Evolutionary conserved NSL complex/BRD4 axis controls transcription activation via histone acetylation.


Journal

Nature communications
ISSN: 2041-1723
Titre abrégé: Nat Commun
Pays: England
ID NLM: 101528555

Informations de publication

Date de publication:
07 05 2020
Historique:
received: 19 09 2019
accepted: 14 04 2020
entrez: 9 5 2020
pubmed: 10 5 2020
medline: 18 8 2020
Statut: epublish

Résumé

Cells rely on a diverse repertoire of genes for maintaining homeostasis, but the transcriptional networks underlying their expression remain poorly understood. The MOF acetyltransferase-containing Non-Specific Lethal (NSL) complex is a broad transcription regulator. It is essential in Drosophila, and haploinsufficiency of the human KANSL1 subunit results in the Koolen-de Vries syndrome. Here, we perform a genome-wide RNAi screen and identify the BET protein BRD4 as an evolutionary conserved co-factor of the NSL complex. Using Drosophila and mouse embryonic stem cells, we characterise a recruitment hierarchy, where NSL-deposited histone acetylation enables BRD4 recruitment for transcription of constitutively active genes. Transcriptome analyses in Koolen-de Vries patient-derived fibroblasts reveals perturbations with a cellular homeostasis signature that are evoked by the NSL complex/BRD4 axis. We propose that BRD4 represents a conserved bridge between the NSL complex and transcription activation, and provide a new perspective in the understanding of their functions in healthy and diseased states.

Identifiants

pubmed: 32382029
doi: 10.1038/s41467-020-16103-0
pii: 10.1038/s41467-020-16103-0
pmc: PMC7206058
doi:

