Long non-coding RNA LncKdm2bregulates cortical neuronal differentiation by cis-activating Kdm2b

Abstract

The mechanisms underlying spatial and temporal control of cortical neurogenesis of the brain are largely elusive. Long non-coding RNAs (lncRNAs) have emerged as essential cell fate regulators. Here we found LncKdm2b(also known as Kancr), a lncRNA divergently transcribed from a bidirectional promoter of Kdm2b,is transiently expressed during early differentiation of cortical projection neurons. Interestingly, Kdm2b’s transcription is positively regulated in cisby LncKdm2b, which has intrinsic-activating function and facilitates a permissive chromatin environment at the Kdm2b’s promoter by associating with hnRNPAB. Lineage tracing experiments and phenotypic analyses indicated LncKdm2band Kdm2bare crucial in proper differentiation and migration of cortical projection neurons. These observations unveiled a lncRNA-dependent machinery in regulating cortical neuronal differentiation.

Keywords

long non-coding RNA / neuronal differentiation / cerebral cortex / KDM2B / divergent lncRNA

References

[1] Aprea J, Prenninger S, Dori M, Ghosh T, Monasor LS, Wessendorf E, Zocher S, Massalini S, Alexopoulou D, Lesche M (2013) Transcriptome sequencing during mouse brain development identifies long non-coding RNAs functionally involved in neurogenic commitment . EMBO J 32:3145–3160

[2] Arron JR, Winslow MM, Polleri A, Chang CP, Wu H, Gao X, Neilson JR, Chen L, Heit JJ, Kim SK (2006) NFAT dysregulation by increased dosage of DSCR2 and DYRK1A on chromosome 21 . Nature 441:595–600

[3] Ayala R, Shu T, Tsai LH (2007) Trekking across the brain: the journey of neuronal migration . Cell 128:29–43

[4] Ayoub AE, Oh S, Xie Y, Leng J, Cotney J, Dominguez MH, Noonan JP, Rakic P (2011) Transcriptional programs in transient embryonic zones of the cerebral cortex defined by high-resolution mRNA sequencing . Proc Natl Acad Sci USA 108:14950–14955

[5] Baek ST, Kerjan G, Bielas SL, Lee JE, Fenstermaker AG, Novarino G, Gleeson JG (2014) Off-target effect of doublecortin family shRNA on neuronal migration associated with endogenous microRNA dysregulation . Neuron 82:1255–1262

[6] Bassett AR, Akhtar A, Barlow DP, Bird AP, Brockdorff N, Duboule D, Ephrussi A, Ferguson-Smith AC, Gingeras TR, Haerty W (2014) Considerations when investigating lncRNA function in vivo . Elife 3:e03058

[7] Bauer M, Kinkl N, Meixner A, Kremmer E, Riemenschneider M, Forstl H, Gasser T, Ueffing M (2009) Prevention of interferonstimulated gene expression using microRNA-designed hairpins . Gene Ther 16:142–147

[8] Belgard TG, Marques AC, Oliver PL, Abaan HO, Sirey TM, HoerderSuabedissen A, Garcia-Moreno F, Molnar Z, Margulies EH, Ponting CP (2011) A transcriptomic atlas of mouse neocortical layers. Neuron 71:605–616

[9] Benavides-Piccione R, Dierssen M, Ballesteros-Yanez I, Martinez de Lagran M, Arbones ML, Fotaki V, DeFelipe J, Elston GN (2005) Alterations in the phenotype of neocortical pyramidal cells in the Dyrk1A+/mouse . Neurobiol Dis 20:115–122

[10] Berghoff EG, Clark MF, Chen S, Cajigas I, Leib DE, Kohtz JD (2013) Evf2 (Dlx6as) lncRNA regulates ultraconserved enhancer methylation and the differential transcriptional control of adjacent genes . Development 140:4407–4416

[11] Cabianca DS, Casa V, Bodega B, Xynos A, Ginelli E, Tanaka Y, Gabellini D (2012) A long ncRNA links copy number variation to a polycomb/trithorax epigenetic switch in FSHD muscular dystrophy . Cell 149:819–831

