An intronic enhancer of Cebpa regulates adipocyte differentiation and adipose tissue development via long-range loop formation

Abstract

Cebpa is a master transcription factor gene for adipogenesis. However, the mechanisms of enhancer–promoter chromatin interactions controlling Cebpa transcriptional regulation during adipogenic differentiation remain largely unknown. To reveal how the three-dimensional structure of Cebpa changes during adipogenesis, we generated high-resolution chromatin interactions of Cebpa in 3T3-L1 preadipocytes and 3T3-L1 adipocytes using circularized chromosome conformation capture sequencing (4C-seq). We revealed dramatic changes in chromatin interactions and chromatin status at interaction sites during adipogenic differentiation. Based on this, we identified five active enhancers of Cebpa in 3T3-L1 adipocytes through epigenomic data and luciferase reporter assays. Next, epigenetic repression of Cebpa-L1-AD-En2 or -En3 by the dCas9-KRAB system significantly down-regulated Cebpa expression and inhibited adipocyte differentiation. Furthermore, experimental depletion of cohesin decreased the interaction intensity between Cebpa-L1-AD-En2 and the Cebpa promoter and down-regulated Cebpa expression, indicating that long-range chromatin loop formation was mediated by cohesin. Two transcription factors, RXRA and PPARG, synergistically regulate the activity of Cebpa-L1-AD-En2. To test whether Cebpa-L1-AD-En2 plays a role in adipose tissue development, we injected dCas9-KRAB-En2 lentivirus into the inguinal white adipose tissue (iWAT) of mice to suppress the activity of Cebpa-L1-AD-En2. Repression of Cebpa-L1-AD-En2 significantly decreased Cebpa expression and adipocyte size, altered iWAT transcriptome, and affected iWAT development. We identified functional enhancers regulating Cebpa expression and clarified the crucial roles of Cebpa-L1-AD-En2 and Cebpa promoter interaction in adipocyte differentiation and adipose tissue development.

References

[1] Kershaw EE, Flier JS. Adipose tissue as an endocrine organ. J Clin Endocrinol Metabol. 2004;89(6):2548-2556.

[2] Scherer PE. Adipose tissue: from lipid storage compartment to endocrine organ. Diabetes. 2006;55(6):1537-1545.

[3] Cawthorn WP, Scheller EL, MacDougald OA. Adipose tissue stem cells meet preadipocyte commitment: going back to the future. J Lipid Res. 2012;53(2):227-246.

[4] Cristancho AG, Lazar MA. Forming functional fat: a growing understanding of adipocyte differentiation. Nat Rev Mol Cell Biol. 2011;12(11):722-734.

[5] Siersbæk R, Mandrup S. Transcriptional networks controlling adipocyte differentiation. Cold Spring Harb Symp Quant Biol. 2011;76:247-255.

[6] Siersbæk R, Nielsen R, John S, et al. Extensive chromatin remodelling and establishment of transcription factor 'hotspots' during early adipogenesis. EMBO J. 2011;30(8):1459-1472.

[7] Siersbæk R, Nielsen R, Mandrup S. Transcriptional networks and chromatin remodeling controlling adipogenesis. Trends Endocrinol Metab. 2012;23(2):56-64.

[8] Tang QQ, Zhang JW, Daniel LM. Sequential gene promoter interactions of C/EBPbeta, C/EBPalpha, and PPARgamma during adipogenesis. Biochem Biophys Res Commun. 2004;319(1):235-239.

[9] Rosen ED, Hsu CH, Wang X, et al. C/EBPalpha induces adipogenesis through PPARgamma: a unified pathway. Genes Dev. 2002;16(1):22-26.

[10] Wu Z, Rosen ED, Brun R, et al. Cross-regulation of C/EBPα and PPARγ controls the transcriptional pathway of adipogenesis and insulin sensitivity. Mol Cell. 1999;3(2):151-158.

[11] Lefterova MI, Lazar MA. New developments in adipogenesis. Trends Endocrinol Metab. 2009;20(3):107-114.

[12] Freytag SO, Paielli DL, Gilbert JD. Ectopic expression of the CCAAT/enhancer-binding protein alpha promotes the adipogenic program in a variety of mouse fibroblastic cells. Genes Dev. 1994;8(14):1654-1663.

