Tip60 complex binds to active Pol II promoters and a subset of enhancers and co-regulates the c-Myc network in mouse embryonic stem cells

Epigenetics & Chromatin

Laszlo Tora²  Matthieu Stierle²  Tao Ye¹  Changwei Yu²  Sarina Ravens² 

[1] Microarrays and Deep Sequencing Platform, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS UMR 7104, INSERM U964, UdS, BP 10142, CU de Strasbourg, Illkirch Cedex, 67404, France;Cellular Signalling and Nuclear Dynamics Programme, Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), CNRS UMR 7104, INSERM U964, Université de Strasbourg (UdS), BP 10142, 1 Rue Laurent Fries, CU de Strasbourg, Illkirch Cedex, 67404, France

关键词: MSL;    NSL;    Mof;    c-Myc;    Bivalent genes;    Pluripotency;    Mouse;    Super enhancers;    Enhancers;    H3K4me3;    H3K27ac;    KAT5;    Histone acetyltransferase (HAT);   

Others  :  1231090
DOI  :  10.1186/s13072-015-0039-z

 received in 2015-06-12, accepted in 2015-10-29,  发布年份 2015

【 摘 要 】

Background

Tip60 (KAT5) is the histone acetyltransferase (HAT) of the mammalian Tip60/NuA4 complex. While Tip60 is important for early mouse development and mouse embryonic stem cell (mESC) pluripotency, the function of Tip60 as reflected in a genome-wide context is not yet well understood.

Results

Gel filtration of nuclear mESCs extracts indicate incorporation of Tip60 into large molecular complexes and exclude the existence of large quantities of “free” Tip60 within the nuclei of ESCs. Thus, monitoring of Tip60 binding to the genome should reflect the behaviour of Tip60-containing complexes. The genome-wide mapping of Tip60 binding in mESCs by chromatin immunoprecipitation (ChIP) coupled with high-throughput sequencing (ChIP-seq) shows that the Tip60 complex is present at promoter regions of predominantly active genes that are bound by RNA polymerase II (Pol II) and contain the H3K4me3 histone mark. The coactivator HAT complexes, Tip60- and Mof (KAT8)-containing (NSL and MSL), show a global overlap at promoters, whereas distinct binding profiles at enhancers suggest different regulatory functions of each essential HAT complex. Interestingly, Tip60 enrichment peaks at about 200 bp downstream of the transcription start sites suggesting a function for the Tip60 complexes in addition to histone acetylation. The comparison of genome-wide binding profiles of Tip60 and c-Myc, a somatic cell reprogramming factor that binds predominantly to active genes in mESCs, demonstrate that Tip60 and c-Myc co-bind at 50–60 % of their binding sites. We also show that the Tip60 complex binds to a subset of bivalent developmental genes and defines a set of mESC-specific enhancer as well as super-enhancer regions.

Conclusions

Our study suggests that the Tip60 complex functions as a global transcriptional co-activator at most active Pol II promoters, co-regulates the ESC-specific c-Myc network, important for ESC self-renewal and cell metabolism and acts at a subset of active distal regulatory elements, or super enhancers, in mESCs.

