Catalytic activity of Setd2 is essential for embryonic development in mice: establishment of a mouse model harboring patient-derived Setd2 mutation

Shubei Chen, Dianjia Liu, Bingyi Chen, Zijuan Li, Binhe Chang, Chunhui Xu, Ningzhe Li, Changzhou Feng, Xibo Hu, Weiying Wang, Yuanliang Zhang, Yinyin Xie, Qiuhua Huang, Yingcai Wang, Stephen D. Nimer, Saijuan Chen, Zhu Chen, Lan Wang, Xiaojian Sun

Front. Med. ›› 2024, Vol. 18 ›› Issue (5) : 831-849.

PDF(14879 KB)
Front. Med. All Journals
PDF(14879 KB)
Front. Med. ›› 2024, Vol. 18 ›› Issue (5) : 831-849. DOI: 10.1007/s11684-024-1095-1
RESEARCH ARTICLE

Catalytic activity of Setd2 is essential for embryonic development in mice: establishment of a mouse model harboring patient-derived Setd2 mutation

Author information +
History +

Abstract

SETD2 is the only enzyme responsible for transcription-coupled histone H3 lysine 36 trimethylation (H3K36me3). Mutations in SETD2 cause human diseases including cancer and developmental defects. In mice, Setd2 is essential for embryonic vascular remodeling. Given that many epigenetic modifiers have recently been found to possess noncatalytic functions, it is unknown whether the major function(s) of Setd2 is dependent on its catalytic activity or not. Here, we established a site-specific knockin mouse model harboring a cancer patient-derived catalytically dead Setd2 (Setd2-CD). We found that the essentiality of Setd2 in mouse development is dependent on its methyltransferase activity, as the Setd2CD/CD and Setd2−/− mice showed similar embryonic lethal phenotypes and largely comparable gene expression patterns. However, compared with Setd2−/−, the Setd2CD/CD mice showed less severe defects in allantois development, and single-cell RNA-seq analysis revealed differentially regulated allantois-specific 5′ Hoxa cluster genes in these two models. Collectively, this study clarifies the importance of Setd2 catalytic activity in mouse development and provides a new model for comparative study of previously unrecognized Setd2 functions.

Keywords

Setd2 / H3K36 methylation / epigenetics / embryonic development / cancer

Cite this article

Download citation ▾
Shubei Chen, Dianjia Liu, Bingyi Chen, Zijuan Li, Binhe Chang, Chunhui Xu, Ningzhe Li, Changzhou Feng, Xibo Hu, Weiying Wang, Yuanliang Zhang, Yinyin Xie, Qiuhua Huang, Yingcai Wang, Stephen D. Nimer, Saijuan Chen, Zhu Chen, Lan Wang, Xiaojian Sun. Catalytic activity of Setd2 is essential for embryonic development in mice: establishment of a mouse model harboring patient-derived Setd2 mutation. Front. Med., 2024, 18(5): 831‒849 https://doi.org/10.1007/s11684-024-1095-1

1 Introduction

In eukaryotes, genomic DNA is compacted together with histones to form highly ordered chromatin. To exert its functions such as transcription and replication, chromatin is modulated by a variety of regulatory proteins, including several families of enzymes that catalyze covalent chemical modifications on DNA and histones. These chromatin modifications contribute to establishment and maintenance of relatively stable states of gene expression, thus representing an important epigenetic regulatory mechanism [13]. Notably, although the catalytic activities of these epigenetic modifiers are usually considered to be essential for their functions, recent studies have revealed that many of them possess important noncatalytic functions (for reviews, see [46]). While being somewhat surprising, this notion is plausible considering that these enzymes in fact have acquired many extra functional domains, have been involved in multi-protein complexes, and have expanded their family members so that their functions become redundant in many regulatory processes.
The human SETD2 (also known as HYPB) gene, orthologous to yeast Set2 [7], encodes the only histone methyltransferase responsible for the transcription-coupled trimethylation of histone H3 lysine 36 (H3K36me3) [8]. The catalytic activity of the SETD2 protein is undertaken by the evolutionarily conserved SET domain (named after the Drosophila genes Su(var)3-9, E(z) and trx) together with the adjacent N-terminal AWS (associate with SET) and C-terminal PostSET domains [8]. The direct coupling of SETD2 with gene transcription is determined by its SRI (Set2-Rpb1 interacting) domain that specifically binds to the hyperphosphorylated, elongating form of RNA polymerase II (Pol II) [811]. Besides these domains, SETD2 also contains a WW domain (named for two conserved W residues) which may mediate protein–protein interactions [1215], a lowly charged region which shows transcriptional activation activity [8], a SHI (SETD2-hnRNP interacting) domain which interacts with heterogeneous nuclear ribonucleoprotein L (hnRNP L) [1618], and several potentially functional disordered regions [19]. Although SETD2 has several homologous family members, including ASH1L, NSD1, NSD2 (also known as WHSC1), and NSD3 (also known as WHSC1L1), SETD2 serves its unique role as the only transcription-coupled H3K36me3 methyltransferase, whereas its other family members tend to catalyze H3K36me1/2 but not H3K36me3 [2027]; this is unlike the situation of many other epigenetic modifiers that share redundant activities and functions with their family members. Notably, because of its direct binding to elongating Pol II, SETD2 seems to indiscriminately leave the H3K36me3 mark on virtually all protein-coding genes that are actively transcribed by Pol II [28]. Thus, it remains a mystery of whether SETD2 acts just equally on all these genes or, under any circumstances, could preferentially regulate any specific target gene. In this regard, an objective approach to dissect the biological functions of SETD2 would be generating specific mutants of SETD2 to determine what function(s) of SETD2 is dependent on which domains or activities.
Since the first identification of recurrent mutations in the human SETD2 gene in clear cell renal cell carcinoma (ccRCC) [29], it has now been well documented that SETD2 mutations are associated with various types of cancers and some developmental defects [2932]. To study the physiologic functions of SETD2, we previously have generated constitutive Setd2 knockout mouse and zebrafish models [27,33]. Our studies show that loss of Setd2 in mice causes embryonic lethality at embryonic day (E) 10.5 due to severe defects in vascular remodeling [27] and, subsequently, our cross-species comparative studies between the mouse and zebrafish models suggest that this vascular phenotype is likely related to metabolic stress that is withstood by the mouse but not the zebrafish embryos [33]. Meanwhile, we and other groups have also generated several conditional Setd2 knockout mouse models [3442]. Some of these models, upon crossing with various tissue-specific Cre recombinase expressing mice, have been widely used to study tumorigenesis and the results have recapitulated many aspects of human cancers caused by SETD2 loss-of-function [38,4251]. However, there is still lacking an animal model harboring a SETD2 mutation derived from patients.
In this study, we first identified a ccRCC patient-derived single-nucleotide mutation in SETD2 (C1685F) [29] to produce a catalytically dead (CD) SETD2 protein. This SETD2-CD protein was confirmed to only lose its histone methyltransferase activity but retain its specific interaction with hyperphosphorylated Pol II. We then introduced the corresponding mutation in mouse Setd2 gene (C1659F) into mouse embryonic stem (ES) cells using homologous recombination technology and subsequently generated a new Setd2-CD knockin mouse model. A side-by-side comparative study between this Setd2-CD and our original Setd2 constitutive knockout mouse models was performed to clarify the catalytically dependent and independent Setd2 functions.

2 Materials and methods

2.1 Plasmids, antibodies, and mouse strains

The pGEX-5X-1 based plasmid containing glutathione S-transferase (GST)-fused human SETD2 fragment was the same one used in our previous study [8]. The corresponding fragment of mouse Setd2 was cloned into the same vector. The mammalian expression plasmids of human SETD2 were generated by cloning the C-terminal fragments of SETD2 into a customized lentiviral vector (OBiO Tech), in which the expression of FLAG-tagged SETD2 is driven by a CMV promoter. Point mutations in these plasmids were generated with site-directed mutagenesis strategy.
The following antibodies that can distinguish different modification states of histone H3 and Pol II (represented by its large subunit Rpb1) were used: H3K36me1 (Abcam, ab9048), H3K36me2 (Cell Signaling Technology, 2901), H3K36me3 (Abcam, ab9050), total H3 (Cell Signaling Technology, 4499S), Ser2-phosphorylated Rpb1 (Cell Signaling Technology, 13499), Ser5-phosphorylated Rpb1 (Cell Signaling Technology, 13523), and total Rpb1 (Cell Signaling Technology, 14958). A customized polyclonal rabbit antibody for SETD2 was developed by immunizing rabbits with a peptide embracing amino acids 916-1038 (according to GenBank protein accession number NP_054878.5) expressed and purified from bacteria (ABclonal Biotechnology). This antibody can also detect mouse Setd2. The GAPDH antibody was purchased from Proteintech (60004-1-Ig).
The C57BL/6J mice were purchased from Shanghai Model Organisms Center. The mice were grown and used according to animal care standards, and the animal studies were approved by the Committee of Animal Use at Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences.

2.2 In vitro histone methyltransferase activity assay

The GST-fusion enzyme proteins were expressed in Escherichia coli strain BL21 and purified with Glutathione-Sepharose 4B according to the manufacture’s protocol (Cytiva). Protein concentration was determined by Coomassie blue staining (Yeasen) of SDS-PAGE gels, using bovine serum albumin as a standard. Recombinant polynucleosomes were purchased from Active Motif (31466) and were used as substrates. The in vitro histone methyltransferase activity assay was performed by adding 1.2 μg purified GST-fusion enzymes, 1.2 μg recombinant polynucleosomes, 10 μmol/L S-adenosylmethionine to a final volume of 30 μL methylation buffer (50 mmol/L Tris pH8.0, 50 mmol/L NaCl, 1 mmol/L MgCl2, 2 mmol/L DTT, 5% glycerol). The reaction system was incubated at 30 °C for 1.5 h and stopped by adding 7.5 μL 5× SDS sample buffer. A part of the reaction products was separated by SDS-PAGE and visualized by Coomassie blue staining as loading controls, and the others were subjected to immunoblot analysis with specific antibodies for H3K36me1, H3K36me2, and H3K36me3.

2.3 Generation of SETD2 knockout cell lines

Monoclonal SETD2 knockout HEK293T cell lines were generated using CRISPR/Cas9 technology. Two sgRNAs (5′-TTAAAGAACCAGTTGATACGAGG-3′; 5′-GTTGTGTATGATCGAACTCAAGG-3′) were designed to target exon 3 of human SETD2, and the targeting plasmids were constructed using the pSpCas9-Puro (PX459) vector. HEK293T cells were transfected with the targeting plasmids and selected with puromycin. Monoclonal cell clones were isolated using the limiting dilution method, and the knockout of SETD2 in the cell lines were validated by sequencing the genomic PCR products and TA clones, as well as immunoblot analysis of protein expression.