[13] Lin FT, Lane MD. Antisense CCAAT/enhancer-binding protein RNA suppresses coordinate gene expression and triglyceride accumulation during differentiation of 3T3-L1 preadipocytes. Genes Dev. 1992;6(4):533-544.

[14] Shao H-Y, Hsu H-Y, Wu K-S, Hee S-W, Chuang L-M, Yeh J-I. Prolonged induction activates Cebpα independent Adipogenesis in NIH/3T3 cells. PLoS One. 2013;8(1):e51459.

[15] Wang ND, Finegold MJ, Bradley A, et al. Impaired energy homeostasis in C/EBP alpha knockout mice. Science. 1995;269(5227):1108-1112.

[16] Linhart HG, Ishimura-Oka K, DeMayo F, et al. C/EBPalpha is required for differentiation of white, but not brown, adipose tissue. Proc Natl Acad Sci U S A. 2001;98(22):12532-12537.

[17] Olofsson LE, Orho-Melander M, William-Olsson L, et al. CCAAT/enhancer binding protein alpha (C/EBPα) in adipose tissue regulates genes in lipid and glucose metabolism and a genetic variation in C/EBPα is associated with serum levels of triglycerides. J Clin Endocrinol Metab. 2008;93(12):4880-4886.

[18] Delgado-Lista J, Perez-Martinez P, Garcia-Rios A, et al. A gene variation (rs12691) in the CCAT/enhancer binding protein α modulates glucose metabolism in metabolic syndrome. Nutr Metab Cardiovasc Dis. 2013;23(5):417-423.

[19] Bennett CE, Nsengimana J, Bostock JA, et al. CCAAT/enhancer binding protein α, β and δ gene variants: associations with obesity related phenotypes in the Leeds family study. Diab Vasc Dis Res. 2010;7(3):195-203.

[20] Misteli T, Soutoglou E. The emerging role of nuclear architecture in DNA repair and genome maintenance. Nat Rev Mol Cell Biol. 2009;10(4):243-254.

[21] Rowley MJ, Corces VG. Organizational principles of 3D genome architecture. Nat Rev Genet. 2018;19(12):789-800.

[22] Schoenfelder S, Fraser P. Long-range enhancer–promoter contacts in gene expression control. Nat Rev Genet. 2019;20(8):437-455.

[23] Zheng H, Xie W. The role of 3D genome organization in development and cell differentiation. Nat Rev Mol Cell Biol. 2019;20(9):535-550.

[24] Panigrahi A, O'Malley BW. Mechanisms of enhancer action: the known and the unknown. Genome Biol. 2021;22(1):108.

[25] Pennacchio LA, Bickmore W, Dean A, Nobrega MA, Bejerano G. Enhancers: five essential questions. Nat Rev Genet. 2013;14(4):288-295.

[26] Creyghton MP, Cheng AW, Welstead GG, et al. Histone H3K27ac separates active from poised enhancers and predicts developmental state. Proc Natl Acad Sci U S A. 2010;107(50):21931-21936.

[27] Heintzman ND, Stuart RK, Hon G, et al. Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nat Genet. 2007;39(3):311-318.

[28] Daugherty AC, Yeo RW, Buenrostro JD, Greenleaf WJ, Kundaje A, Brunet A. Chromatin accessibility dynamics reveal novel functional enhancers in C. elegans. Genome Res. 2017;27(12):2096-2107.

[29] Stępniak K, Machnicka MA, Mieczkowski J, et al. Mapping chromatin accessibility and active regulatory elements reveals pathological mechanisms in human gliomas. Nat Commun. 2021;12(1):3621.

[30] Visel A, Blow MJ, Li Z, et al. ChIP-seq accurately predicts tissue-specific activity of enhancers. Nature. 2009;457(7231):854-858.

[31] DeMare LE, Leng J, Cotney J, et al. The genomic landscape of cohesin-associated chromatin interactions. Genome Res. 2013;23(8):1224-1234.

[32] Grubert F, Srivas R, Spacek DV, et al. Landscape of cohesin-mediated chromatin loops in the human genome. Nature. 2020;583(7818):737-743.

[33] Li Y, Haarhuis JHI, Sedeño Cacciatore Á, et al. The structural basis for cohesin–CTCF-anchored loops. Nature. 2020;578(7795):472-476.