Substances chimiques

Chromatin 0
Drosophila Proteins 0
Histones 0
Nuclear Proteins 0

Types de publication

Journal Article Research Support, Non-U.S. Gov't

Langues

eng

Sous-ensembles de citation

IM

Pagination

2243

Références

Allis, C. D. & Jenuwein, T. The molecular hallmarks of epigenetic control. Nat. Rev. Genet. 17, 487 (2016).
pubmed: 27346641 doi: 10.1038/nrg.2016.59
Sheikh, B. N. & Akhtar, A. The many lives of KATs—detectors, integrators and modulators of the cellular environment. Nat. Rev. Genet. 20, 7–23 (2018).
doi: 10.1038/s41576-018-0072-4
Rodríguez-Paredes, M. & Esteller, M. Cancer epigenetics reaches mainstream oncology. Nat. Med 17, 330–339 (2011).
pubmed: 21386836 doi: 10.1038/nm.2305
Boycott, K. M. et al. International cooperation to enable the diagnosis of all rare genetic diseases. Am. J. Hum. Genet. 100, 695–705 (2017).
pubmed: 28475856 pmcid: 5420351 doi: 10.1016/j.ajhg.2017.04.003
Mendjan, S. et al. Nuclear pore components are involved in the transcriptional regulation of dosage compensation in Drosophila. Mol. Cell 21, 811–823 (2006).
pubmed: 16543150 doi: 10.1016/j.molcel.2006.02.007
Koolen, D. A. et al. Mutations in the chromatin modifier gene KANSL1 cause the 17q21. 31 microdeletion syndrome. Nat. Genet 44, 639–641 (2012).
pubmed: 22544363 doi: 10.1038/ng.2262
Zollino, M. et al. Mutations in KANSL1 cause the 17q21. 31 microdeletion syndrome phenotype. Nat. Genet 44, 636–638 (2012).
pubmed: 22544367 doi: 10.1038/ng.2257
Koolen D. A., de Vries B. B. KANSL1-related intellectual disability syndrome. In Gene Reviews (eds Adam, M. P., Ardinger, H. H., Pagon, R. A. et al.) 1993–2018 (University of Washington, WA, Seattle, 2010).
Li, L. et al. Lysine acetyltransferase 8 is involved in cerebral development and syndromic intellectual disability. J. Clin. Investig. 130, 1431–1445 (2019).
doi: 10.1172/JCI131145
Gilissen, C. et al. Genome sequencing identifies major causes of severe intellectual disability. Nature 511, 344–347 (2014).
pubmed: 24896178 doi: 10.1038/nature13394
Chelmicki, T. et al. MOF-associated complexes ensure stem cell identity and Xist repression. Elife 3, e02024 (2014).
pubmed: 24842875 pmcid: 4059889 doi: 10.7554/eLife.02024
Feller, C. et al. The MOF-containing NSL complex associates globally with housekeeping genes, but activates only a defined subset. Nucleic Acids Res. 40, 1509–1522 (2012).
pubmed: 22039099 doi: 10.1093/nar/gkr869
Lam, K. C. et al. The NSL complex regulates housekeeping genes in Drosophila. PLoS Genet 8, e1002736 (2012).
pubmed: 22723752 pmcid: 3375229 doi: 10.1371/journal.pgen.1002736
Sheikh B. N., Guhathakurta S., Akhtar A. The non‐specific lethal (NSL) complex at the crossroads of transcriptional control and cellular homeostasis. EMBO Rep. 20, e47630 (2019).
Raja, S. J. et al. The nonspecific lethal complex is a transcriptional regulator in Drosophila. Mol. Cell 38, 827–841 (2010).
pubmed: 20620954 doi: 10.1016/j.molcel.2010.05.021
Lam, K. C. et al. The NSL complex–mediated nucleosome landscape is required to maintain transcription fidelity and suppression of transcription noise. Genes Dev. 33, 1–14 (2019).
doi: 10.1101/gad.321489.118
Wangler, M. F. et al. Model organisms facilitate rare disease diagnosis and therapeutic research. Genetics 207, 9–27 (2017).
pubmed: 28874452 pmcid: 5586389 doi: 10.1534/genetics.117.203067
Horn, T., Sandmann, T. & Boutros, M. Design and evaluation of genome-wide libraries for RNA interference screens. Genome Biol. 11, R61 (2010).
pubmed: 20550664 pmcid: 2911109 doi: 10.1186/gb-2010-11-6-r61
Zhang, J.-H., Chung, T. D. & Oldenburg, K. R. A simple statistical parameter for use in evaluation and validation of high throughput screening assays. J. Biomol. Screen 4, 67–73 (1999).
pubmed: 10838414 doi: 10.1177/108705719900400206
Van Bortle, K. et al. Insulator function and topological domain border strength scale with architectural protein occupancy. Genome Biol. 15, R82 (2014).
pubmed: 24981874 pmcid: 4226948 doi: 10.1186/gb-2014-15-5-r82
Xu, C. & Corces, V. G. Towards a predictive model of chromatin 3D organization. Semin. Cell Dev. Biol. 57, 24–30 (2016).
pubmed: 26658098 doi: 10.1016/j.semcdb.2015.11.013
Spencer, E., Jiang, J. & Chen, Z. J. Signal-induced ubiquitination of IκBα by the F-box protein Slimb/β-TrCP. Genes Dev. 13, 284–294 (1999).
pubmed: 9990853 pmcid: 316434 doi: 10.1101/gad.13.3.284
Virshup, D. M. & Shenolikar, S. From promiscuity to precision: protein phosphatases get a makeover. Mol. Cell 33, 537–545 (2009).
pubmed: 19285938 doi: 10.1016/j.molcel.2009.02.015
Szklarczyk, D. et al. STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Nucleic Acids Res. 47, D607–D613 (2018).