2.4 Cell transfection and coimmunoprecipitation (co-IP)

SETD2 knockout HEK293T cells were transfected with FLAG-tagged wild-type (WT) or mutant C-terminal SETD2 plasmids using Polyethylenimine Linear (PEI) MW40000 (Yeasen, 40816ES03). The transfected cells were harvested 48 h after transfection and lysed with T/G lysis buffer (20 mmol/L Tris HCl, pH 7.5, 300 mmol/L NaCl, 50 mmol/L NaF, 2 mmol/L EDTA, 1% Triton X-100, and 20% glycerol) [52]. Cell lysates were incubated with anti-FLAG magnetic beads (MedChemExpress, HY-K0207) and rotated for 4 h at 4 °C. The beads were precipitated and washed 3 times with T/G lysis buffer. The bound proteins were eluted with SDS sample buffer at 95 °C for 10 min and subjected to immunoblot analysis with antibodies for different modification states of Pol II. Meanwhile, whole cell lysates of these transfected cells were also prepared with SDS sample buffer for immunoblot analysis of the H3K36me1, H3K36me2, and H3K36me3 levels.

2.5 Generation of Setd2 knockin mice

The targeting vector was electroporated into 129/Sv mouse ES cells. The targeted ES cell clones were selected with neomycin and validated by genomic PCR with a pair of primers (forward, 5′-TACTCATTATACTGCTTTTC-3′; reverse, 5′-AAAAAGAATTCTGACTTAAGG-3′) and sequencing of the PCR products. The heterozygous ES cells were microinjected into C57BL/6J blastocysts, followed by implantation into pseudopregnant foster mothers. Male chimeras were mated with C57BL/6J females to generate F1 mice, which were further mated with Ddx4-Cre (Shanghai Model Organisms Center, NM-KI-225028) C57BL/6J females to generate Neo deleted F2 progeny. The F2 mice were backcrossed to the C57BL/6J strain for eight generations to examine the persistence of the phenotypes. Genotypes of the mice were determined by genomic PCR with a pair of primers spanning the LoxP site (forward, 5′-GCAGTGATGCTGTCTGTTTCA-3′; reverse, 5′-TGCCCTCAGAAGGGCTAATA-3′) and a pair of primers spanning exon 9 (forward, 5′-GGGGCTGAAAATGAAGCATA-3′; reverse, 5′-GATGATCTGGGTTTGATCCCTG-3′). The PCR products were further validated by sequencing. The Setd2 constitutive knockout C57BL/6J mice were obtained from our previous work [27].

2.6 Embryo dissection, immunoblot, and histology analysis

Embryos were collected at multiple stages for genotyping, RNA-seq, immunoblot, and histology analyses. For immunoblot analysis, the embryos were lysed with SDS sample buffer and facilitated with a homogenizer. The lysates were incubated at 95 °C for 10–15 min, centrifuged at 12 000 rpm for 10 min, and the supernatant were collected for immunoblot. For histology analysis, the embryos together with yolk sacs were fixed in 4% paraformaldehyde overnight and then subjected to paraffin embedding. The embedded embryos and yolk sacs were cut into 5 μm sections. The sections were dewaxed by immersion in xylene and decreasing alcohol concentration, stained with hematoxylin and eosin (H&E) (Servicebio), and imaged under microscope.

2.7 RNA-seq and data analysis

Total RNA was extracted from whole embryos or yolk sacs using TRIzol reagent (Invitrogen, 15596018). RNA-seq libraries was constructed with KAPA RNA HyperPrep Kits (Roche) and sequenced using NovaSeq 6000 (Illumina). Raw reads were filtered by fastp (0.22.0) with default set. Clean sequenced reads were aligned to the mm10 reference genome by HISAT2 (2.2.1). Aligned reads were extracted by featureCounts (2.0.1) with default parameters and normalized by DEseq2 (1.32.0). Fragments per kilobase of exon model per million mapped reads (FPKM) were calculated using a protocol as described previously [53]. Principal component analysis (PCA) and hierarchical clustering analysis were performed with Cluster (3.0) and the heatmap was drawn with Java TreeView (1.1.6r4) as described previously [54]. Gene set enrichment analysis (GSEA) was performed with the version 2023.1 of the Molecular Signatures Database (MSigDB) [55]. The RNA-seq data have been deposited in the Gene Expression Omnibus with accession number GSE241154.

2.8 Single-cell RNA sequencing (scRNA-seq) and data analysis

Embryos were dissociated, and single-cell suspensions were prepared following a previously established protocol [56]. In brief, embryos were incubated with TrypLE Express dissociation reagent (Gibco) at 37 °C for 15 min, followed by quenching with heat-inactivated fetal bovine serum (FBS). The resulting single-cell suspension was then washed and filtered through a 40-μm cell strainer before being resuspended in PBS containing 1% FBS. Cell concentration was assessed using a Countstar, and cells were subsequently processed for single-cell RNA sequencing using the 10x Genomics Chromium Single Cell 3′ v3 platform. Sequencing data were aligned to the mm10 reference genome using Cell Ranger to generate gene expression matrices, which were then subjected to downstream analysis using Seurat (4.1.0). Data preprocessing involved filtering cells expressing between 500 and 5000 genes, with mitochondrial content less than 15%. The expression data was log-normalized and scaled, and the variable genes were identified based on their expression patterns. Next, these variable genes were utilized to conduct PCA. Subsequently, cells were clustered based on a shared nearest neighbor graph constructed using the first 30 principal components, with a resolution set at 0.8. Integration of different samples was achieved using the “FindIntegrationAnchors” and “IntegrateData” functions in Seurat. Identification of specific markers for each cluster was conducted using the “FindAllMarkers” function. Finally, cell types were assigned to each cluster through manual review of gene expression profiles, focusing on classic markers.

3 Results

3.1 Identification of the cancer patient-derived SETD2 CD mutation

While many types of human cancers have been documented to be associated with SETD2 mutations, ccRCC remains at the top of the list [30,57,58] and the contribution of the SETD2 mutations to ccRCC pathology has been relatively better studied [47,48,5964]. We therefore focused on analyzing the SETD2 mutations in ccRCC. From the Catalogue of Somatic Mutations (COSMIC) database, we retrieved 360 ccRCC cases containing SETD2 mutations. Relatively high numbers of nonsense mutations (100 cases; 27.78%) and frame-shift mutations (127 cases; 35.28%) suggest that SETD2 loss-of-function may serve as an important mechanism in tumorigenesis (Fig.1). Meanwhile, single-nucleotide missense mutations in SETD2 were found in 124 ccRCC cases (34.44%). Notably, although these mutations seemingly located throughout the whole protein, they showed a considerable enrichment in the AWS-SET-PostSET (abbreviated as ASP) catalytic domains of SETD2 (Fig.1), thus suggesting that the catalytic activity of SETD2 is probably more important for its tumor suppressive functions.
Fig.1 Identification of a cancer patient-derived catalytically dead (CD) SETD2 mutation. (A) Lollipop plots of the mutations in SETD2 identified in patients with clear cell renal cell carcinoma (ccRCC). Data are retrieved from the Catalogue of Somatic Mutations (COSMIC) database. The top panel shows various types of mutations, whereas the bottom panel shows the missense mutations. The Lollipop plots were generated with the OmicStudio tools. Red arrow denotes the C1685F mutation. Residue positions are according to GenBank protein accession number NP_054878.5. (B) Amino acid sequence alignment of the catalytic domains of SETD2 and its orthologs in various species, as well as its close paralogs in human. Hs, Homo sapiens; Mm, Mus musculus; Gg, Gallus gallus; Xt, Xenopus tropicalis; Dr, Danio rerio; Dm, Drosophila melanogaster; Ce, Caenorhabditis elegans; Sp, Schizosaccharomyces pombe; Sc, Saccharomyces cerevisiae. Red arrow denotes the conserved C1685 in human SETD2, corresponding to C1659 in mouse Setd2. (C) Structure of SETD2 catalytic domains in complex with a nucleosome containing H3.3K36M (PDB: 7EA8). Note that the C1685 residue (yellow) interacts with a zinc ion (blue) and locates close to the catalytic site and the substrate histone H3 tail (orange). (D) Experimental design, showing the domain architectures of the GST-tagged wild-type and CD SETD2 fragments used in the in vitro histone methyltransferase activity assays, and a summary of the experimental results. Note that, while only human SETD2 is illustrated, the experiments using the human and mouse versions of the enzymes produce the same results. The fragment containing the AWS-SET-PostSET domains is abbreviated as ASP, and the mutation is denoted with an asterisk. (E, F) Results of the in vitro histone methyltransferase activity assays showing that the CD mutants of human SETD2 (E) and mouse Setd2 (F) completely lose their activities to catalyze mono-, di- and trimethylation of H3K36 in polynucleosomes. The H3K36 methylation states were determined by specific antibodies and the loading controls were visualized by Coomassie blue staining. (G) Experimental design, showing the domain architectures of the FLAG-tagged wild-type (WT) and CD SETD2 fragments used in the coimmunoprecipitation (co-IP) and H3K36me3 restoration assays, and a summary of the experimental results. The fragment containing the AWS-SET-PostSET, WW, and SRI domains is abbreviated as ASPWS, and the mutation is denoted with an asterisk. (H) Results of the co-IP assays showing that the WT and CD SETD2(ASPWS) proteins similarly interact with the hyperphosphorylated, but not the unphosphorylated, RNA polymerase II (Pol II). (I) Immunoblot analysis of H3K36 methylation states in the SETD-knockout HEK293T cells transfected with WT or CD SETD2(ASPWS) proteins. Note the failure of the CD SETD2(ASPWS) protein to restore the H3K36me3 in the cells. Total H3 was used as a loading control.

Full size|PPT slide

We then screened several SETD2 missense mutations within the ASP domains using in vitro histone methyltransferase activity assays [8] and identified the C1685F mutation [29] for further analysis because this mutation could abolish the catalytic activity of SETD2 while barely affecting the stability of the GST-fused SETD2(ASP) protein (see below). The C1685 of human SETD2 is equivalent to C1659 of mouse Setd2. It locates within the PostSET domain of SETD2 and is highly conserved through the evolution from yeasts to humans, as well as in the SETD2 paralogs including ASH1L, NSD1, NSD2, and NSD3 (Fig.1). According to the structural studies of human SETD2 [65,66], the C1685 combines with C1631, C1678, and C1680 to tetrahedrally coordinate a zinc ion near the active site (Fig.1), and the C1685F mutation is thus supposed to affect the catalytic activity of SETD2. We then purified both human and mouse versions of the GST-SETD2(ASP) WT and mutant proteins for in vitro histone methyltransferase activity assays, and the results showed that, while the WT proteins could catalyze mono-, di-, and trimethylation of H3K36 on recombinant nucleosomes, the C1685F/C1659F mutations completely abolished all these catalytic activities but barely affected the stability of the human and mouse GST-SETD2(ASP) proteins (Fig.1–1F).
Next, we asked whether the WT and mutant SETD2 could equally bind to the hyperphosphorylated elongating Pol II and, if they could, whether they indeed show dramatic difference in catalyzing the transcription-coupled H3K36me3 in cells. To answer these questions, we first generated a SETD2 knockout HEK293T cell line using the CRISPR/Cas9 technology. Compared with the control cells, the SETD2 knockout cells showed dramatically decreased H3K36me3 but not H3K36me1/2 levels. Given the difficulty in ectopically expressing the full-length SETD2 protein [8,67,68], we transfected these cells with the C-terminal part of the WT and C1685F mutant SETD2, which contained the ASP, WW, and SRI domains (abbreviated as ASPWS) (Fig.1), and results of the co-IP assays showed that both the WT and mutant SETD2(ASPWS) protein could bind to the hyperphosphorylated, but not the unphosphorylated Pol II (Fig.1). Meanwhile, we performed immunoblot analysis of the H3K36 methylation levels in these cells. The results showed that only the WT, but not the mutant, SETD2(ASPWS) protein could substantially restore the H3K36me3 level in the SETD2 knockout cells; in contrast, the H3K36me1/2 levels showed no difference upon expression of either WT or mutant SETD2(ASPWS) proteins (Fig.1). Collectively, these results indicate that this ccRCC patient-derived SETD2 mutation can specifically abolish its catalytic activity while retaining its Pol II-interaction, thus providing a rational tool for dissecting the functions of SETD2 dependent or independent of its catalytic activity.