[34] Kagey MH, Newman JJ, Bilodeau S, et al. Mediator and cohesin connect gene expression and chromatin architecture. Nature. 2010;467(7314):430-435.

[35] Siersbæk R, Madsen JGS, Javierre BM, et al. Dynamic rewiring of promoter-anchored chromatin loops during adipocyte differentiation. Mol Cell. 2017;66(3):420-435.e425.

[36] He M, Li Y, Tang Q, et al. Genome-wide chromatin structure changes during Adipogenesis and Myogenesis. Int J Biol Sci. 2018;14(11):1571-1585.

[37] Siersbæk R, Rabiee A, Nielsen R, et al. Transcription factor cooperativity in early adipogenic hotspots and super-enhancers. Cell Rep. 2014;7(5):1443-1455.

[38] Lee JE, Park YK, Park S, et al. Brd4 binds to active enhancers to control cell identity gene induction in adipogenesis and myogenesis. Nat Commun. 2017;8(1):2217.

[39] Banerji J, Rusconi S, Schaffner W. Expression of a beta-globin gene is enhanced by remote SV40 DNA sequences. Cell. 1981;27(2 Pt 1):299-308.

[40] Ross SR, Graves RA, Greenstein A, et al. A fat-specific enhancer is the primary determinant of gene expression for adipocyte P2 in vivo. Proc Natl Acad Sci U S A. 1990;87(24):9590-9594.

[41] Segawa K, Matsuda M, Fukuhara A, et al. Identification of a novel distal enhancer in human adiponectin gene. J Endocrinol. 2009;200(1):107-116.

[42] LeBlanc SE, Wu Q, Lamba P, Sif S, Imbalzano AN. Promoter-enhancer looping at the PPARγ2 locus during adipogenic differentiation requires the Prmt5 methyltransferase. Nucleic Acids Res. 2016;44(11):5133-5147.

[43] Brown JD, Feldman ZB, Doherty SP, et al. BET bromodomain proteins regulate enhancer function during adipogenesis. Proc Natl Acad Sci U S A. 2018;115(9):2144-2149.

[44] Christy RJ, Yang VW, Ntambi JM, et al. Differentiation-induced gene expression in 3T3-L1 preadipocytes: CCAAT/enhancer binding protein interacts with and activates the promoters of two adipocyte-specific genes. Genes Dev. 1989;3(9):1323-1335.

[45] Kiefer FW, Vernochet C, O'Brien P, et al. Retinaldehyde dehydrogenase 1 regulates a thermogenic program in white adipose tissue. Nat Med. 2012;18(6):918-925.

[46] Livak KJ, Schmittgen TD. Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) method. Methods. 2001;25(4):402-408.

[47] Krijger PHL, Geeven G, Bianchi V, Hilvering CRE, de Laat W. 4C-seq from beginning to end: a detailed protocol for sample preparation and data analysis. Methods. 2020;170:17-32.

[48] van de Werken HJ, de Vree PJ, Splinter E, et al. 4C technology: protocols and data analysis. Methods Enzymol. 2012;513:89-112.

[49] Thongjuea S, Stadhouders R, Grosveld FG, Soler E, Lenhard B. r3Cseq: an R/Bioconductor package for the discovery of long-range genomic interactions from chromosome conformation capture and next-generation sequencing data. Nucleic Acids Res. 2013;41(13):e132.

[50] Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15(12):550.

[51] Stephens M. False discovery rates: a new deal. Biostatistics. 2016;18(2):275-294.

[52] Langmead B, Salzberg SL. Fast gapped-read alignment with bowtie 2. Nat Methods. 2012;9(4):357-359.

[53] Nagari A, Murakami S, Malladi VS, Kraus WL. Computational approaches for mining GRO-Seq data to identify and characterize active enhancers. Methods Mol Biol. 2017;1468:121-138.

[54] Fang B, Everett LJ, Jager J, et al. Circadian enhancers coordinate multiple phases of rhythmic gene transcription In vivo. Cell. 2014;159(5):1140-1152.

[55] Haeussler M, Schönig K, Eckert H, et al. Evaluation of off-target and on-target scoring algorithms and integration into the guide RNA selection tool CRISPOR. Genome Biol. 2016;17(1):148.

[56] Liu H, Wei Z, Dominguez A, Li Y, Wang X, Qi LS. CRISPR-ERA: a comprehensive design tool for CRISPR-mediated gene editing, repression and activation. Bioinformatics. 2015;31(22):3676-3678.