【 授权许可】

   
2015 Ravens et al.

【 图 表 】

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【 参考文献 】

• [1]Squatrito M, Gorrini C, Amati B. Tip60 in DNA damage response and growth control: many tricks in one HAT. Trends Cell Biol. 2006; 16(9):433-442.
• [2]Voss AK, Thomas T. MYST family histone acetyltransferases take center stage in stem cells and development. BioEssays News Rev Mol Cell Develop Biol. 2009; 31(10):1050-1061.
• [3]Doyon Y, Selleck W, Lane WS, Tan S, Cote J. Structural and functional conservation of the NuA4 histone acetyltransferase complex from yeast to humans. Mol Cell Biol. 2004; 24(5):1884-1896.
• [4]Sapountzi V, Cote J. MYST-family histone acetyltransferases: beyond chromatin. Cell Mol Life Sci CMLS. 2011; 68(7):1147-1156.
• [5]Boudreault AA, Cronier D, Selleck W, Lacoste N, Utley RT, Allard S et al.. Yeast enhancer of polycomb defines global Esa1-dependent acetylation of chromatin. Genes Dev. 2003; 17(11):1415-1428.
• [6]Doyon Y, Cote J. The highly conserved and multifunctional NuA4 HAT complex. Curr Opin Genet Dev. 2004; 14(2):147-154.
• [7]Ikura T, Ogryzko VV, Grigoriev M, Groisman R, Wang J, Horikoshi M et al.. Involvement of the TIP60 histone acetylase complex in DNA repair and apoptosis. Cell. 2000; 102(4):463-473.
• [8]Auger A, Galarneau L, Altaf M, Nourani A, Doyon Y, Utley RT et al.. Eaf1 is the platform for NuA4 molecular assembly that evolutionarily links chromatin acetylation to ATP-dependent exchange of histone H2A variants. Mol Cell Biol. 2008; 28(7):2257-2270.
• [9]Fuchs M, Gerber J, Drapkin R, Sif S, Ikura T, Ogryzko V et al.. The p400 complex is an essential E1A transformation target. Cell. 2001; 106(3):297-307.
• [10]Samuelson AV, Narita M, Chan HM, Jin J, de Stanchina E, McCurrach ME et al.. p400 is required for E1A to promote apoptosis. J Biol Chem. 2005; 280(23):21915-21923.
• [11]Park JH, Sun XJ, Roeder RG. The SANT domain of p400 ATPase represses acetyltransferase activity and coactivator function of TIP60 in basal p21 gene expression. Mol Cell Biol. 2010; 30(11):2750-2761.
• [12]Kim J, Woo AJ, Chu J, Snow JW, Fujiwara Y, Kim CG et al.. A Myc network accounts for similarities between embryonic stem and cancer cell transcription programs. Cell. 2010; 143(2):313-324.
• [13]Hu Y, Fisher JB, Koprowski S, McAllister D, Kim MS, Lough J. Homozygous disruption of the Tip60 gene causes early embryonic lethality. Develop Dyn Off Publ Am Assoc Anat. 2009; 238(11):2912-2921.
• [14]Fazzio TG, Huff JT, Panning B. An RNAi screen of chromatin proteins identifies Tip60-p400 as a regulator of embryonic stem cell identity. Cell. 2008; 134(1):162-174.
• [15]Chen PB, Hung JH, Hickman TL, Coles AH, Carey JF, Weng Z et al.. Hdac6 regulates Tip60-p400 function in stem cells. eLife. 2013; 2:e01557.
• [16]Gupta A, Guerin-Peyrou TG, Sharma GG, Park C, Agarwal M, Ganju RK et al.. The mammalian ortholog of Drosophila MOF that acetylates histone H4 lysine 16 is essential for embryogenesis and oncogenesis. Mol Cell Biol. 2008; 28(1):397-409.
• [17]Thomas T, Dixon MP, Kueh AJ, Voss AK. Mof (MYST1 or KAT8) is essential for progression of embryonic development past the blastocyst stage and required for normal chromatin architecture. Mol Cell Biol. 2008; 28(16):5093-5105.
• [18]Ravens S, Fournier M, Ye T, Stierle M, Dembele D, Chavant V et al.. Mof-associated complexes have overlapping and unique roles in regulating pluripotency in embryonic stem cells and during differentiation. eLife. 2014.
• [19]Chelmicki T, Dundar F, Turley MJ, Khanam T, Aktas T, Ramirez F et al.. MOF-associated complexes ensure stem cell identity and Xist repression. eLife. 2014; 3:e02024.
• [20]Frank SR, Parisi T, Taubert S, Fernandez P, Fuchs M, Chan HM et al.. MYC recruits the TIP60 histone acetyltransferase complex to chromatin. EMBO Rep. 2003; 4(6):575-580.