3.2 Generation of the site-specific Setd2-CD knockin mouse model

We employed the targeted homologous recombination technique to generate a mouse model harboring the ccRCC patient-derived SETD2 mutation. Both the C1685 of human SETD2 and the C1659 of mouse Setd2 proteins are encoded by a TGC codon, in which a substitution for the second letter G by T causes a missense amino acid mutation from C to F. As the C1659 of mouse Setd2 locates in exon 9, we cloned an XbaI/KpnI-digested genomic fragment embracing exons 7–9 into the targeting vector, while making the G-to-T mutation in exon 9 and inserting a LoxP-Neo-LoxP cassette in intron 8 and a Tk cassette downstream of the 3′ homologous arm as positive and negative selection markers, respectively (Fig.2). Besides the G-to-T mutation, the targeting strategy only leaves a single LoxP site in the middle of intron 8 upon Cre-Lox recombination, so that it provides a marker for genotyping but barely affects the expression of the Setd2 gene. After introducing the targeting vector into mouse ES cells by electroporation, we selected the neomycin-resistant ES cell clones and validated them by genomic PCR and sequencing (Fig.2 and 2C). Subsequently, we chose clone #9 for blastocyst microinjection and transferred the injected blastocysts into pseudopregnant mice. Chimeras were bred to obtain germline-transmitted heterozygous knockin mice, and their Neo cassettes in the genome were removed by mating with a Ddx4 (also known as Vasa) promoter-driven Cre transgenic mouse line, in which the Cre recombinase is specifically expressed in germ cells [69]. The WT and heterozygous Setd2 C1659F knockin (Setd2+/CD) mice were genotyped with PCR primers flanking the remaining single LoxP site in the genome (Fig.2), and the C1659F mutation site was validated by sequencing the PCR products of the genomic region containing exon 9 (Fig.2 and 2F). We then crossed the Setd2+/CD mice to obtain homozygous Setd2 C1659F knockin (Setd2CD/CD) offsprings. However, genotyping of multiple litters showed that, while the numbers of the WT and Setd2+/CD littermates showed a normal ratio of roughly 1:2, there was not any Setd2CD/CD mouse born (Fig.2). This finding suggested that the Setd2CD/CD mice might die in utero, which was reminiscent of the embryonic lethality phenotype of our Setd2−/− model [27]. Therefore, we sought to perform a side-by-side comparative study between these two mouse models.
Fig.2 Generation of the site-specific Setd2-CD knockin mouse model. (A) Schematic diagram of the targeting strategy. Asterisk denotes the G-to-T mutation in exon 9, which causes the C1659F mutation in mouse Setd2 protein. A Neo cassette flanked with two LoxP sites and a reversed Tk cassette are used as positive and negative selection markers in the targeted embryonic stem (ES) cells. Green and orange arrows indicate the positions of PCR primers for genotyping the targeted ES cells and mice, respectively, and the corresponding numbers indicated the expected sizes of PCR products. (B) Genomic PCR experiments confirming the targeted ES cell clones. Clone #9 was used for blastocyst microinjection. (C) Sequencing results of the genomic PCR products of the clone #9 ES cells, showing the junction sites between the genomic and inserted DNA sequences. (D) Genomic PCR for genotyping the newborn mice produced by heterozygous parents. Note that there was no homozygous mouse born, while the WT (+/+) and heterozygous (+/CD) littermates showed a normal ratio of roughly 1:2. (E) Representative genomic PCR products containing exon 9 of the WT and heterozygous mice. (F) Sequencing results of the PCR products of the WT and heterozygous mice as shown in panel (E). Note the double-peaks at the G-to-T mutation site in the heterozygous mice. Deduced amino acid sequences are written beneath, and the region of the PostSET domain is indicated. (G) Genotype statistics of the littermates produced by heterozygous intercrosses. Note the absence of homozygous (Setd2CD/CD) offspring.

Full size|PPT slide

3.3 Comparable embryonic lethality phenotypes and reduced H3K36me3 levels in the Setd2CD/CD and Setd2−/− mice

To determine whether the embryonic lethality of the Setd2CD/CD and Setd2−/− mice occurred at the same developmental stage, we collected and analyzed their embryos at multiple time points. The results revealed that both Setd2CD/CD and Setd2−/− embryos died at E10.5 as there was no embryo found viable beyond this stage. At E10.5, the Setd2CD/CD and Setd2−/− embryos exhibited comparable levels of overall phenotypes including pale and shriveled yolk sacs and severely retarded growth of the embryos proper; in contrast, the heterozygous embryos of both models (Setd2+/CD and Setd2+/−) showed no apparent defect compared with their WT littermates (Fig.3 and 3B). To exclude the possibility that the Setd2 null-like phenotypes of the Setd2CD/CD embryos were just caused by complete elimination of Setd2 protein by the C1659F mutation, we performed immunoblot analysis of the WT, heterozygous and homozygous Setd2-CD and Setd2 knockout embryos at E10.5. The results showed that, although the Setd2-CD protein level was relatively lower, the Setd2CD/CD embryos still contained a considerable amount of Setd2-CD protein (Fig.3); in contrast, Setd2 proteins in the Setd2−/− embryos were entirely absent (Fig.3). This observation indicates that the C1659F mutation cannot eliminate Setd2 protein in the embryos, and that the limited decrease of protein level may unlikely be able to causes such severe Setd2 null-like phenotypes. We also verified whether the specific loss of Setd2 catalytic activity in the Setd2CD/CD embryos could cause comparable levels of reduced H3K36me3 compared with the Setd2−/− embryos. As a result, immunoblot and quantification analysis showed that the H3K36me3 levels in the Setd2CD/CD and Setd2−/− embryos were similarly reduced to 20%–30% levels relative to their WT littermates, whereas their levels of H3K36me1 and H3K36me2, which might be catalyzed by other methyltransferases, were not reduced (Fig.3–3H). Collectively, these results demonstrated that the loss of H3K36me3 methyltransferase activity of Setd2 per se could cause similar embryonic lethality phenotypes as the complete knockout of the whole Setd2, thus implying that the catalytic activity of Setd2 is essential for its functions in supporting embryonic development.
Fig.3 Comparable embryonic lethality phenotypes and reduced H3K36me3 levels in the Setd2CD/CD and Setd2−/− mice. (A, B) Bright-field microscopy images of the wild-type, heterozygous and homozygous Setd2-CD (A) and Setd2 knockout (B) embryos at E10.5. The top panels show embryos enclosed in the yolk sacs, and the bottom panels show isolated embryos proper. Scale bar = 1 mm. (C, D) Immunoblot analysis of Setd2 protein levels in the wild-type, heterozygous and homozygous Setd2-CD (C) and Setd2 knockout (D) embryos at E10.5. Each sample was loaded in 2-fold serial dilution to facilitate quantification. Gapdh was used as a loading control. (E, F) Immunoblot analysis of the different H3K36 methylation states of the wild-type, heterozygous and homozygous Setd2-CD (E) and Setd2 knockout (F) embryos at E10.5. Each sample was loaded in 2-fold serial dilution to facilitate quantification. Total H3 was used as a loading control. (G, H) Quantification of H3K36 methylation levels in the heterozygous and homozygous Setd2-CD (G) and Setd2 knockout (H) embryos relative to their wild-type littermates. Note that the Setd2CD/CD and Setd2−/− embryos similarly show dramatic reduction of H3K36me3 but not H3K36me1/2 levels.

Full size|PPT slide

3.4 Vascular remodeling defects and gene expression profiling of the Setd2CD/CD and Setd2−/− yolk sac

To further characterize the developmental defects of the Setd2CD/CD and Setd2−/− mice and to understand the molecular mechanisms, we performed a comparative gene expression profiling based on RNA-seq analysis of their yolk sacs at E9.5. This relatively early developmental stage was chosen because the Setd2CD/CD and Setd2−/− yolk sacs at E9.5 were still apparently normal and thus would be more suitable for identifying earlier molecular mechanisms underlying the phenotypes. PCA analysis of the highly variable genes among the 6 groups of yolk sac samples (i.e., the yolk sacs of the Setd2CD/CD and Setd2−/− mice, as well as those of their heterozygous and WT littermates; 2 samples in each group) showed that the Setd2CD/CD and Setd2−/− yolk sacs (4 samples) were closely clustered, whereas all the heterozygous and WT samples were clustered into another group (Fig.4). This result indicates that, consistent with their comparable phenotypes, the Setd2CD/CD and Setd2−/− yolk sacs also share considerable similarities at transcriptomic level.
Fig.4 Similar vascular remodeling defects in the Setd2CD/CD and Setd2−/− mice. (A) Principal component analysis (PCA) of the highly variable genes in the wild-type (WT), heterozygous (HE) and homozygous (HO) Setd2-CD and Setd2 knockout (KO) yolk sacs at E9.5. Note that the Setd2-CD and Setd2-KO HO samples were closely clustered, whereas all the HE and WT samples were clustered into another group. (B) Gene set enrichment analysis (GSEA) of the RNA-seq data showing that the angiogenesis hallmark genes are similarly downregulated in the Setd2CD/CD and Setd2−/− yolk sacs compared with their WT littermates. (C) Unsupervised hierarchical clustering analysis of the 12 indicated yolk sac samples and the angiogenesis hallmark genes used in panel (B), validating the consistent downregulation of these genes in the 4 HO samples. (D, E) Applying RNA-seq data to re-analyze the previously reported cDNA microarray gene signature of the Setd2-KO yolk sacs. The left and right panels show the downregulated and upregulated genes, respectively, in the previous signatures which are largely recapitulated by the RNA-seq analysis of the Setd2-CD (D) and Setd2-KO (E) yolk sacs. (F, G) Microscopy images of the hematoxylin and eosin (H&E) stained yolk sac sections of the Setd2CD/CD (F) and Setd2−/− (G) mice at E9.5 in comparison with their WT littermates. Scale bars in the top panels represent 100 μm, and those in the bottom panels represent 10 μm.