[57] Labun K, Montague TG, Krause M, Torres Cleuren YN, Tjeldnes H, Valen E. CHOPCHOP v3: expanding the CRISPR web toolbox beyond genome editing. Nucleic Acids Res. 2019;47(W1):W171-W174.

[58] Hodgkins A, Farne A, Perera S, et al. WGE: a CRISPR database for genome engineering. Bioinformatics. 2015;31(18):3078-3080.

[59] Bae S, Park J, Kim J-S. Cas-OFFinder: a fast and versatile algorithm that searches for potential off-target sites of Cas9 RNA-guided endonucleases. Bioinformatics. 2014;30(10):1473-1475.

[60] Hagège H, Klous P, Braem C, et al. Quantitative analysis of chromosome conformation capture assays (3C-qPCR). Nat Protoc. 2007;2(7):1722-1733.

[61] Naumova N, Smith EM, Zhan Y, Dekker J. Analysis of long-range chromatin interactions using chromosome conformation capture. Methods. 2012;58(3):192-203.

[62] Krivega I, Dean A. Chromosome conformation capture (3C and higher) with erythroid samples. Methods Mol Biol. 2018;1698:237-243.

[63] Montavon T, Soshnikova N, Mascrez B, et al. A regulatory archipelago controls Hox genes transcription in digits. Cell. 2011;147(5):1132-1145.

[64] Deng W, Lee J, Wang H, et al. Controlling long-range genomic interactions at a native locus by targeted tethering of a looping factor. Cell. 2012;149(6):1233-1244.

[65] Hu H, Miao Y-R, Jia L-H, Yu Q-Y, Zhang Q, Guo A-Y. AnimalTFDB 3.0: a comprehensive resource for annotation and prediction of animal transcription factors. Nucleic Acids Res. 2019;47(D1):D33-D38.

[66] Fornes O, Castro-Mondragon JA, Khan A, et al. JASPAR 2020: update of the open-access database of transcription factor binding profiles. Nucleic Acids Res. 2020;48(D1):D87-D92.

[67] Balkow A, Hoffmann LS, Klepac K, et al. Direct lentivirus injection for fast and efficient gene transfer into brown and beige adipose tissue. J Biol Methods. 2016;3(3):e48.

[68] Ding H, Zheng S, Garcia-Ruiz D, et al. Fasting induces a subcutaneous-to-visceral fat switch mediated by microRNA-149-3p and suppression of PRDM16. Nat Commun. 2016;7(1):11533.

[69] Green H, Kehinde O. An established preadipose cell line and its differentiation in culture. II. Factors affecting the adipose conversion. Cell. 1975;5(1):19-27.

[70] Gregoire FM, Smas CM, Sul HS. Understanding adipocyte differentiation. Physiol Rev. 1998;78(3):783-809.

[71] Rosen ED, MacDougald OA. Adipocyte differentiation from the inside out. Nat Rev Mol Cell Biol. 2006;7(12):885-896.

[72] Sarusi Portuguez A, Schwartz M, Siersbaek R, et al. Hierarchical role for transcription factors and chromatin structure in genome organization along adipogenesis. FEBS J. 2017;284(19):3230-3244.

[73] Stachecka J, Kolodziejski PA, Noak M, Szczerbal I. Alteration of active and repressive histone marks during adipogenic differentiation of porcine mesenchymal stem cells. Sci Rep. 2021;11(1):1325.

[74] Shlyueva D, Stampfel G, Stark A. Transcriptional enhancers: from properties to genome-wide predictions. Nat Rev Genet. 2014;15(4):272-286.

[75] Core LJ, Waterfall JJ, Lis JT. Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters. Science. 2008;322(5909):1845-1848.

[76] Core LJ, Martins AL, Danko CG, Waters CT, Siepel A, Lis JT. Analysis of nascent RNA identifies a unified architecture of initiation regions at mammalian promoters and enhancers. Nat Genet. 2014;46(12):1311-1320.

[77] Nardone J, Lee DU, Ansel KM, Rao A. Bioinformatics for the ‘bench biologist’: how to find regulatory regions in genomic DNA. Nat Immunol. 2004;5(8):768-774.