[12] Cheng M, Jin X, Mu L, Wang F, Li W, Zhong X, Liu X, Shen W, Liu Y, Zhou Y (2016) Combination of the clustered regularly interspaced short palindromic repeats (CRISPR)-associated 9 technique with the piggybac transposon system for mouse in utero electroporation to study cortical development . J Neurosci Res 94:814–824

[13] Corish P, Tyler-Smith C (1999) Attenuation of green fluorescent protein half-life in mammalian cells . Protein Eng 12:1035–1040

[14] da Huang W, Sherman BT, Lempicki RA (2009) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources . Nat Protoc 4:44–57

[15] Diez-Roux G, Banfi S, Sultan M, Geffers L, Anand S, Rozado D, Magen A, Canidio E, Pagani M, Peluso I (2011) A highresolution anatomical atlas of the transcriptome in the mouse embryo . PLoS Biol 9:e1000582

[16] Dillman AA, Hauser DN, Gibbs JR, Nalls MA, McCoy MK, Rudenko IN, Galter D, Cookson MR (2013) mRNA expression, splicing and editing in the embryonic and adult mouse cerebral cortex . Nat Neurosci 16:499–506

[17] Engreitz JM, Haines JE, Perez EM, Munson G, Chen J, Kane M, McDonel PE, Guttman M, Lander ES (2016) Local regulation of gene expression by lncRNA promoters, transcription and splicing . Nature 539:452–455

[18] Fietz SA, Huttner WB (2011) Cortical progenitor expansion, selfrenewal and neurogenesis-a polarized perspective . Curr Opin Neurobiol 21:23–35

[19] Fotaki V, Dierssen M, Alcantara S, Martinez S, Marti E, Casas C, Visa J, Soriano E, Estivill X, Arbones ML (2002) Dyrk1A haploinsufficiency affects viability and causes developmental delay and abnormal brain morphology in mice . Mol Cell Biol 22:6636–6647

[20] Fu XD (2014) Non-coding RNA: a new frontier in regulatory biology . Natl Sci Rev 1:190–204

[21] Gaspard N, Bouschet T, Hourez R, Dimidschstein J, Naeije G, van den Ameele J, Espuny-Camacho I, Herpoel A, Passante L, Schiffmann SN (2008) An intrinsic mechanism of corticogenesis from embryonic stem cells . Nature 455:351–357

[22] Ghosh A, Greenberg ME (1995) Distinct roles for bFGF and NT-3 in the regulation of cortical neurogenesis . Neuron 15:89–103

[23] Goecks J, Nekrutenko A, Taylor J, Galaxy T (2010) Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences . Genome Biol 11:R86

[24] Greig LC, Woodworth MB, Galazo MJ, Padmanabhan H, Macklis JD (2013) Molecular logic of neocortical projection neuron specification, development and diversity . Nat Rev Neurosci 14:755–769

[25] Grote P, Wittler L, Hendrix D, Koch F, Wahrisch S, Beisaw A, Macura K, Blass G, Kellis M, Werber M (2013) The tissue-specific lncRNA Fendrr is an essential regulator of heart and body wall development in the mouse . Dev Cell 24:206–214

[26] Guo C, Eckler MJ, McKenna WL, McKinsey GL, Rubenstein JL, Chen B (2013) Fezf2 expression identifies a multipotent progenitor for neocortical projection neurons, astrocytes, and oligodendrocytes . Neuron 80:1167–1174

[27] Guttman M, Garber M, Levin JZ, Donaghey J, Robinson J, Adiconis X, Fan L, Koziol MJ, Gnirke A, Nusbaum C (2010) Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs . Nat Biotechnol 28:503–510

[28] Hagege H, Klous P, Braem C, Splinter E, Dekker J, Cathala G, de Laat W, Forne T (2007) Quantitative analysis of chromosome conformation capture assays (3C-qPCR) . Nat Protoc 2:1722–1733

[29] Heintzman ND, Hon GC, Hawkins RD, Kheradpour P, Stark A, Harp LF, Ye Z, Lee LK, Stuart RK, Ching CW (2009) Histone modifications at human enhancers reflect global cell-type-specific gene expression . Nature 459:108–112