Full size|PPT slide

Relevant to the fact that the Setd2−/− embryos die of vascular remodeling defects, our GSEA analysis showed that the angiogenesis hallmark genes were similarly downregulated in both Setd2CD/CD and Setd2−/− yolk sacs compared with their WT littermates (Fig.4), and these results were further validated by an unsupervised hierarchy clustering analysis of the above-mentioned 6 groups of yolk sac samples (Fig.4). Furthermore, since we previously used cDNA microarray techniques to identify a transcriptomic signature including several differentially expressed genes in Setd2−/− yolk sacs compared with their WT littermates [27], we herein used RNA-seq to re-analyze these genes. As a result, this signature was largely recapitulated by the RNA-seq analysis of both Setd2CD/CD and Setd2−/− yolk sacs, as majority of the previously identified genes showed similar downregulation (Gja4, Plg, Angptl6, and Vegfb) and upregulation (Ccn2, Ccn1, Lama1, and Foxo3); meanwhile, probably due to technical difference between the RNA-seq and microarray platforms, several previously identified differentially expressed genes by microarray showed no significant change in the RNA-seq results (Fig.4 and 4E). Nevertheless, the side-by-side comparison of gene expression patterns of Setd2CD/CD and Setd2−/− yolk sacs demonstrated clear similarity between these two mouse models. To validate their vascular remodeling defects, we performed histological section analysis of the Setd2CD/CD and Setd2−/− yolk sacs. The results showed that both Setd2CD/CD and Setd2−/− yolk sacs contained a number of widely enlarged cavities between the visceral endoderm and mesoderm, which were very rarely observed in the yolk sacs of their WT littermates (Fig.4 and 4G).
Apart from the above-mentioned angiogenic genes, we also performed a broader analysis of the gene expression profiles to gain more insights into the potential mechanisms underlying the vascular remodeling defects of the Setd2CD/CD and Setd2−/− yolk sacs. Notably, our previous cross-species comparative studies between Setd2 knockout mouse and zebrafish models have suggested that the embryonic lethal vascular remodeling phenotypes are likely related to metabolic stress that is withstood by the mouse but not the zebrafish embryos [33]. Therefore, it would be important to continue searching for stress-related genes and more upstream differentially expressed genes that could be directly regulated by Setd2. In particular, GSEA analysis of the RNA-seq data against the hallmark gene sets [70] suggested that the p53 pathway and the heme metabolism were activated, whereas the coagulation and epithelial-mesenchymal transition pathways were suppressed, in both Setd2CD/CD and Setd2−/− yolk sacs (Fig.5). These observations imply that the tissues might suffer certain types of stress (e.g., DNA damage and hypoxia) and related dysfunctions. Notably, a comparison between the gene expression profiles of the homozygous and heterozygous Setd2-CD and Setd2 knockout mice can further exclude the possibility that the phenotypes of the Setd2CD/CD mice were caused by decreased Setd2 protein levels rather than loss-of-activity, as if this possibility is real, the gene expression pattern of the Setd2CD/CD mice, which still contain considerable amount of Setd2 protein, would be more like Setd2+/−. However, the gene expression profiling showed a close similarity between Setd2CD/CD and Setd2−/−, but not with Setd2+/− (Fig.5), thus suggesting that the Setd2 null-like phenotypes of the Setd2CD/CD mice are caused by Setd2 loss-of-activity rather than protein instability.
Fig.5 Global gene expression profiling of the homozygous, heterozygous and wild-type (WT) Setd2-CD and Setd2 knockout yolk sacs. (A) A summary of gene set enrichment analysis (GSEA) of the homozygous and heterozygous Setd2-CD and Setd2 knockout yolk sacs compared with their WT littermates, showing the significantly enriched and depleted hallmark gene sets, as well as their nominal P-values. Dashed vertical lines indicate the threshold of nominal P-values at 0.05. The dashed horizontal line divides between enriched and depleted gene sets in the Setd2CD/CD versus WT data analysis. Note that these two models show comparable global tendencies with relatively minor differences. (B) GSEA results showing that the collagen assembly related genes are similarly downregulated in the Setd2CD/CD and Setd2−/− yolk sac compared with their WT littermates. (C) Unsupervised hierarchical clustering analysis of the 12 indicated yolk sac samples and the collagen assembly related genes used in panel (B), validating the consistent downregulation of these genes in the 4 HO samples.

Full size|PPT slide

Furthermore, GSEA analysis against the Gene Ontology gene sets [71] showed that collagen assembly related genes were downregulated in the Setd2CD/CD and Setd2−/− yolk sacs (Fig.5), and this result was confirmed by an unsupervised hierarchical clustering analysis of all samples of the homozygous, heterozygous and WT yolk sacs (Fig.5). Notably, the immediate relevance of collagen proteins to angiogenesis [72] and the special genomic features of the collagen genes (i.e., most collagen genes are very long and highly interrupted) [73] imply that these genes may serve as candidate genes preferentially regulated by Setd2 and H3K36me3 in the developmental processes (for more detailed historical and logical discussions on this point, see Discussion section). Taken together, these results suggest that certain stress response, metabolism and cellular communication pathways might play important roles in the vascular remodeling defects of the Setd2CD/CD and Setd2−/− yolk sacs.

3.5 Setd2CD/CD embryos exhibit slightly milder developmental defects than Setd2−/−

To investigate the developmental defects of the Setd2CD/CD and Setd2−/− embryos proper, we isolated the embryos at E9.5 and performed comparative gene expression profiling together with the embryos of their heterozygous and WT littermates. Notably, relative to the closely comparable gene expression patterns between the Setd2CD/CD and Setd2−/− yolk sacs, their embryos showed bigger differences in gene expression alterations. For example, in the Setd2−/− embryos, we found that 293 and 257 genes were up- and downregulated, respectively, compared with those of their WT littermates; in contrast, there were only 88 and 144 genes were found to be up- and downregulated, respectively, in the Setd2CD/CD embryos (Fig.6). Nonetheless, the similarity between the Setd2CD/CD and Setd2−/− embryos was still evident because their genes were largely regulated in the same direction, i.e., the upregulated genes in the Setd2CD/CD embryos were overlapped with the upregulated genes in the Setd2−/− embryos, and vice versa (Fig.6). To further evaluate the level of change of each gene, we ranked the shared upregulated genes along their fold changes in Setd2−/−, and the fold changes in Setd2CD/CD were generally less dramatic (Fig.6, left). The same trend was also observed in the downregulated genes (Fig.6, right). These results suggested that gene expression alterations in the Setd2CD/CD embryos were less dramatic than those in the Setd2−/− embryos.
Fig.6 The Setd2-CD mice exhibit slightly milder developmental defects than the Setd2 knockout mice. (A) Venn diagram showing the numbers and overlapping of the upregulated and downregulated genes in the Setd2CD/CD and Setd2−/− embryos compared with their WT littermates. (B) Comparisons of gene expression alteration levels of the shared upregulated (left) and downregulated (right) genes between the Setd2CD/CD and Setd2−/− embryos compared with their WT littermates. The genes are ranked along their fold changes in the Setd2−/− embryos. Note that the fold changes in the Setd2CD/CD embryos are generally less dramatic than those in the Setd2−/− embryos. (C) Bright-field microscopy images of the Setd2CD/CD and Setd2−/− embryos at E10.5, showing different ratios of incomplete chorioallantoic attachment. Scale bar = 1 mm. (D) Representative images of histological section analysis showing different levels of severeness of the developmental defects in the Setd2CD/CD and Setd2−/− placentas. Note the normal and thinner labyrinthine layers in the wild-type and Setd2CD/CD embryos, respectively, and the lack of labyrinthine layer in a representative Setd2−/− embryo. Scale bar = 100 μm. (E) Statistics of the frequencies of chorioallantoic attachment defects in the Setd2CD/CD and Setd2−/− embryos.

Full size|PPT slide

We therefore further compared the phenotypes of the Setd2CD/CD and Setd2−/− embryos in detail, especially taking their heterogeneities into consideration. As reported in our previous study [27], the Setd2−/− embryos showed a considerable degree of heterogeneity in their growth retardation phenotypes, which could be measured by their asynchronous completeness of developmental milestone events. In particular, at E9.5, close to half of the Setd2−/− embryos were found showing incomplete attachment of their allantoides to the chorion; in contrast, although the incomplete chorioallantoic attachment was also observed in some Setd2CD/CD embryos, the majority of them had completed this milestone event (Fig.6). Furthermore, histological section analysis showed different levels of developmental defects in the Setd2CD/CD and Setd2−/− placentas. Compared with the WT placentas, in which the labyrinthine layer was well developed to have blood vessels invaded and interdigitated properly, the majority of Setd2CD/CD placentas contained a much thinner labyrinthine layer with blood vessels remained at the periphery, whereas the placentas of those Setd2−/− embryos with incomplete chorioallantoic attachment showed no labyrinthine layer (Fig.6 and 6E). Therefore, this different severeness of developmental defects between the Setd2CD/CD and Setd2−/− placentas, though only notable when considering their heterogeneities, suggests that the Setd2-CD protein could still retain minor functions in regulation of mouse embryonic development.

3.6 scRNA-seq analysis reveals differential regulation of allantois-specific 5′ Hoxa cluster genes in Setd2CD/CD and Setd2−/− embryos

To further characterize the differences between the Setd2CD/CD and Setd2−/− embryos at single cellular level, we isolated the embryos at E8.5 and performed scRNA-seq analysis. At this stage, the allantoides of the Setd2CD/CD and Setd2−/− embryos had not been attached to the chorion and thus there was not apparent phenotypic difference between them. Our uniform manifold approximation and projection (UMAP) analysis of the scRNA-seq data led to identification of 20 distinct cell clusters (Fig.7), whose identities were annotated by specific marker genes (Fig.7). All of these clusters, including the allantois (annotated by marker genes including Pitx1, Slc38a4, Amot, Hoxa9, Plac1, and Sgce), were similarly observed in the Setd2CD/CD and Setd2−/− embryos (Fig.7), and the frequencies of each cluster were also correlated (Fig.7). These results suggested that the cellular identities and compositions in the Setd2CD/CD and Setd2−/− embryos were closely comparable.
Fig.7 Single cell RNA sequencing (scRNA-seq) analysis of the Setd2CD/CD and Setd2−/− E8.5 embryos reveals differential regulation of allantois-specific 5′ Hoxa cluster genes. (A) Uniform manifold approximation and projection (UMAP) analysis of the scRNA-seq data of wild-type (WT) E8.5 embryos leading to identification of 20 distinct cell clusters. (B) Hierarchical clustering heatmap illustrating the relative expression levels of marker genes in each identified cell type. (C) Single cells of the Setd2CD/CD and Setd2−/− embryos projected to the reference map using the mutual nearest neighbors (MNNs) algorithm. The cells are assigned to, and colored as, one of the 20 WT cell types as shown in panel (A). WT cells are shown as background in gray. Red arrows denote allantois cells. Two asterisks in each panel denote the clusters of erythrocytes (lower) and blood progenitors (upper), which tend to be lost during harvesting the samples so that they are not included in calculating frequencies as shown in panel (D). (D) A scatter plot showing the frequencies of the 18 clusters of cells in the Setd2CD/CD versus Setd2−/− embryos. Red arrow denotes the allantois cells. Two dashed lines denote the degree of 50% similarity, indicating that the frequencies of all these clusters share higher similarities than this degree. (E) Results of scRNA-seq analysis of WT embryos showing that the 5′ Hoxa cluster genes are relatively highly expressed in the allantois cells. (F) Violin plots of expression levels of the 5′ Hoxa cluster genes in the Setd2CD/CD and Setd2−/− allantois cells compared with their WT littermates. Note that these genes are dramatically downregulated in the Setd2−/− but not the Setd2CD/CD allantois cells.