• [21]Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE et al.. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 2008; 9(9):R137. BioMed Central Full Text
• [22]Ye T, Krebs AR, Choukrallah MA, Keime C, Plewniak F, Davidson I et al.. seqMINER: an integrated ChIP-seq data interpretation platform. Nucleic Acids Res. 2011; 39(6):e35.
• [23]Adelman K, Lis JT. Promoter-proximal pausing of RNA polymerase II: emerging roles in metazoans. Nat Rev Genet. 2012; 13(10):720-731.
• [24]Wang ZB, Zang CZ, Cui KR, DE Schones, Barski A, Peng WQ et al.. Genome-wide mapping of HATs and HDACs reveals distinct functions in active and inactive genes. Cell. 2009; 138(5):1019-1031.
• [25]Wang Z, Zang C, Rosenfeld JA, Schones DE, Barski A, Cuddapah S et al.. Combinatorial patterns of histone acetylations and methylations in the human genome. Nat Genet. 2008; 40(7):897-903.
• [26]Cai Y, Jin J, Swanson SK, Cole MD, Choi SH, Florens L et al.. Subunit composition and substrate specificity of a MOF-containing histone acetyltransferase distinct from the male-specific lethal (MSL) complex. J Biol Chem. 2010; 285(7):4268-4272.
• [27]Mendjan S, Taipale M, Kind J, Holz H, Gebhardt P, Schelder M et al.. Nuclear pore components are involved in the transcriptional regulation of dosage compensation in Drosophila. Mol Cell. 2006; 21(6):811-823.
• [28]Li X, Li L, Pandey R, Byun JS, Gardner K, Qin Z et al.. The histone acetyltransferase MOF is a key regulator of the embryonic stem cell core transcriptional network. Cell Stem Cell. 2012; 11(2):163-178.
• [29]Amati B, Brooks MW, Levy N, Littlewood TD, Evan GI, Land H. Oncogenic activity of the c-Myc protein requires dimerization with Max. Cell. 1993; 72(2):233-245.
• [30]Patel JH, Loboda AP, Showe MK, Showe LC, McMahon SB. Analysis of genomic targets reveals complex functions of MYC. Nat Rev Cancer. 2004; 4(7):562-568.
• [31]Chen X, Xu H, Yuan P, Fang F, Huss M, Vega VB et al.. Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell. 2008; 133(6):1106-1117.
• [32]Kim J, Chu J, Shen X, Wang J, Orkin SH. An extended transcriptional network for pluripotency of embryonic stem cells. Cell. 2008; 132(6):1049-1061.
• [33]Yeo JC, Ng HH. The transcriptional regulation of pluripotency. Cell Res. 2013; 23(1):20-32.
• [34]Kidder BL, Yang J, Palmer S. Stat3 and c-Myc genome-wide promoter occupancy in embryonic stem cells. PLoS One. 2008; 3(12):e3932.
• [35]Martinato F, Cesaroni M, Amati B, Guccione E. Analysis of Myc-induced histone modifications on target chromatin. PLoS One. 2008; 3(11):e3650.
• [36]Barski A, Cuddapah S, Cui K, Roh TY, Schones DE, Wang Z et al.. High-resolution profiling of histone methylations in the human genome. Cell. 2007; 129(4):823-837.
• [37]Creyghton MP, Cheng AW, Welstead GG, Kooistra T, Carey BW, Steine EJ et al.. Histone H3K27ac separates active from poised enhancers and predicts developmental state. Proc Natl Acad Sci USA. 2010; 107(50):21931-21936.
• [38]Heintzman ND, Stuart RK, Hon G, Fu YT, Ching CW, Hawkins RD et al.. Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nat Genet. 2007; 39(3):311-318.
• [39]Bernstein BE, Mikkelsen TS, Xie X, Kamal M, Huebert DJ, Cuff J et al.. A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell. 2006; 125(2):315-326.
• [40]Voigt P, Tee WW, Reinberg D. A double take on bivalent promoters. Genes Dev. 2013; 27(12):1318-1338.
• [41]Whyte WA, Orlando DA, Hnisz D, Abraham BJ, Lin CY, Kagey MH et al.. Master transcription factors and mediator establish super-enhancers at key cell identity genes. Cell. 2013; 153(2):307-319.
• [42]Eberhardy SR, D’Cunha CA, Farnham PJ. Direct examination of histone acetylation on Myc target genes using chromatin immunoprecipitation. J Biol Chem. 2000; 275(43):33798-33805.
• [43]Sabo A, Amati B. Genome recognition by MYC. Cold Spring Harb Perspect Med. 2014.