pmcid: 6323986 doi: 10.1093/nar/gky1131
Kockmann, T. et al. The BET protein FSH functionally interacts with ASH1 to orchestrate global gene activity in Drosophila. Genome Biol. 14, R18 (2013).
pubmed: 23442797 pmcid: 4053998 doi: 10.1186/gb-2013-14-2-r18
Kwak, H. & Lis, J. T. Control of transcriptional elongation. Annu Rev. Genet 47, 483–508 (2013).
pubmed: 24050178 pmcid: 3974797 doi: 10.1146/annurev-genet-110711-155440
Di Micco, R. et al. Control of embryonic stem cell identity by BRD4-dependent transcriptional elongation of super-enhancer-associated pluripotency genes. Cell Rep. 9, 234–247 (2014).
pubmed: 25263550 pmcid: 4317728 doi: 10.1016/j.celrep.2014.08.055
Lovén, J. et al. Selective inhibition of tumor oncogenes by disruption of super-enhancers. Cell 153, 320–334 (2013).
pubmed: 23582323 pmcid: 3760967 doi: 10.1016/j.cell.2013.03.036
Sabari, B. R. et al. Coactivator condensation at super-enhancers links phase separation and gene control. Science 361, eaar3958 (2018).
pubmed: 29930091 pmcid: 6092193 doi: 10.1126/science.aar3958
Chatterjee, A. et al. MOF acetyl transferase regulates transcription and respiration in mitochondria. Cell 167, 722–738. e723 (2016).
pubmed: 27768893 doi: 10.1016/j.cell.2016.09.052
Filippakopoulos, P. et al. Selective inhibition of BET bromodomains. Nature 468, 1067–1073 (2010).
pubmed: 3010259 pmcid: 3010259 doi: 10.1038/nature09504
Nicodeme, E. et al. Suppression of inflammation by a synthetic histone mimic. Nature 468, 1119–1123 (2010).
pubmed: 21068722 pmcid: 5415086 doi: 10.1038/nature09589
Winter, G. E. et al. BET bromodomain proteins function as master transcription elongation factors independent of CDK9 recruitment. Mol. Cell 67, 5–18. e19 (2017).
pubmed: 28673542 pmcid: 5663500 doi: 10.1016/j.molcel.2017.06.004
Tagwerker, C. et al. A tandem affinity tag for two-step purification under fully denaturing conditions application in ubiquitin profiling and protein complex identification combined with in vivocross-linking. Mol. Cell Proteom. 5, 737–748 (2006).
doi: 10.1074/mcp.M500368-MCP200
Cai, Y. et al. Subunit composition and substrate specificity of a MOF-containing histone acetyltransferase distinct from the male-specific lethal (MSL) complex. J. Biol. Chem. 285, 4268–4272 (2010).
pubmed: 20018852 doi: 10.1074/jbc.C109.087981
Filippakopoulos, P. et al. Histone recognition and large-scale structural analysis of the human bromodomain family. Cell 149, 214–231 (2012).
pubmed: 22464331 pmcid: 3326523 doi: 10.1016/j.cell.2012.02.013
Vollmuth, F., Blankenfeldt, W. & Geyer, M. Structures of the dual bromodomains of the P-TEFb-activating protein Brd4 at atomic resolution. J. Biol. Chem. 284, 36547–36556 (2009).
pubmed: 19828451 pmcid: 2794770 doi: 10.1074/jbc.M109.033712
Morinière, J. et al. Cooperative binding of two acetylation marks on a histone tail by a single bromodomain. Nature 461, 664–668 (2009).
pubmed: 19794495 doi: 10.1038/nature08397
Umehara, T. et al. Structural basis for acetylated histone H4 recognition by the human BRD2 bromodomain. J. Biol. Chem. 285, 7610–7618 (2010).
pubmed: 20048151 pmcid: 2844208 doi: 10.1074/jbc.M109.062422
Conrad, T. et al. The MOF chromobarrel domain controls genome-wide H4K16 acetylation and spreading of the MSL complex. Dev. Cell 22, 610–624 (2012).
pubmed: 22421046 doi: 10.1016/j.devcel.2011.12.016
Smith, E. R. et al. A human protein complex homologous to the Drosophila MSL complex is responsible for the majority of histone H4 acetylation at lysine 16. Mol. Cell Biol. 25, 9175–9188 (2005).
pubmed: 16227571 pmcid: 1265810 doi: 10.1128/MCB.25.21.9175-9188.2005
Bhagwat, A. S. et al. BET bromodomain inhibition releases the mediator complex from select cis-regulatory elements. Cell Rep. 15, 519–530 (2016).
pubmed: 27068464 pmcid: 4838499 doi: 10.1016/j.celrep.2016.03.054
Gonzales-Cope, M., Sidoli, S., Bhanu, N. V., Won, K.-J. & Garcia, B. A. Histone H4 acetylation and the epigenetic reader Brd4 are critical regulators of pluripotency in embryonic stem cells. BMC Genomics 17, 95 (2016).
pubmed: 26847871 pmcid: 4740988 doi: 10.1186/s12864-016-2414-y
Xiao, T. et al. Histone H2B ubiquitylation is associated with elongating RNA polymerase II. Mol. Cell Biol. 25, 637–651 (2005).
pubmed: 15632065 pmcid: 543430 doi: 10.1128/MCB.25.2.637-651.2005
Dawson, M. A. et al. Inhibition of BET recruitment to chromatin as an effective treatment for MLL-fusion leukaemia. Nature 478, 529–533 (2011).
pubmed: 21964340 pmcid: 3679520 doi: 10.1038/nature10509
Baldi, S. & Becker, P. B. The variant histone H2A. V of Drosophila—three roles, two guises. Chromosoma 122, 245–258 (2013).