Full size|PPT slide

To explore the potential mechanism relevant to the different severeness of allantois developmental defects observed at later stage (E9.5), we then focused on analyzing the genes that were enriched and known to play important roles in the allantois of the Setd2CD/CD and Setd2−/− embryos. Notably, previous studies have shown that the spatiotemporal expression of the 5′ Hoxa cluster genes in the allantois is important for placental labyrinth development in mice [74,75]. Indeed, our scRNA-seq data showed that Hoxa9, Hoxa10, Hoxa11, and Hoxa13 were relatively highly expressed in the allantois cells (Fig.7). Comparison between the Setd2CD/CD and Setd2−/− embryos showed that, while these 5′ Hoxa cluster genes were dramatically downregulated in the Setd2−/− allantois cells compared with the WT littermates, their changes in the Setd2CD/CD allantois cells were very little (Fig.7). These results suggest that the inactivation of the 5′ Hoxa cluster genes specifically in the Setd2−/− allantois cells may provide a mechanism underlying the severer allantois developmental defects in the Setd2−/− embryos, and that the spatiotemporal activation of the 5′ Hoxa cluster genes may require the entire functions of Setd2 besides its catalytic activity.

4 Discussion

In this study, we have generated the first Setd2-CD mouse model by knocking-in a single-point mutation which is derived from cancer patients. This mutation has been verified to specifically abolish the catalytic activity but not the transcriptional coupling of Setd2. This model provides a vital tool for determine whether the physiologic function of Setd2 is dependent on its catalytic activity. A side-by-side comparative study between the Setd2CD/CD and Setd2−/− mice at both phenotypic and molecular levels is important for properly interpreting the phenotypes and for drawing unbiased conclusions. Our results demonstrate both similarities and differences between these two models. On the one hand, they show very similar phenotypes, including embryonic lethality at E10.5, vascular defects, and the developmental retardation, all of which are underlain by closely comparable transcriptomic alterations. On the other hand, they also show certain differences, though being relatively subtle, in specific developmental events such as the chorioallantoic developmental defects which could be explained by differential regulations of the allantois-specific 5′ Hoxa cluster genes. Taken together, these results suggest that the essential functions of Setd2 in supporting mouse embryonic development is largely dependent on its catalytic activity, whereas in specific circumstances the Setd2-CD protein may still be able to exert minor noncatalytic functions.
Although epigenetic modifiers are usually thought to function mainly through their catalytic activities, their noncatalytic functions recently have attracted much attention owing to several elegant studies on specific CD mutants in comparison with complete knockout of the whole proteins. For example, in a mouse ES cell model harboring CD mutants of the H3K4me1 methyltransferases Mll3 and Mll4, studies showed that, despite the loss of H3K4me1 on the enhancers of the Mll3/4-target genes, transcriptional levels of these genes had much smaller changes in the Mll3/4-CD cells than that of those in the Mll3/4 double knockout cells, thus suggesting an important noncatalytic function of Mll3/4 [76]. This notion was further explored by a series of studies on a Drosophila model harboring the CD mutants of Trr (ortholog of mammalian Mll3/4), in which Trr-CD could rescue the embryonic lethality caused by Trr knockout, indicating that the viability of the embryos requires only the noncatalytic but not the whole functions of Trr [77]. Subsequently, a new domain within Trr was identified to mediate this noncatalytic function through interacting with, and stabilizing, the H3K27 demethylase Utx [78]. Furthermore, noncatalytic functions of several histone acetyltransferases such as Drosophila Nejire (ortholog of mammalian Cbp/p300) and Gcn5 (ortholog of mammalian Gcn5/Pcaf) have also been reported [79]. Based on these studies, it has been thoughtfully conceived that the noncatalytic activities of these epigenetic modifiers would be related to their involvement in multiprotein complexes through protein–protein interactions and/or the nature of functional redundancies among the different chromatin modifications [6]. In contrast, however, our study provides an example in the opposite side because the major physiologic function of Setd2 in mouse embryonic development is largely dependent on its catalytic activity. Notably, another example supporting this side is that the mouse model harboring a CD mutation in the DNA methyltransferase Dnmt1 showed similar embryonic lethal phenotypes as the Dnmt1 complete knockout mice [80]. Therefore, given the fact that both Setd2 and Dnmt1 play relatively nonredundant roles in H3K36me3 and DNA methylation maintenance, respectively, these studies jointly suggest that Setd2 and Dnmt1 may represent a class of epigenetic modifiers whose functions are heavily dependent on their catalytic activities because they themselves, and their catalyzed chromatin modifications, are basically irreplaceable.
Setd2 and H3K36me3 have been implicated into many aspects of genomic regulation, including gene transcriptional elongation, repression of intragenic cryptic transcription, repair of DNA damage, and mRNA splicing (for review, see [81,82]). However, as SETD2 catalyzes H3K36me3 on virtually all actively transcribed protein-coding genes, it remains unclear whether Setd2 tends to just indiscriminately regulate all target genes or preferentially regulate specific genes in any circumstance. If the latter possibility is real, those target genes that are preferentially regulated by SETD2 shall have special structural features (e.g., gene length, genomic structure or regulatory elements). Interestingly, previous studies have shown that, in yeasts, Set2-mediated H3K36 methylation preferentially regulates longer and infrequently transcribed genes [83], although this finding remains controversial due to variable statistical methodology [84]. Potentially related to this notion, we herein found that many collagen genes, which are highly interrupted and thus contain large numbers of exons [73], are downregulated in the Setd2CD/CD and Setd2−/− yolk sacs at very early developmental stage, therefore suggesting that these collagen genes could be considered as model genes in mammals to study whether the long and highly interrupted genes tend to be more dependent on Setd2 and H3K36me3. Furthermore, regarding the potential catalytically independent functions Setd2, we found that the 5′ Hoxa cluster genes are differentially regulated between the Setd2CD/CD and Setd2−/− embryos. This observation is possibly related to previous studies showing that, in Drosophila, the Hox cluster genes are more sensitive to the H3K36R and H3K36A mutants which could affect the crosstalk between H3K36me3 and PRC2-mediated H3K27me3 [85]. Besides these mechanisms, it has also been found that, in yeasts, overlapping genes (including those containing antisense RNAs within gene body) can be regulated by Set2 in a special way because of the possible promoter-locating H3K36me3 left by Set2 from the cDNA strand [86,87]. In this regard, considering that the mammalian genomes also contain some overlapping genes [8890], it would be interesting to investigate whether these genes may rely more on Setd2 either dependent or independent of the catalytic activity.
Since the discovery of SETD2 mutations in cancer, to our knowledge, there have been at least 10 Setd2 knockout mouse models independently generated by different research groups (including 1 constitutive and 9 conditional Setd2-knockout models) [27,3442]. In the present study, we generated the first Setd2 point mutation knockin mouse model. In addition to determining the catalytically dependent and independent functions of Setd2, we have also characterized this new model by comparing the heterozygous Setd2-CD and Setd2 null embryos. Significant difference between the Setd2+/CD and Setd2−/− mice suggests that the herein studied mutant Setd2 protein does not function as a dominant-negative factor against the WT Setd2 protein, while the similarity between Setd2CD/CD and Setd2−/−, but not Setd2+/−, suggests that the loss of catalytic activity, rather than protein instability, represents the key mechanism for this mutant Setd2 protein to cause the phenotypes in the mice. Lastly, although the embryonic lethality restricts the immediate use of this model to study tumorigenesis, crossing this model with the conditional Setd2 knockout models would be an option to create a window to evaluate the tissue-specific role of this patient-derived mutation, and the same approach would be useful to study many other patient-derived SETD2 mutations in the future.