[78] Visel A, Minovitsky S, Dubchak I, Pennacchio LA. VISTA enhancer browser—a database of tissue-specific human enhancers. Nucleic Acids Res. 2007;35(Database issue):D88-D92.

[79] Chen L, Fish AE, Capra JA. Prediction of gene regulatory enhancers across species reveals evolutionarily conserved sequence properties. PLoS Comput Biol. 2018;14(10):e1006484.

[80] Odaka YS, Tohmonda T, Toyoda A, Aruga J. An evolutionarily conserved mesodermal enhancer in vertebrate Zic3. Sci Rep. 2018;8(1):14954.

[81] Snetkova V, Ypsilanti AR, Akiyama JA, et al. Ultraconserved enhancer function does not require perfect sequence conservation. Nat Genet. 2021;53(4):521-528.

[82] Anwar S, Minhas R, Ali S, et al. Identification and functional characterization of novel transcriptional enhancers involved in regulating human GLI3 expression during early development. Dev Growth Differ. 2015;57(8):570-580.

[83] Bonello GB, Pham MH, Begum K, Sigala J, Sataranatarajan K, Mummidi S. An evolutionarily conserved TNF-alpha-responsive enhancer in the far upstream region of human CCL2 locus influences its gene expression. J Immunol. 2011;186(12):7025-7038.

[84] Pellegrinelli V, Rodriguez-Cuenca S, Rouault C, et al. Dysregulation of macrophage PEPD in obesity determines adipose tissue fibro-inflammation and insulin resistance. Nat Metab. 2022;4(4):476-494.

[85] Rao SSP, Huang S-C, Glenn St Hilaire B, et al. Cohesin loss eliminates all loop domains. Cell. 2017;171(2):305-320.e324.

[86] Chien R, Zeng W, Kawauchi S, et al. Cohesin mediates chromatin interactions that regulate mammalian β-globin expression. J Biol Chem. 2011;286(20):17870-17878.

[87] Gong Y, Lazaris C, Sakellaropoulos T, et al. Stratification of TAD boundaries reveals preferential insulation of super-enhancers by strong boundaries. Nat Commun. 2018;9(1):542.

[88] Lupiáñez DG, Kraft K, Heinrich V, et al. Disruptions of topological chromatin domains cause pathogenic rewiring of gene-enhancer interactions. Cell. 2015;161(5):1012-1025.

[89] Hanssen LLP, Kassouf MT, Oudelaar AM, et al. Tissue-specific CTCF-cohesin-mediated chromatin architecture delimits enhancer interactions and function in vivo. Nat Cell Biol. 2017;19(8):952-961.

[90] Bahr C, von Paleske L, Uslu VV, et al. A Myc enhancer cluster regulates normal and leukaemic haematopoietic stem cell hierarchies. Nature. 2018;553(7689):515-520.

[91] Symmons O, Uslu VV, Tsujimura T, et al. Functional and topological characteristics of mammalian regulatory domains. Genome Res. 2014;24(3):390-400.

[92] Dixon JR, Selvaraj S, Yue F, et al. Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature. 2012;485(7398):376-380.

[93] Ramasamy S, Aljahani A, Karpinska MA, Cao TBN, Cruz JN, Oudelaar AM. The mediator complex regulates enhancer-promoter interactions. Nat Struct Mol Biol. 2023;30(7):991-1000.

[94] Spitz F, Furlong EEM. Transcription factors: from enhancer binding to developmental control. Nat Rev Genet. 2012;13(9):613-626.

[95] Hirsch N, Eshel R, Bar Yaacov R, et al. Unraveling the transcriptional regulation of TWIST1 in limb development. PLoS Genet. 2018;14(10):e1007738.

[96] Chen L, Cao W, Aita R, et al. Three-dimensional interactions between enhancers and promoters during intestinal differentiation depend upon HNF4. Cell Rep. 2021;34(4):108679.

[97] Ito S, Das ND, Umehara T, Koseki H. Factors and mechanisms that influence chromatin-mediated enhancer–promoter interactions and transcriptional regulation. Cancer (Basel). 2022;14(21):5404.

[98] Hiraike Y, Waki H, Yu J, et al. NFIA co-localizes with PPARγ and transcriptionally controls the brown fat gene program. Nat Cell Biol. 2017;19(9):1081-1092.