• [44]Perna D, Faga G, Verrecchia A, Gorski MM, Barozzi I, Narang V et al.. Genome-wide mapping of Myc binding and gene regulation in serum-stimulated fibroblasts. Oncogene. 2012; 31(13):1695-1709.
• [45]Kusch T, Mei A, Nguyen C. Histone H3 lysine 4 trimethylation regulates cotranscriptional H2A variant exchange by Tip60 complexes to maximize gene expression. Proc Natl Acad Sci USA. 2014; 111(13):4850-4855.
• [46]Krebs AR, Karmodiya K, Lindahl-Allen M, Struhl K, Tora L. SAGA and ATAC histone acetyl transferase complexes regulate distinct sets of genes and ATAC defines a class of p300-independent enhancers. Mol Cell. 2011; 44(3):410-423.
• [47]Sapountzi V, Logan IR, Robson CN. Cellular functions of TIP60. Int J Biochem Cell Biol. 2006; 38(9):1496-1509.
• [48]Bonnet J, Wang CY, Baptista T, Vincent SD, Hsiao WC, Stierle M et al.. The SAGA coactivator complex acts on the whole transcribed genome and is required for RNA polymerase II transcription. Genes Dev. 2014; 28(18):1999-2012.
• [49]Sun M, Schwalb B, Schulz D, Pirkl N, Etzold S, Lariviere L et al.. Comparative dynamic transcriptome analysis (cDTA) reveals mutual feedback between mRNA synthesis and degradation. Genome Res. 2012; 22(7):1350-1359.
• [50]Helenius K, Yang Y, Tselykh TV, Pessa HK, Frilander MJ, Makela TP. Requirement of TFIIH kinase subunit Mat1 for RNA Pol II C-terminal domain Ser5 phosphorylation, transcription and mRNA turnover. Nucleic Acids Res. 2011; 39(12):5025-5035.
• [51]Mayer A, di Iulio J, Maleri S, Eser U, Vierstra J, Reynolds A et al.. Native elongating transcript sequencing reveals human transcriptional activity at nucleotide resolution. Cell. 2015; 161(3):541-554.
• [52]Hooper M, Hardy K, Handyside A, Hunter S, Monk M. HPRT-deficient (Lesch-Nyhan) mouse embryos derived from germline colonization by cultured cells. Nature. 1987; 326(6110):292-295.
• [53]Langmead B. Aligning short sequencing reads with Bowtie. Current protocols in bioinformatics/editoral board, Andreas D Baxevanis [et al]. 2010; Chapter 11: Unit 11 7. doi:10.1002/0471250953.bi1107s32.
• [54]Karmodiya K, Krebs AR, Oulad-Abdelghani M, Kimura H, Tora L. H3K9 and H3K14 acetylation co-occur at many gene regulatory elements, while H3K14ac marks a subset of inactive inducible promoters in mouse embryonic stem cells. BMC Genom. 2012; 13:424. BioMed Central Full Text
• [55]Taylor GC, Eskeland R, Hekimoglu-Balkan B, Pradeepa MM, Bickmore WA. H4K16 acetylation marks active genes and enhancers of embryonic stem cells, but does not alter chromatin compaction. Genome Res. 2013; 23(12):2053-2065.
• [56]Shen Y, Yue F, McCleary DF, Ye Z, Edsall L, Kuan S et al.. A map of the cis-regulatory sequences in the mouse genome. Nature. 2012; 488(7409):116-120.
• [57]Mikkelsen TS, Ku M, Jaffe DB, Issac B, Lieberman E, Giannoukos G et al.. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature. 2007; 448(7153):553-560.
• [58]Robert F, Hardy S, Nagy Z, Baldeyron C, Murr R, Dery U et al.. The transcriptional histone acetyltransferase cofactor TRRAP associates with the MRN repair complex and plays a role in DNA double-strand break repair. Mol Cell Biol. 2006; 26(2):402-412.
• [59]Heinz S, Benner C, Spann N, Bertolino E, Lin YC, Laslo P et al.. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol Cell. 2010; 38(4):576-589.
• [60]Trapnell C, Pachter L, Salzberg SL. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics. 2009; 25(9):1105-1111.
• [61]Roberts A, Pimentel H, Trapnell C, Pachter L. Identification of novel transcripts in annotated genomes using RNA-Seq. Bioinformatics. 2011; 27(17):2325-2329.
• [62]Tassy O, Pourquie O. Manteia, a predictive data mining system for vertebrate genes and its applications to human genetic diseases. Nucleic Acids Res. 2014; 42(Database issue):D882-D891.