Shubei Chen et al

References

[1]
Bird AP. CpG-rich islands and the function of DNA methylation. Nature 1986; 321(6067): 209–213
CrossRef Google scholar
[2]
Bestor TH, Verdine GL. DNA methyltransferases. Curr Opin Cell Biol 1994; 6(3): 380–389
CrossRef Google scholar
[3]
Jenuwein T, Allis CD. Translating the histone code. Science 2001; 293(5532): 1074–1080
CrossRef Google scholar
[4]
Aubert Y, Egolf S, Capell BC. The unexpected noncatalytic roles of histone modifiers in development and disease. Trends Genet 2019; 35(9): 645–657
CrossRef Google scholar
[5]
Morgan MAJ, Shilatifard A. Reevaluating the roles of histone-modifying enzymes and their associated chromatin modifications in transcriptional regulation. Nat Genet 2020; 52(12): 1271–1281
CrossRef Google scholar
[6]
Morgan MAJ, Shilatifard A. Epigenetic moonlighting: catalytic-independent functions of histone modifiers in regulating transcription. Sci Adv 2023; 9(16): eadg6593
CrossRef Google scholar
[7]
Strahl BD, Grant PA, Briggs SD, Sun ZW, Bone JR, Caldwell JA, Mollah S, Cook RG, Shabanowitz J, Hunt DF, Allis CD. Set2 is a nucleosomal histone H3-selective methyltransferase that mediates transcriptional repression. Mol Cell Biol 2002; 22(5): 1298–1306
CrossRef Google scholar
[8]
Sun XJ, Wei J, Wu XY, Hu M, Wang L, Wang HH, Zhang QH, Chen SJ, Huang QH, Chen Z. Identification and characterization of a novel human histone H3 lysine 36-specific methyltransferase. J Biol Chem 2005; 280(42): 35261–35271
CrossRef Google scholar
[9]
Kizer KO, Phatnani HP, Shibata Y, Hall H, Greenleaf AL, Strahl BD. A novel domain in Set2 mediates RNA polymerase II interaction and couples histone H3 K36 methylation with transcript elongation. Mol Cell Biol 2005; 25(8): 3305–3316
CrossRef Google scholar
[10]
Li M, Phatnani HP, Guan Z, Sage H, Greenleaf AL, Zhou P. Solution structure of the Set2-Rpb1 interacting domain of human Set2 and its interaction with the hyperphosphorylated C-terminal domain of Rpb1. Proc Natl Acad Sci USA 2005; 102(49): 17636–17641
CrossRef Google scholar
[11]
Vojnic E, Simon B, Strahl BD, Sattler M, Cramer P. Structure and carboxyl-terminal domain (CTD) binding of the Set2 SRI domain that couples histone H3 Lys36 methylation to transcription. J Biol Chem 2006; 281(1): 13–15
CrossRef Google scholar
[12]
Faber PW, Barnes GT, Srinidhi J, Chen J, Gusella JF, MacDonald ME. Huntingtin interacts with a family of WW domain proteins. Hum Mol Genet 1998; 7(9): 1463–1474
CrossRef Google scholar
[13]
Passani LA, Bedford MT, Faber PW, McGinnis KM, Sharp AH, Gusella JF, Vonsattel JP, MacDonald ME. Huntingtin’s WW domain partners in Huntington’s disease post-mortem brain fulfill genetic criteria for direct involvement in Huntington’s disease pathogenesis. Hum Mol Genet 2000; 9(14): 2175–2182
CrossRef Google scholar
[14]
Hesselberth JR, Miller JP, Golob A, Stajich JE, Michaud GA, Fields S. Comparative analysis of Saccharomyces cerevisiae WW domains and their interacting proteins. Genome Biol 2006; 7(4): R30
CrossRef Google scholar
[15]
Seervai RNH, Jangid RK, Karki M, Tripathi DN, Jung SY, Kearns SE, Verhey KJ, Cianfrocco MA, Millis BA, Tyska MJ, Mason FM, Rathmell WK, Park IY, Dere R, Walker CL. The Huntingtin-interacting protein SETD2/HYPB is an actin lysine methyltransferase. Sci Adv 2020; 6(40): eabb7854
CrossRef Google scholar
[16]
Yuan W, Xie J, Long C, Erdjument-Bromage H, Ding X, Zheng Y, Tempst P, Chen S, Zhu B, Reinberg D. Heterogeneous nuclear ribonucleoprotein L Is a subunit of human KMT3a/Set2 complex required for H3 Lys-36 trimethylation activity in vivo. J Biol Chem 2009; 284(23): 15701–15707
CrossRef Google scholar
[17]
Bhattacharya S, Levy MJ, Zhang N, Li H, Florens L, Washburn MP, Workman JL. The methyltransferase SETD2 couples transcription and splicing by engaging mRNA processing factors through its SHI domain. Nat Commun 2021; 12(1): 1443
CrossRef Google scholar
[18]
Bhattacharya S, Wang S, Reddy D, Shen S, Zhang Y, Zhang N, Li H, Washburn MP, Florens L, Shi Y, Workman JL, Li F. Structural basis of the interaction between SETD2 methyltransferase and hnRNP L paralogs for governing co-transcriptional splicing. Nat Commun 2021; 12(1): 6452
CrossRef Google scholar
[19]
Bhattacharya S, Lange JJ, Levy M, Florens L, Washburn MP, Workman JL. The disordered regions of the methyltransferase SETD2 govern its function by regulating its proteolysis and phase separation. J Biol Chem 2021; 297(3): 101075
CrossRef Google scholar
[20]
Li J, Moazed D, Gygi SP. Association of the histone methyltransferase Set2 with RNA polymerase II plays a role in transcription elongation. J Biol Chem 2002; 277(51): 49383–49388
CrossRef Google scholar
[21]
Krogan NJ, Kim M, Tong A, Golshani A, Cagney G, Canadien V, Richards DP, Beattie BK, Emili A, Boone C, Shilatifard A, Buratowski S, Greenblatt J. Methylation of histone H3 by Set2 in Saccharomyces cerevisiae is linked to transcriptional elongation by RNA polymerase II. Mol Cell Biol 2003; 23(12): 4207–4218
CrossRef Google scholar
[22]
Li B, Howe L, Anderson S, Yates JR 3rd, Workman JL. The Set2 histone methyltransferase functions through the phosphorylated carboxyl-terminal domain of RNA polymerase II. J Biol Chem 2003; 278(11): 8897–8903
CrossRef Google scholar
[23]
Xiao T, Hall H, Kizer KO, Shibata Y, Hall MC, Borchers CH, Strahl BD. Phosphorylation of RNA polymerase II CTD regulates H3 methylation in yeast. Genes Dev 2003; 17(5): 654–663
CrossRef Google scholar
[24]
Schaft D, Roguev A, Kotovic KM, Shevchenko A, Sarov M, Shevchenko A, Neugebauer KM, Stewart AF. The histone 3 lysine 36 methyltransferase, SET2, is involved in transcriptional elongation. Nucleic Acids Res 2003; 31(10): 2475–2482
CrossRef Google scholar
[25]
Edmunds JW, Mahadevan LC, Clayton AL. Dynamic histone H3 methylation during gene induction: HYPB/Setd2 mediates all H3K36 trimethylation. EMBO J 2008; 27(2): 406–420
CrossRef Google scholar
[26]
Sun XJ, Xu PF, Zhou T, Hu M, Fu CT, Zhang Y, Jin Y, Chen Y, Chen SJ, Huang QH, Liu TX, Chen Z. Genome-wide survey and developmental expression mapping of zebrafish SET domain-containing genes. PLoS One 2008; 3(1): e1499
CrossRef Google scholar
[27]
Hu M, Sun XJ, Zhang YL, Kuang Y, Hu CQ, Wu WL, Shen SH, Du TT, Li H, He F, Xiao HS, Wang ZG, Liu TX, Lu H, Huang QH, Chen SJ, Chen Z. Histone H3 lysine 36 methyltransferase Hypb/Setd2 is required for embryonic vascular remodeling. Proc Natl Acad Sci USA 2010; 107(7): 2956–2961
CrossRef Google scholar
[28]
Barski A, Cuddapah S, Cui K, Roh TY, Schones DE, Wang Z, Wei G, Chepelev I, Zhao K. High-resolution profiling of histone methylations in the human genome. Cell 2007; 129(4): 823–837
CrossRef Google scholar
[29]
Dalgliesh GL, Furge K, Greenman C, Chen L, Bignell G, Butler A, Davies H, Edkins S, Hardy C, Latimer C, Teague J, Andrews J, Barthorpe S, Beare D, Buck G, Campbell PJ, Forbes S, Jia M, Jones D, Knott H, Kok CY, Lau KW, Leroy C, Lin ML, McBride DJ, Maddison M, Maguire S, McLay K, Menzies A, Mironenko T, Mulderrig L, Mudie L, O’Meara S, Pleasance E, Rajasingham A, Shepherd R, Smith R, Stebbings L, Stephens P, Tang G, Tarpey PS, Turrell K, Dykema KJ, Khoo SK, Petillo D, Wondergem B, Anema J, Kahnoski RJ, Teh BT, Stratton MR, Futreal PA. Systematic sequencing of renal carcinoma reveals inactivation of histone modifying genes. Nature 2010; 463(7279): 360–363
CrossRef Google scholar
[30]
Kandoth C, McLellan MD, Vandin F, Ye K, Niu B, Lu C, Xie M, Zhang Q, McMichael JF, Wyczalkowski MA, Leiserson MDM, Miller CA, Welch JS, Walter MJ, Wendl MC, Ley TJ, Wilson RK, Raphael BJ, Ding L. Mutational landscape and significance across 12 major cancer types. Nature 2013; 502(7471): 333–339
CrossRef Google scholar
[31]
Luscan A, Laurendeau I, Malan V, Francannet C, Odent S, Giuliano F, Lacombe D, Touraine R, Vidaud M, Pasmant E, Cormier-Daire V. Mutations in SETD2 cause a novel overgrowth condition. J Med Genet 2014; 51(8): 512–517
CrossRef Google scholar
[32]
D’Gama AM, Pochareddy S, Li M, Jamuar SS, Reiff RE, Lam AN, Sestan N, Walsh CA. Targeted DNA sequencing from autism spectrum disorder brains implicates multiple genetic mechanisms. Neuron 2015; 88(5): 910–917
CrossRef Google scholar
[33]
Liu DJ, Zhang F, Chen Y, Jin Y, Zhang YL, Chen SB, Xie YY, Huang QH, Zhao WL, Wang L, Xu PF, Chen Z, Chen SJ, Li B, Zhang A, Sun XJ. setd2 knockout zebrafish is viable and fertile: differential and developmental stress-related requirements for Setd2 and histone H3K36 trimethylation in different vertebrate animals. Cell Discov 2020; 6(1): 72
CrossRef Google scholar
[34]
Park IY, Powell RT, Tripathi DN, Dere R, Ho TH, Blasius TL, Chiang YC, Davis IJ, Fahey CC, Hacker KE, Verhey KJ, Bedford MT, Jonasch E, Rathmell WK, Walker CL. Dual chromatin and cytoskeletal remodeling by SETD2. Cell 2016; 166(4): 950–962
CrossRef Google scholar
[35]
Chen K, Liu J, Liu S, Xia M, Zhang X, Han D, Jiang Y, Wang C, Cao X. Methyltransferase SETD2-mediated methylation of STAT1 is critical for interferon antiviral activity. Cell 2017; 170(3): 492–506.e14
CrossRef Google scholar
[36]
Mar BG, Chu SH, Kahn JD, Krivtsov AV, Koche R, Castellano CA, Kotlier JL, Zon RL, McConkey ME, Chabon J, Chappell R, Grauman PV, Hsieh JJ, Armstrong SA, Ebert BL. SETD2 alterations impair DNA damage recognition and lead to resistance to chemotherapy in leukemia. Blood 2017; 130(24): 2631–2641
CrossRef Google scholar
[37]
Moffitt AB, Ondrejka SL, McKinney M, Rempel RE, Goodlad JR, Teh CH, Leppa S, Mannisto S, Kovanen PE, Tse E, Au-Yeung RKH, Kwong YL, Srivastava G, Iqbal J, Yu J, Naresh K, Villa D, Gascoyne RD, Said J, Czader MB, Chadburn A, Richards KL, Rajagopalan D, Davis NS, Smith EC, Palus BC, Tzeng TJ, Healy JA, Lugar PL, Datta J, Love C, Levy S, Dunson DB, Zhuang Y, Hsi ED, Dave SS. Enteropathy-associated T cell lymphoma subtypes are characterized by loss of function of SETD2. J Exp Med 2017; 214(5): 1371–1386
CrossRef Google scholar
[38]
Zhang YL, Sun JW, Xie YY, Zhou Y, Liu P, Song JC, Xu CH, Wang L, Liu D, Xu AN, Chen Z, Chen SJ, Sun XJ, Huang QH. Setd2 deficiency impairs hematopoietic stem cell self-renewal and causes malignant transformation. Cell Res 2018; 28(4): 476–490
CrossRef Google scholar
[39]
Zhou Y, Yan X, Feng X, Bu J, Dong Y, Lin P, Hayashi Y, Huang R, Olsson A, Andreassen PR, Grimes HL, Wang QF, Cheng T, Xiao Z, Jin J, Huang G. Setd2 regulates quiescence and differentiation of adult hematopoietic stem cells by restricting RNA polymerase II elongation. Haematologica 2018; 103(7): 1110–1123
CrossRef Google scholar
[40]
Zuo X, Rong B, Li L, Lv R, Lan F, Tong MH. The histone methyltransferase SETD2 is required for expression of acrosin-binding protein 1 and protamines and essential for spermiogenesis in mice. J Biol Chem 2018; 293(24): 9188–9197
CrossRef Google scholar
[41]
Xu L, Zheng Y, Li X, Wang A, Huo D, Li Q, Wang S, Luo Z, Liu Y, Xu F, Wu X, Wu M, Zhou Y. Abnormal neocortex arealization and Sotos-like syndrome-associated behavior in Setd2 mutant mice. Sci Adv 2021; 7(1): eaba1180
CrossRef Google scholar
[42]
Xie Y, Sahin M, Wakamatsu T, Inoue-Yamauchi A, Zhao W, Han S, Nargund AM, Yang S, Lyu Y, Hsieh JJ, Leslie CS, Cheng EH. SETD2 regulates chromatin accessibility and transcription to suppress lung tumorigenesis. JCI Insight 2023; 8(4): e154120
CrossRef Google scholar
[43]
Yuan H, Li N, Fu D, Ren J, Hui J, Peng J, Liu Y, Qiu T, Jiang M, Pan Q, Han Y, Wang X, Li Q, Qin J. Histone methyltransferase SETD2 modulates alternative splicing to inhibit intestinal tumorigenesis. J Clin Invest 2017; 127(9): 3375–3391
CrossRef Google scholar
[44]
Chen BY, Song J, Hu CL, Chen SB, Zhang Q, Xu CH, Wu JC, Hou D, Sun M, Zhang YL, Liu N, Yu PC, Liu P, Zong LJ, Zhang JY, Dai RF, Lan F, Huang QH, Zhang SJ, Nimer SD, Chen Z, Chen SJ, Sun XJ, Wang L. SETD2 deficiency accelerates MDS-associated leukemogenesis via S100a9 in NHD13 mice and predicts poor prognosis in MDS. Blood 2020; 135(25): 2271–2285
CrossRef Google scholar
[45]
Niu N, Lu P, Yang Y, He R, Zhang L, Shi J, Wu J, Yang M, Zhang ZG, Wang LW, Gao WQ, Habtezion A, Xiao GG, Sun Y, Li L, Xue J. Loss of Setd2 promotes Kras-induced acinar-to-ductal metaplasia and epithelia-mesenchymal transition during pancreatic carcinogenesis. Gut 2020; 69(4): 715–726
CrossRef Google scholar
[46]
Yuan H, Han Y, Wang X, Li N, Liu Q, Yin Y, Wang H, Pan L, Li L, Song K, Qiu T, Pan Q, Chen Q, Zhang G, Zang Y, Tan M, Zhang J, Li Q, Wang X, Jiang J, Qin J. SETD2 restricts prostate cancer metastasis by integrating EZH2 and AMPK signaling pathways. Cancer Cell 2020; 38(3): 350–365.e7
CrossRef Google scholar
[47]