[30] Homem CC, Repic M, Knoblich JA (2015) Proliferation control in neural stem and progenitor cells . Nat Rev Neurosci 16:647–659

[31] Imayoshi I, Kageyama R (2014) bHLH factors in self-renewal, multipotency, and fate choice of neural progenitor cells . Neuron 82:9–23

[32] Klattenhoff CA, Scheuermann JC, Surface LE, Bradley RK, Fields PA, Steinhauser ML, Ding H, Butty VL, Torrey L, Haas S (2013) Braveheart, a long noncoding RNA required for cardiovascular lineage commitment . Cell 152:570–583

[33] Kottakis F, Polytarchou C, Foltopoulou P, Sanidas I, Kampranis SC, Tsichlis PN (2011) FGF-2 regulates cell proliferation, migration, and angiogenesis through an NDY1/KDM2B-miR-101-EZH2 pathway . Mol Cell 43:285–298

[34] Kwan KY, Sestan N, Anton ES (2012) Transcriptional co-regulation of neuronal migration and laminar identity in the neocortex . Development 139:1535–1546

[35] Labonne JD, Lee KH, Iwase S, Kong IK, Diamond MP, Layman LC, Kim CH, Kim HG (2016) An atypical 12q24.31 microdeletion implicates six genes including a histone demethylase KDM2B and a histone methyltransferase SETD1B in syndromic intellectual disability . Hum Genet 135:757–771

[36] Lepoivre C, Belhocine M, Bergon A, Griffon A, Yammine M, Vanhille L, Zacarias-Cabeza J, Garibal MA, Koch F, Maqbool MA (2013) Divergent transcription is associated with promoters of transcriptional regulators . BMC Genomics 14:914

[37] Li W, Notani D, Ma Q, Tanasa B, Nunez E, Chen AY, Merkurjev D, Zhang J, Ohgi K, Song X (2013) Functional roles of enhancer RNAs for oestrogen-dependent transcriptional activation . Nature 498:516–520

[38] Li Y, Wang W, Wang F, Wu Q, Li W, Zhong X, Tian K, Zeng T, Gao L, Liu Y (2017) Paired related homeobox 1 transactivates dopamine D2 receptor to maintain propagation and tumorigenicity of glioma-initiating cells . J Mol Cell Biol 9:302–314

[39] Lin N, Chang KY, Li Z, Gates K, Rana ZA, Dang J, Zhang D, Han T, Yang CS, Cunningham TJ (2014) An evolutionarily conserved long noncoding RNA TUNA controls pluripotency and neural lineage commitment . Mol Cell 53:1005–1019

[40] Liu B, Ye B, Yang L, Zhu X, Huang G, Zhu P, Du Y, Wu J, Qin X, Chen R (2017) Long noncoding RNA lncKdm2b is required for ILC3 maintenance by initiation of Zfp292 expression . Nat Immunol 18:499–508

[41] Lu J, Sheen V (2005) Periventricular heterotopia . Epilepsy Behav 7:143–149

[42] Luo S, Lu JY, Liu L, Yin Y, Chen C, Han X, Wu B, Xu R, Liu W, Yan P (2016) Divergent lncRNAs regulate gene expression and lineage differentiation in pluripotent cells . Cell Stem Cell 18:637–652

[43] Mercer TR, Qureshi IA, Gokhan S, Dinger ME, Li G, Mattick JS, Mehler MF (2010) Long noncoding RNAs in neuronal-glial fate specification and oligodendrocyte lineage maturation . BMC Neurosci 11:14

[44] Molyneaux BJ, Goff LA, Brettler AC, Chen HH, Hrvatin S, Rinn JL, Arlotta P (2015) DeCoN: genome-wide analysis of in vivo transcriptional dynamics during pyramidal neuron fate selection in neocortex . Neuron 85:275–288

[45] Ng SY, Bogu GK, Soh BS, Stanton LW (2013) The long noncoding RNA RMST interacts with SOX2 to regulate neurogenesis . Mol Cell 51:349–359