[99] Waki H, Nakamura M, Yamauchi T, et al. Global mapping of cell type–specific open chromatin by FAIRE-seq reveals the regulatory role of the NFI family in adipocyte differentiation. PLoS Genet. 2011;7(10):e1002311.

[100] Grosschedl R, Giese K, Pagel J. HMG domain proteins: architectural elements in the assembly of nucleoprotein structures. Trends Genet. 1994;10(3):94-100.

[101] Reeves R. Structure and function of the HMGI(Y) family of architectural transcription factors. Environ Health Perspect. 2000;108(Suppl 5):803-809.

[102] Ozturk N, Singh I, Mehta A, Braun T, Barreto G. HMGA proteins as modulators of chromatin structure during transcriptional activation. Front Cell Dev Biol. 2014;2:5.

[103] Maekawa T, Jin W, Ishii S. The role of ATF-2 family transcription factors in adipocyte differentiation: antiobesity effects of p38 inhibitors. Mol Cell Biol. 2010;30(3):613-625.

[104] Tontonoz P, Graves RA, Budavari AI, et al. Adipocyte-specific transcription factor ARF6 is a heterodimeric complex of two nuclear hormone receptors, PPAR gamma and RXRa. Nucleic Acids Res. 1994;22(25):5628-5634.

[105] Tontonoz P, Hu E, Graves RA, Budavari AI, Spiegelman BM. mPPAR gamma 2: tissue-specific regulator of an adipocyte enhancer. Genes Dev. 1994;8(10):1224-1234.

[106] Chandra V, Huang P, Hamuro Y, et al. Structure of the intact PPAR-γ–RXR-α nuclear receptor complex on DNA. Nature. 2008;456(7220):350-356.

[107] Zamir I, Zhang J, Lazar MA. Stoichiometric and steric principles governing repression by nuclear hormone receptors. Genes Dev. 1997;11(7):835-846.

[108] Ricote M, Glass CK. PPARs and molecular mechanisms of transrepression. Biochim Biophys Acta. 2007;1771(8):926-935.

[109] Stanya KJ, Kao H-Y. New insights into the functions and regulation of the transcriptional corepressors SMRT and N-CoR. Cell Div. 2009;4(1):7.

[110] Yu C, Markan K, Temple KA, Deplewski D, Brady MJ, Cohen RN. The nuclear receptor corepressors NCoR and SMRT decrease peroxisome proliferator-activated receptor gamma transcriptional activity and repress 3T3-L1 adipogenesis. J Biol Chem. 2005;280(14):13600-13605.

[111] Schulman Ira G, Shao G, Heyman RA. Transactivation by retinoid X receptor–peroxisome proliferator-activated receptor γ (PPARγ) heterodimers: intermolecular synergy requires only the PPARγ hormone-dependent activation function. Mol Cell Biol. 1998;18(6):3483-3494.

[112] Kojetin DJ, Matta-Camacho E, Hughes TS, et al. Structural mechanism for signal transduction in RXR nuclear receptor heterodimers. Nat Commun. 2015;6(1):8013.

[113] Aranda A, Pascual A. Nuclear hormone receptors and gene expression. Physiol Rev. 2001;81(3):1269-1304.

[114] Graves RA, Tontonoz P, Ross SR, Spiegelman BM. Identification of a potent adipocyte-specific enhancer: involvement of an NF-1-like factor. Genes Dev. 1991;5(3):428-437.

[115] Ulianov SV, Galitsyna AA, Flyamer IM, et al. Activation of the alpha-globin gene expression correlates with dramatic upregulation of nearby non-globin genes and changes in local and large-scale chromatin spatial structure. Epigenetics Chromatin. 2017;10(1):35.

[116] Strahl BD, Allis CD. The language of covalent histone modifications. Nature. 2000;403(6765):41-45.

[117] Li K, Han J, Wang Z. Histone modifications centric-regulation in osteogenic differentiation. Cell Death Discov. 2021;7(1):91.

[118] Choy M-K, Javierre BM, Williams SG, et al. Promoter interactome of human embryonic stem cell-derived cardiomyocytes connects GWAS regions to cardiac gene networks. Nat Commun. 2018;9(1):2526.

[119] Li G, Ruan X, Auerbach RK, et al. Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation. Cell. 2012;148(1–2):84-98.

[120] Osterwalder M, Barozzi I, Tissières V, et al. Enhancer redundancy provides phenotypic robustness in mammalian development. Nature. 2018;554(7691):239-243.