Rao H, Li X, Liu M, Liu J, Feng W, Tang H, Xu J, Gao WQ, Li L. Multilevel regulation of beta-catenin activity by SETD2 suppresses the transition from polycystic kidney disease to clear cell renal cell carcinoma. Cancer Res 2021; 81(13): 3554–3567
CrossRef Google scholar
[48]
Rao H, Liu C, Wang A, Ma C, Xu Y, Ye T, Su W, Zhou P, Gao WQ, Li L, Ding X. SETD2 deficiency accelerates sphingomyelin accumulation and promotes the development of renal cancer. Nat Commun 2023; 14(1): 7572
CrossRef Google scholar
[49]
Song J, Du L, Liu P, Wang F, Zhang B, Xie Y, Lu J, Jin Y, Zhou Y, Lv G, Zhang J, Chen S, Chen Z, Sun X, Zhang Y, Huang Q. Intra-heterogeneity in transcription and chemoresistant property of leukemia-initiating cells in murine Setd2−/− acute myeloid leukemia. Cancer Commun (Lond) 2021; 41(9): 867–888
CrossRef Google scholar
[50]
Ma C, Liu M, Feng W, Rao H, Zhang W, Liu C, Xu Y, Wang Z, Teng Y, Yang X, Ni L, Xu J, Gao WQ, Lu B, Li L. Loss of SETD2 aggravates colorectal cancer progression caused by SMAD4 deletion through the RAS/ERK signalling pathway. Clin Transl Med 2023; 13(11): e1475
CrossRef Google scholar
[51]
Zheng X, Luo Y, Xiong Y, Liu X, Zeng C, Lu X, Wang X, Cheng Y, Wang S, Lan H, Wang K, Weng Z, Bi W, Gan X, Jia X, Wang L, Wang Y. Tumor cell-intrinsic SETD2 inactivation sensitizes cancer cells to immune checkpoint blockade through the NR2F1-STAT1 pathway. J Immunother Cancer 2023; 11(12): e007678
CrossRef Google scholar
[52]
Sun XJ, Wang Z, Wang L, Jiang Y, Kost N, Soong TD, Chen WY, Tang Z, Nakadai T, Elemento O, Fischle W, Melnick A, Patel DJ, Nimer SD, Roeder RG. A stable transcription factor complex nucleated by oligomeric AML1-ETO controls leukaemogenesis. Nature 2013; 500(7460): 93–97
CrossRef Google scholar
[53]
Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods 2008; 5(7): 621–628
CrossRef Google scholar
[54]
Zhang F, Zeng QY, Xu H, Xu AN, Liu DJ, Li NZ, Chen Y, Jin Y, Xu CH, Feng CZ, Zhang YL, Liu D, Liu N, Xie YY, Yu SH, Yuan H, Xue K, Shi JY, Liu TX, Xu PF, Zhao WL, Zhou Y, Wang L, Huang QH, Chen Z, Chen SJ, Zhou XL, Sun XJ. Selective and competitive functions of the AAR and UPR pathways in stress-induced angiogenesis. Cell Discov 2021; 7(1): 98
CrossRef Google scholar
[55]
Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, Paulovich A, Pomeroy SL, Golub TR, Lander ES, Mesirov JP. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci USA 2005; 102(43): 15545–15550
CrossRef Google scholar
[56]
Grosswendt S, Kretzmer H, Smith ZD, Kumar AS, Hetzel S, Wittler L, Klages S, Timmermann B, Mukherji S, Meissner A. Epigenetic regulator function through mouse gastrulation. Nature 2020; 584(7819): 102–108
CrossRef Google scholar
[57]
Fahey CC, Davis IJ. SETting the stage for cancer development: SETD2 and the consequences of lost methylation. Cold Spring Harb Perspect Med 2017; 7(5): a026468
CrossRef Google scholar
[58]
Patnaik MM, Abdel-Wahab O. SETD2—linking stem cell survival and transformation. Cell Res 2018; 28(4): 393–394
CrossRef Google scholar
[59]
Gerlinger M, Rowan AJ, Horswell S, Math M, Larkin J, Endesfelder D, Gronroos E, Martinez P, Matthews N, Stewart A, Tarpey P, Varela I, Phillimore B, Begum S, McDonald NQ, Butler A, Jones D, Raine K, Latimer C, Santos CR, Nohadani M, Eklund AC, Spencer-Dene B, Clark G, Pickering L, Stamp G, Gore M, Szallasi Z, Downward J, Futreal PA, Swanton C. Intratumor heterogeneity and branched evolution revealed by multiregion sequencing. N Engl J Med 2012; 366(10): 883–892
CrossRef Google scholar
[60]
The Cancer Genome Atlas Research Network. Comprehensive molecular characterization of clear cell renal cell carcinoma. Nature 2013; 499(7456): 43–49
CrossRef Google scholar
[61]
Kanu N, Gronroos E, Martinez P, Burrell RA, Yi Goh X, Bartkova J, Maya-Mendoza A, Mistrik M, Rowan AJ, Patel H, Rabinowitz A, East P, Wilson G, Santos CR, McGranahan N, Gulati S, Gerlinger M, Birkbak NJ, Joshi T, Alexandrov LB, Stratton MR, Powles T, Matthews N, Bates PA, Stewart A, Szallasi Z, Larkin J, Bartek J, Swanton C. SETD2 loss-of-function promotes renal cancer branched evolution through replication stress and impaired DNA repair. Oncogene 2015; 34(46): 5699–5708
CrossRef Google scholar
[62]
González-Rodríguez P, Engskog-Vlachos P, Zhang H, Murgoci AN, Zerdes I, Joseph B. SETD2 mutation in renal clear cell carcinoma suppress autophagy via regulation of ATG12. Cell Death Dis 2020; 11(1): 69
CrossRef Google scholar
[63]
Xie Y, Sahin M, Sinha S, Wang Y, Nargund AM, Lyu Y, Han S, Dong Y, Hsieh JJ, Leslie CS, Cheng EH. SETD2 loss perturbs the kidney cancer epigenetic landscape to promote metastasis and engenders actionable dependencies on histone chaperone complexes. Nat Cancer 2022; 3(2): 188–202
CrossRef Google scholar
[64]
Liu XD, Zhang YT, McGrail DJ, Zhang X, Lam T, Hoang A, Hasanov E, Manyam G, Peterson CB, Zhu H, Kumar SV, Akbani R, Pilie PG, Tannir NM, Peng G, Jonasch E. SETD2 loss and ATR inhibition synergize to promote cGAS signaling and immunotherapy response in renal cell carcinoma. Clin Cancer Res 2023; 29(19): 4002–4015
CrossRef Google scholar
[65]
Yang S, Zheng X, Lu C, Li GM, Allis CD, Li H. Molecular basis for oncohistone H3 recognition by SETD2 methyltransferase. Genes Dev 2016; 30(14): 1611–1616
CrossRef Google scholar
[66]
Liu Y, Zhang Y, Xue H, Cao M, Bai G, Mu Z, Yao Y, Sun S, Fang D, Huang J. Cryo-EM structure of SETD2/Set2 methyltransferase bound to a nucleosome containing oncohistone mutations. Cell Discov 2021; 7(1): 32
CrossRef Google scholar
[67]
Zhu K, Lei PJ, Ju LG, Wang X, Huang K, Yang B, Shao C, Zhu Y, Wei G, Fu XD, Li L, Wu M. SPOP-containing complex regulates SETD2 stability and H3K36me3-coupled alternative splicing. Nucleic Acids Res 2017; 45(1): 92–105
CrossRef Google scholar
[68]
Bhattacharya S, Lange JJ, Levy M, Florens L, Washburn MP, Workman JL. The disordered regions of the methyltransferase SETD2 govern its function by regulating its proteolysis and phase separation. J Biol Chem 2021; 297(3): 101075
CrossRef Google scholar
[69]
Gallardo T, Shirley L, John GB, Castrillon DH. Generation of a germ cell-specific mouse transgenic Cre line, Vasa-Cre. Genesis 2007; 45(6): 413–417
CrossRef Google scholar
[70]
Liberzon A, Birger C, Thorvaldsdottir H, Ghandi M, Mesirov JP, Tamayo P. The Molecular Signatures Database (MSigDB) hallmark gene set collection. Cell Syst 2015; 1(6): 417–425
CrossRef Google scholar
[71]
Gene Ontology Consortium; Aleksander SA, Balhoff J, Carbon S, Cherry JM, Drabkin HJ, Ebert D, Feuermann M, Gaudet P, Harris NL, Hill DP, Lee R, Mi H, Moxon S, Mungall CJ, Muruganugan A, Mushayahama T, Sternberg PW, Thomas PD, Van Auken K, Ramsey J, Siegele DA, Chisholm RL, Fey P, Aspromonte MC, Nugnes MV, Quaglia F, Tosatto S, Giglio M, Nadendla S, Antonazzo G, Attrill H, Dos Santos G, Marygold S, Strelets V, Tabone CJ, Thurmond J, Zhou P, Ahmed SH, Asanitthong P, Luna Buitrago D, Erdol MN, Gage MC, Ali Kadhum M, Li KYC, Long M, Michalak A, Pesala A, Pritazahra A, Saverimuttu SCC, Su R, Thurlow KE, Lovering RC, Logie C, Oliferenko S, Blake J, Christie K, Corbani L, Dolan ME, Drabkin HJ, Hill DP, Ni L, Sitnikov D, Smith C, Cuzick A, Seager J, Cooper L, Elser J, Jaiswal P, Gupta P, Jaiswal P, Naithani S, Lera-Ramirez M, Rutherford K, Wood V, De Pons JL, Dwinell MR, Hayman GT, Kaldunski ML, Kwitek AE, Laulederkind SJF, Tutaj MA, Vedi M, Wang SJ, D'Eustachio P, Aimo L, Axelsen K, Bridge A, Hyka-Nouspikel N, Morgat A, Aleksander SA, Cherry JM, Engel SR, Karra K, Miyasato SR, Nash RS, Skrzypek MS, Weng S, Wong ED, Bakker E, Berardini TZ, Reiser L, Auchincloss A, Axelsen K, Argoud-Puy G, Blatter MC, Boutet E, Breuza L, Bridge A, Casals-Casas C, Coudert E, Estreicher A, Livia Famiglietti M, Feuermann M, Gos A, Gruaz-Gumowski N, Hulo C, Hyka-Nouspikel N, Jungo F, Le Mercier P, Lieberherr D, Masson P, Morgat A, Pedruzzi I, Pourcel L, Poux S, Rivoire C, Sundaram S, Bateman A, Bowler-Barnett E, Bye-A-Jee H, Denny P, Ignatchenko A, Ishtiaq R, Lock A, Lussi Y, Magrane M, Martin MJ, Orchard S, Raposo P, Speretta E, Tyagi N, Warner K, Zaru R, Diehl AD, Lee R, Chan J, Diamantakis S, Raciti D, Zarowiecki M, Fisher M, James-Zorn C, Ponferrada V, Zorn A, Ramachandran S, Ruzicka L, Westerfield M. The Gene Ontology knowledgebase in 2023. Genetics 2023; 224(1): iyad031
CrossRef Google scholar
[72]
Myllyharju J, Kivirikko KI. Collagens and collagen-related diseases. Ann Med 2001; 33(1): 7–21
CrossRef Google scholar
[73]
ChuML. Structural Proteins: Genes for Collagen. Encyclopedia of Life Sciences. 2011
[74]
Shaut CA, Keene DR, Sorensen LK, Li DY, Stadler HS. HOXA13 is essential for placental vascular patterning and labyrinth endothelial specification. PLoS Genet 2008; 4(5): e1000073
CrossRef Google scholar
[75]
Scotti M, Kmita M. Recruitment of 5′ Hoxa genes in the allantois is essential for proper extra-embryonic function in placental mammals. Development 2012; 139(4): 731–739
CrossRef Google scholar
[76]
Dorighi KM, Swigut T, Henriques T, Bhanu NV, Scruggs BS, Nady N, Still CD 2nd, Garcia BA, Adelman K, Wysocka J. Mll3 and Mll4 facilitate enhancer RNA synthesis and transcription from promoters independently of H3K4 monomethylation. Mol Cell 2017; 66(4): 568–576.e4
CrossRef Google scholar
[77]
Rickels R, Herz HM, Sze CC, Cao K, Morgan MA, Collings CK, Gause M, Takahashi YH, Wang L, Rendleman EJ, Marshall SA, Krueger A, Bartom ET, Piunti A, Smith ER, Abshiru NA, Kelleher NL, Dorsett D, Shilatifard A. Histone H3K4 monomethylation catalyzed by Trr and mammalian COMPASS-like proteins at enhancers is dispensable for development and viability. Nat Genet 2017; 49(11): 1647–1653
CrossRef Google scholar
[78]
Rickels R, Wang L, Iwanaszko M, Ozark PA, Morgan MA, Piunti A, Khalatyan N, Soliman SHA, Rendleman EJ, Savas JN, Smith ER, Shilatifard A. A small UTX stabilization domain of Trr is conserved within mammalian MLL3–4/COMPASS and is sufficient to rescue loss of viability in null animals. Genes Dev 2020; 34(21–22): 1493–1502
CrossRef Google scholar
[79]
Ciabrelli F, Rabbani L, Cardamone F, Zenk F, Loser E, Schachtle MA, Mazina M, Loubiere V, Iovino N. CBP and Gcn5 drive zygotic genome activation independently of their catalytic activity. Sci Adv 2023; 9(16): eadf2687
CrossRef Google scholar
[80]
Takebayashi S, Tamura T, Matsuoka C, Okano M. Major and essential role for the DNA methylation mark in mouse embryogenesis and stable association of DNMT1 with newly replicated regions. Mol Cell Biol 2007; 27(23): 8243–8258
CrossRef Google scholar
[81]
McDaniel SL, Strahl BD. Shaping the cellular landscape with Set2/SETD2 methylation. Cell Mol Life Sci 2017; 74(18): 3317–3334
CrossRef Google scholar
[82]
Li J, Ahn JH, Wang GG. Understanding histone H3 lysine 36 methylation and its deregulation in disease. Cell Mol Life Sci 2019; 76(15): 2899–2916
CrossRef Google scholar
[83]
Li B, Gogol M, Carey M, Pattenden SG, Seidel C, Workman JL. Infrequently transcribed long genes depend on the Set2/Rpd3S pathway for accurate transcription. Genes Dev 2007; 21(11): 1422–1430
CrossRef Google scholar
[84]
Lickwar CR, Rao B, Shabalin AA, Nobel AB, Strahl BD, Lieb JD. The Set2/Rpd3S pathway suppresses cryptic transcription without regard to gene length or transcription frequency. PLoS One 2009; 4(3): e4886
CrossRef Google scholar
[85]
Finogenova K, Bonnet J, Poepsel S, Schafer IB, Finkl K, Schmid K, Litz C, Strauss M, Benda C, Muller J. Structural basis for PRC2 decoding of active histone methylation marks H3K36me2/3. eLife 2020; 9: e61964
CrossRef Google scholar
[86]
Kim JH, Lee BB, Oh YM, Zhu C, Steinmetz LM, Lee Y, Kim WK, Lee SB, Buratowski S, Kim T. Modulation of mRNA and lncRNA expression dynamics by the Set2-Rpd3S pathway. Nat Commun 2016; 7(1): 13534
CrossRef Google scholar
[87]
Venkatesh S, Li H, Gogol MM, Workman JL. Selective suppression of antisense transcription by Set2-mediated H3K36 methylation. Nat Commun 2016; 7(1): 13610
CrossRef Google scholar
[88]
Adelman JP, Bond CT, Douglass J, Herbert E. Two mammalian genes transcribed from opposite strands of the same DNA locus. Science 1987; 235(4795): 1514–1517
CrossRef Google scholar
[89]
Rosikiewicz W, Suzuki Y, Makalowska I. OverGeneDB: a database of 5′ end protein coding overlapping genes in human and mouse genomes. Nucleic Acids Res 2018; 46(D1): D186–D193
CrossRef Google scholar
[90]
Liu D, Xu C, Liu Y, Ouyang W, Lin S, Xu A, Zhang Y, Xie Y, Huang Q, Zhao W, Chen Z, Wang L, Chen S, Huang J, Wu ZB, Sun X. A systematic survey of LU domain-containing proteins reveals a novel human gene, LY6A, which encodes the candidate ortholog of mouse Ly-6A/Sca-1 and is aberrantly expressed in pituitary tumors. Front Med 2023; 17(3): 458–475
CrossRef Google scholar