[46] Noonan FC, Goodfellow PJ, Staloch LJ, Mutch DG, Simon TC (2003) Antisense transcripts at the EMX2 locus in human and mouse . Genomics 81:58–66

[47] Orom UA, Derrien T, Beringer M, Gumireddy K, Gardini A, Bussotti G, Lai F, Zytnicki M, Notredame C, Huang Q (2010) Long noncoding RNAs with enhancer-like function in human cells . Cell 143:46–58

[48] Perino M, Veenstra GJ (2016) Chromatin control of developmental dynamics and plasticity . Dev Cell 38:610–620

[49] Ponjavic J, Oliver PL, Lunter G, Ponting CP (2009) Genomic and transcriptional co-localization of protein-coding and long noncoding RNA pairs in the developing brain . PLoS Genet 5: e1000617

[50] Ramos AD, Diaz A, Nellore A, Delgado RN, Park KY, GonzalesRoybal G, Oldham MC, Song JS, Lim DA (2013) Integration of genome-wide approaches identifies lncRNAs of adult neural stem cells and their progeny in vivo . Cell Stem Cell 12:616–628

[51] Rinn JL, Chang HY (2012) Genome regulation by long noncoding RNAs . Annu Rev Biochem 81:145–166

[52] Roberts TC, Hart JR, Kaikkonen MU, Weinberg MS, Vogt PK, Morris KV (2015) Quantification of nascent transcription by bromouridine immunocapture nuclear run-on RT-qPCR . Nat Protoc 10:1198–1211

[53] Saba LM, Flink SC, Vanderlinden LA, Israel Y, Tampier L, Colombo G, Kiianmaa K, Bell RL, Printz MP, Flodman P (2015) The sequenced rat brain transcriptome—its use in identifying networks predisposing alcohol consumption . FEBS J 282:3556–3578

[54] Sarkisian MR, Bartley CM, Rakic P (2008) Trouble making the first move: interpreting arrested neuronal migration in the cerebral cortex . Trends Neurosci 31:54–61

[55] Scruggs BS, Adelman K (2015) The importance of controlling transcription elongation at coding and noncoding RNA loci . Cold Spring Harb Symp Quant Biol 80:33–44

[56] Scruggs BS, Gilchrist DA, Nechaev S, Muse GW, Burkholder A, Fargo DC, Adelman K (2015) Bidirectional transcription arises from two distinct hubs of transcription factor binding and active chromatin . Mol Cell 58:1101–1112

[57] Shen Q, Wang Y, Dimos JT, Fasano CA, Phoenix TN, Lemischka IR, Ivanova NB, Stifani S, Morrisey EE, Temple S (2006) The timing of cortical neurogenesis is encoded within lineages of individual progenitor cells . Nat Neurosci 9:743–751

[58] Sigova AA, Mullen AC, Molinie B, Gupta S, Orlando DA, Guenther MG, Almada AE, Lin C, Sharp PA, Giallourakis CC (2013) Divergent transcription of long noncoding RNA/mRNA gene pairs in embryonic stem cells . Proc Natl Acad Sci USA 110:2876–2881

[59] Sinnamon JR, Waddell CB, Nik S, Chen EI, Czaplinski K (2012) Hnrpab regulates neural development and neuron cell survival after glutamate stimulation . RNA 18:704–719

[60] Spigoni G, Gedressi C, Mallamaci A (2010) Regulation of Emx2 expression by antisense transcripts in murine cortico-cerebral precursors . PLoS ONE 5:e8658

[61] Trapnell C, Pachter L, Salzberg SL (2009) TopHat: discovering splice junctions with RNA-Seq . Bioinformatics 25:1105–1111

[62] Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, Pimentel H, Salzberg SL, Rinn JL, Pachter L (2012) Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks . Nat Protoc 7:562–578

[63] Trimarchi T, Bilal E, Ntziachristos P, Fabbri G, Dalla-Favera R, Tsirigos A, Aifantis I (2014) Genome-wide mapping and characterization of Notch-regulated long noncoding RNAs in acute leukemia . Cell 158:593–606