[121] Andersson R, Gebhard C, Miguel-Escalada I, et al. An atlas of active enhancers across human cell types and tissues. Nature. 2014;507(7493):455-461.

[122] Kvon EZ, Waymack R, Gad M, Wunderlich Z. Enhancer redundancy in development and disease. Nat Rev Genet. 2021;22(5):324-336.

[123] Popay TM, Dixon JR. Coming full circle: on the origin and evolution of the looping model for enhancer-promoter communication. J Biol Chem. 2022;298(8):102117.

[124] Sanborn AL, Rao SSP, Huang S-C, et al. Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes. Proc Natl Acad Sci U S A. 2015;112(47):E6456-E6465.

[125] Fudenberg G, Imakaev M, Lu C, Goloborodko A, Abdennur N, Mirny LA. Formation of chromosomal domains by loop extrusion. Cell Rep. 2016;15(9):2038-2049.

[126] Davidson IF, Peters JM. Genome folding through loop extrusion by SMC complexes. Nat Rev Mol Cell Biol. 2021;22(7):445-464.

[127] Guo Y, Monahan K, Wu H, et al. CTCF/cohesin-mediated DNA looping is required for protocadherin α promoter choice. Proc Natl Acad Sci U S A. 2012;109(51):21081-21086.

[128] Weintraub AS, Li CH, Zamudio AV, et al. YY1 is a structural regulator of enhancer-promoter loops. Cell. 2017;171(7):1573-1588.e28.

[129] Zhou Q, Yu M, Tirado-Magallanes R, et al. ZNF143 mediates CTCF-bound promoter–enhancer loops required for murine hematopoietic stem and progenitor cell function. Nat Commun. 2021;12(1):43.

[130] Chen XF, Zhu DL, Yang M, et al. An osteoporosis risk SNP at 1p36.12 acts as an allele-specific enhancer to modulate LINC00339 expression via long-range loop formation. Am J Hum Genet. 2018;102(5):776-793.

[131] Nolis IK, McKay DJ, Mantouvalou E, Lomvardas S, Merika M, Thanos D. Transcription factors mediate long-range enhancer–promoter interactions. Proc Natl Acad Sci U S A. 2009;106(48):20222-20227.

[132] Ramirez RN, Chowdhary K, Leon J, Mathis D, Benoist C. FoxP3 associates with enhancer-promoter loops to regulate T(reg)-specific gene expression. Sci Immunol. 2022;7(67):eabj9836.

[133] Kim T-K, Hemberg M, Gray JM, et al. Widespread transcription at neuronal activity-regulated enhancers. Nature. 2010;465(7295):182-187.

[134] Mousavi K, Zare H, Dell'orso S, et al. eRNAs promote transcription by establishing chromatin accessibility at defined genomic loci. Mol Cell. 2013;51(5):606-617.

[135] Hsieh C-L, Fei T, Chen Y, et al. Enhancer RNAs participate in androgen receptor-driven looping that selectively enhances gene activation. Proc Natl Acad Sci U S A. 2014;111(20):7319-7324.

[136] Tan SH, Leong WZ, Ngoc PCT, et al. The enhancer RNA ARIEL activates the oncogenic transcriptional program in T-cell acute lymphoblastic leukemia. Blood. 2019;134(3):239-251.

[137] Bose DA, Donahue G, Reinberg D, Shiekhattar R, Bonasio R, Berger SL. RNA binding to CBP stimulates histone acetylation and transcription. Cell. 2017;168(1):135-149.e122.

[138] Sigova AA, Abraham BJ, Ji X, et al. Transcription factor trapping by RNA in gene regulatory elements. Science. 2015;350(6263):978-981.

[139] Rahnamoun H, Lee J, Sun Z, et al. RNAs interact with BRD4 to promote enhanced chromatin engagement and transcription activation. Nat Struct Mol Biol. 2018;25(8):687-697.

[140] Yang M, Lee JH, Zhang Z, et al. Enhancer RNAs mediate estrogen-induced decommissioning of selective enhancers by recruiting ERα and its cofactor. Cell Rep. 2020;31(12):107803.

RIGHTS & PERMISSIONS

2023 2023 The Authors. Cell Proliferation published by Beijing Institute for Stem Cell and Regenerative Medicine and John Wiley & Sons Ltd.