pubmed: 23553272 doi: 10.1007/s00412-013-0409-x
Weber, C. M., Ramachandran, S. & Henikoff, S. Nucleosomes are context-specific, H2A. Z-modulated barriers to RNA polymerase. Mol. Cell 53, 819–830 (2014).
pubmed: 24606920 doi: 10.1016/j.molcel.2014.02.014
Dey, A., Chitsaz, F., Abbasi, A., Misteli, T. & Ozato, K. The double bromodomain protein Brd4 binds to acetylated chromatin during interphase and mitosis. Proc. Natl Acad. Sci. USA 100, 8758–8763 (2003).
pubmed: 12840145 doi: 10.1073/pnas.1433065100
Roe, J.-S., Mercan, F., Rivera, K., Pappin, D. J. & Vakoc, C. R. BET bromodomain inhibition suppresses the function of hematopoietic transcription factors in acute myeloid leukemia. Mol. Cell 58, 1028–1039 (2015).
pubmed: 25982114 pmcid: 4475489 doi: 10.1016/j.molcel.2015.04.011
Sakamaki, J.-i et al. Bromodomain protein BRD4 is a transcriptional repressor of autophagy and lysosomal function. Mol. Cell 66, 517–532. e519 (2017).
pubmed: 28525743 pmcid: 5446411 doi: 10.1016/j.molcel.2017.04.027
Zippo, A. et al. Histone crosstalk between H3S10ph and H4K16ac generates a histone code that mediates transcription elongation. Cell 138, 1122–1136 (2009).
pubmed: 19766566 doi: 10.1016/j.cell.2009.07.031
Delmore, J. E. et al. BET bromodomain inhibition as a therapeutic strategy to target c-Myc. Cell 146, 904–917 (2011).
pubmed: 3187920 pmcid: 3187920 doi: 10.1016/j.cell.2011.08.017
Muhar, M. et al. SLAM-seq defines direct gene-regulatory functions of the BRD4-MYC axis. Science 360, 800–805 (2018).
pubmed: 29622725 pmcid: 6409205 doi: 10.1126/science.aao2793
Cairns, R. A. & Mak, T. W. The current state of cancer metabolism. Nat. Rev. Cancer 16, 613–614 (2016).
doi: 10.1038/nrc.2016.100
Valerio, D. G. et al. Histone acetyltransferase activity of MOF is required for MLL-AF9 leukemogenesis. Cancer Res. 77, 1753–1762 (2017).
pubmed: 28202522 pmcid: 5501293 doi: 10.1158/0008-5472.CAN-16-2374
Arbogast, T. et al. Mouse models of 17q21. 31 microdeletion and microduplication syndromes highlight the importance of Kansl1 for cognition. PLoS Genet 13, e1006886 (2017).
pubmed: 28704368 pmcid: 5531616 doi: 10.1371/journal.pgen.1006886
Basilicata, M. F. et al. De novo mutations in MSL3 cause an X-linked syndrome marked by impaired histone H4 lysine 16 acetylation. Nat. Genet 50, 1442 (2018).
pubmed: 30224647 doi: 10.1038/s41588-018-0220-y
Nichols, J. & Jones, K. Derivation of mouse embryonic stem (ES) cell lines using small-molecule inhibitors of Erk and Gsk3 signaling (2i). Cold Spring Harb. Protoc. 2017, pdb. prot094086 (2017).
doi: 10.1101/pdb.prot094086
Worby, C. A., Simonson-Leff, N. & Dixon, J. E. RNA interference of gene expression (RNAi) in cultured Drosophila cells. Sci. Signal. 95, pl1 (2001).
doi: 10.1126/stke.2001.95.pl1
Pelz, O., Gilsdorf, M. & Boutros, M. Web cellHTS2: a web-application for the analysis of high-throughput screening data. BMC Bioinform. 11, 185 (2010).
doi: 10.1186/1471-2105-11-185
Liao, Y., Smyth, G. K. & Shi, W. The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote. Nucleic Acids Res. 41, e108–e108 (2013).
pubmed: 23558742 pmcid: 3664803 doi: 10.1093/nar/gkt214
Anders, S., Pyl, P. T. & Huber, W. HTSeq—a Python framework to work with high-throughput sequencing data. Bioinformatics 31, 166–169 (2015).
pubmed: 25260700 doi: 10.1093/bioinformatics/btu638
Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550 (2014).
pubmed: 25516281 pmcid: 4302049 doi: 10.1186/s13059-014-0550-8
Dobin, A. et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15–21 (2013).
pubmed: 23104886 doi: 10.1093/bioinformatics/bts635 pmcid: 23104886
Liao, Y., Smyth, G. K. & Shi, W. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics 30, 923–930 (2013).
pubmed: 24227677 doi: 10.1093/bioinformatics/btt656
Manzo M., et al. Isoform‐specific localization of DNMT3A regulates DNA methylation fidelity at bivalent CpG islands. EMBO J. 36, 3421–3434 (2017).
Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. methods 9, 357–359 (2012).
pubmed: 22388286 pmcid: 3322381 doi: 10.1038/nmeth.1923
Ramírez, F. et al. deepTools2: a next generation web server for deep-sequencing data analysis. Nucleic Acids Res. 44, W160–W165 (2016).
pubmed: 27079975 pmcid: 4987876 doi: 10.1093/nar/gkw257
Feng, J., Liu, T., Qin, B., Zhang, Y. & Liu, X. S. Identifying ChIP-seq enrichment using MACS. Nat. Protoc. 7, 1728–1740 (2012).
pubmed: 22936215 doi: 10.1038/nprot.2012.101
Johansen, K. M. et al. Polytene chromosome squash methods for studying transcription and epigenetic chromatin modification in Drosophila using antibodies. Methods 48, 387–397 (2009).
pubmed: 19272452 pmcid: 2821744 doi: 10.1016/j.ymeth.2009.02.019