[64] Tsai MC, Manor O, Wan Y, Mosammaparast N, Wang JK, Lan F, Shi Y, Segal E, Chang HY (2010) Long noncoding RNA as modular scaffold of histone modification complexes . Science 329:689–693

[65] Venkov CD, Link AJ, Jennings JL, Plieth D, Inoue T, Nagai K, Xu C, Dimitrova YN, Rauscher FJ, Neilson EG (2007) A proximal activator of transcription in epithelial-mesenchymal transition . J Clin Invest 117:482–491

[66] Vescovi AL, Reynolds BA, Fraser DD, Weiss S (1993) bFGF regulates the proliferative fate of unipotent (neuronal) and bipotent (neuronal/astroglial) EGF-generated CNS progenitor cells . Neuron 11:951–966

[67] Vickers TA, Koo S, Bennett CF, Crooke ST, Dean NM, Baker BF (2003) Efficient reduction of target RNAs by small interfering RNA and RNase H-dependent antisense agents. A comparative analysis . J Biol Chem 278:7108–7118

[68] Vierstra J, Rynes E, Sandstrom R, Zhang M, Canfield T, Hansen RS, Stehling-Sun S, Sabo PJ, Byron R, Humbert R (2014) Mouse regulatory DNA landscapes reveal global principles of cisregulatory evolution . Science 346:1007–1012

[69] Walder RY, Walder JA (1988) Role of RNase H in hybrid-arrested translation by antisense oligonucleotides . Proc Natl Acad Sci USA 85:5011–5015

[70] Wang A, Wang J, Liu Y, Zhou Y (2017) Mechanisms of long noncoding RNAs in the assembly and plasticity of neural circuitry . Front Neural Circuits 11:76

[71] Wang KC, Yang YW, Liu B, Sanyal A, Corces-Zimmerman R, Chen Y, Lajoie BR, Protacio A, Flynn RA, Gupta RA (2011) A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression . Nature 472:120–124

[72] Wang Y, He L, Du Y, Zhu P, Huang G, Luo J, Yan X, Ye B, Li C, Xia P (2015) The long noncoding RNA lncTCF7 promotes selfrenewal of human liver cancer stem cells through activation of Wnt signaling . Cell Stem Cell 16:413–425

[73] Wu M, Wang PF, Lee JS, Martin-Brown S, Florens L, Washburn M, Shilatifard A (2008) Molecular regulation of H3K4 trimethylation by Wdr82, a component of human Set1/COMPASS . Mol Cell Biol 28:7337–7344

[74] Xing YH, Yao RW, Zhang Y, Guo CJ, Jiang S, Xu G, Dong R, Yang L, Chen LL (2017) SLERT Regulates DDX21 Rings Associated with Pol I Transcription . Cell 169:664–678.e616

[75] Ye B, Liu B, Yang L, Zhu X, Zhang D, Wu W, Zhu P, Wang Y, Wang S, Xia P (2018) LncKdm2b controls self-renewal of embryonic stem cells via activating expression of transcription factor Zbtb3 . EMBO J 37:e97174

[76] Yin Y, Yan P, Lu J, Song G, Zhu Y, Li Z, Zhao Y, Shen B, Huang X, Zhu H (2015) Opposing roles for the lncRNA haunt and its genomic locus in regulating HOXA gene activation during embryonic stem cell differentiation . Cell Stem Cell 16:504–516

[77] Yue F, Cheng Y, Breschi A, Vierstra J, Wu W, Ryba T, Sandstrom R, Ma Z, Davis C, Pope BD (2014) A comparative encyclopedia of DNA elements in the mouse genome . Nature 515:355–364

[78] Zhou ZJ, Dai Z, Zhou SL, Hu ZQ, Chen Q, Zhao YM, Shi YH, Gao Q, Wu WZ, Qiu SJ (2014) HNRNPAB induces epithelialmesenchymal transition and promotes metastasis of hepatocellular carcinoma by transcriptionally activating SNAIL . Cancer Res 74:2750

RIGHTS & PERMISSIONS

2019 The Author(s)