Acknowledgements

The computations in this study were run on the Siyuan-1 cluster supported by the Center for High Performance Computing at Shanghai Jiao Tong University. This work was supported by the National Key R&D Plan of China (No. 2018YFA0107802 to Xiaojian Sun, Nos. 2018YFA0107200 and 2018YFA0800203 to Lan Wang), the National Natural Science Foundation of China General Program (Nos. 81970150 and 82170156 to Lan Wang), Shanghai “Science and Technology Innovation Action Plan” Excellent Academic/Technical Leader Program (Youth) (No. 21XD1424500 to Lan Wang), Shanghai Collaborative Innovation Program on Regenerative Medicine and Stem Cell Research (No. 2019CXJQ01 to Saijuan Chen and Xiaojian Sun), Samuel Waxman Cancer Research Foundation, and the Shanghai Guangci Translational Medical Research Development Foundation.

Compliance with ethics guidelines

Conflicts of interest Shubei Chen, Dianjia Liu, Bingyi Chen, Zijuan Li, Binhe Chang, Chunhui Xu, Ningzhe Li, Changzhou Feng, Xibo Hu, Weiying Wang, Yuanliang Zhang, Yinyin Xie, Qiuhua Huang, Yingcai Wang, Stephen D. Nimer, Zhu Chen, Lan Wang, and Xiaojian Sun declare no potential conflicts of interest. Saijuan Chen is one of Editors-in-Chief of Frontiers of Medicine, who was excluded from the peer-review process and all editorial decisions related to the acceptance and publication of this article. Peer-review was handled independently by the other editors to minimise bias.
All the procedure of this study was approved by the Institutional Review Board of the Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine. The animal studies were approved by the Committee of Animal Use at Shanghai Institute of Nutrition and Health, Chinese Academy of Sciences. All institutional and national guidelines for the care and use of laboratory animals were followed.

RIGHTS & PERMISSIONS

2024 Higher Education Press
AI Summary AI Mindmap
PDF(14879 KB)

1179

Accesses

1

Citations

9

Altmetric

Detail

Sections
Recommended

/