Auteurs

Aline Gaub (A)

Max Planck Institute of Immunobiology and Epigenetics, Stuebeweg 51, 79108, Freiburg, Germany.

Bilal N Sheikh (BN)

Max Planck Institute of Immunobiology and Epigenetics, Stuebeweg 51, 79108, Freiburg, Germany.

M Felicia Basilicata (MF)

Max Planck Institute of Immunobiology and Epigenetics, Stuebeweg 51, 79108, Freiburg, Germany.

Marie Vincent (M)

CHU Nantes, Service de Génétique Médicale, 38 Boulevard Jean Monnet, 44000, Nantes, France.

Mathilde Nizon (M)

CHU Nantes, Service de Génétique Médicale, 38 Boulevard Jean Monnet, 44000, Nantes, France.

Cindy Colson (C)

Service Génétique, Génétique Clinique, CHU, Avenue Georges Clemenceau CS 30001, 14033, Caen, France.
Normandy University, UNICAEN, BIOTARGEN, Esplanade de la Paix CS 14032, 14032, Caen, France.

Matthew J Bird (MJ)

Department of Chronic Diseases, Metabolism and Ageing, Katholieke Universiteit Leuven, Herestraat 49, 3000, Leuven, Belgium.

James E Bradner (JE)

Novartis Institutes for Biomedical Research, 181 Massachusetts Ave, Cambridge, MA, 02139, USA.

Julien Thevenon (J)

CNRS UMR 5309, INSERM, U1209, Institute of Advanced Biosciences, Université Grenoble-Alpes CHU Grenoble, Allée des Alpes, 38700, La Tronche Grenoble, France.

Michael Boutros (M)

Division of Signaling and Functional Genomics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120, Heidelberg, Germany.
Department of Cell and Molecular Biology, Medical Faculty Mannheim, Heidelberg University, Theodor-Kutzer-Ufer 1-3, 68167, Mannheim, Germany.

Asifa Akhtar (A)

Max Planck Institute of Immunobiology and Epigenetics, Stuebeweg 51, 79108, Freiburg, Germany. akhtar@ie-freiburg.mpg.de.

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