, Spreading of chromosomes was achieved by applying the tip of a 200 rpm Dremel and subsequent flattening was achieved with the use of a MTC-300-1 vice (Avenger Gold Toolmaker). Slides were blocked with 10% goat serum (Invitrogen), followed by primary and secondary antibody incubations. Primary antibodies were used at the following concentrations: anti HA (Covance) 1/400, anti NSL3 1/250, Secondary Antibodies were used at 1/500 dilution. Images were captured on a LSM780 confocal microscope (Carl Zeiss Microscopy) using an alpha Plan-Apochromat 63×/1.4 (DIC) Oil objective. This method was adapted from a previously described method 70 . Generating list of conserved NSL complex-dependent genes, Polytene chromosome immunostainings. Polytene stainings of salivary glands of wandering third instar larvae were carried out as follows. Salivary glands were dissected, fixed for 7 min in fixation solution (1.8% Formaldehyde, 0.45% acetic acid

, ) dBRD4 ChIP-seq from S2 cells: GSE36450 MOF ChIP-seq: GSE37864 KANSL3, MCRS1, MOF ChIP-seq in mESC: GSE51746 Kansl3 knockdown RNA-seq in mESC: GSE57698 BRD4 ChIP-seq: mESC and EB: GSE76760 BRD4 ChIP-seq: MLL-AF9: GSE74536 JQ1 RNA-seq MOLT4 cells: GSE79253 From ArrayExpress NSL3 and MBD-R2 ChIP, Data from public repositories. From NCBI gene expression omnibus

. Gfp-rnai and . Rnai, Pol II ChIP-seq from S2 cells, p.1084

, Further information on experimental design and reagents can be found in the Nature Research Reporting Summary linked to this article. Data availability RNA-seq and ChIP-seq data have been deposited to Gene Expression Omnibus (GEO) under the accession number: GSE135815 and are also accessible under BioProject PRJNA560185. All other relevant data supporting the key findings of this study are available within the article and its Supplementary Information files or from the corresponding author upon reasonable request. The source data underlying Figs. 2a, 3b-d, 4d-g, 5b, 6a,b and Supplementary Figs. 1a, b, 3a-c

C. D. Allis and T. Jenuwein, The molecular hallmarks of epigenetic control, Nat. Rev. Genet, vol.17, p.487, 2016.

B. N. Sheikh and A. Akhtar, The many lives of KATs-detectors, integrators and modulators of the cellular environment, Nat. Rev. Genet, vol.20, pp.7-23, 2018.

M. Rodríguez-paredes and M. Esteller, Cancer epigenetics reaches mainstream oncology, Nat. Med, vol.17, pp.330-339, 2011.

K. M. Boycott, International cooperation to enable the diagnosis of all rare genetic diseases, Am. J. Hum. Genet, vol.100, pp.695-705, 2017.

S. Mendjan, Nuclear pore components are involved in the transcriptional regulation of dosage compensation in Drosophila, Mol. Cell, vol.21, pp.811-823, 2006.

D. A. Koolen, Mutations in the chromatin modifier gene KANSL1 cause the 17q21. 31 microdeletion syndrome, Nat. Genet, vol.44, pp.639-641, 2012.

M. Zollino, Mutations in KANSL1 cause the 17q21. 31 microdeletion syndrome phenotype, Nat. Genet, vol.44, pp.636-638, 2012.

D. A. Koolen, B. De-vries, M. P. Adam, H. H. Ardinger, and R. A. Pagon, KANSL1-related intellectual disability syndrome, Gene Reviews, 1993.

L. Li, Lysine acetyltransferase 8 is involved in cerebral development and syndromic intellectual disability, J. Clin. Investig, vol.130, pp.1431-1445, 2019.

C. Gilissen, Genome sequencing identifies major causes of severe intellectual disability, Nature, vol.511, pp.344-347, 2014.

T. Chelmicki, MOF-associated complexes ensure stem cell identity and Xist repression, Elife, vol.3, p.2024, 2014.

C. Feller, The MOF-containing NSL complex associates globally with housekeeping genes, but activates only a defined subset, Nucleic Acids Res, vol.40, pp.1509-1522, 2012.

K. C. Lam, The NSL complex regulates housekeeping genes in Drosophila, PLoS Genet, vol.8, p.1002736, 2012.

B. N. Sheikh, S. Guhathakurta, and A. Akhtar, The non-specific lethal (NSL) complex at the crossroads of transcriptional control and cellular homeostasis, EMBO Rep, vol.20, p.47630, 2019.

S. J. Raja, The nonspecific lethal complex is a transcriptional regulator in Drosophila, Mol. Cell, vol.38, pp.827-841, 2010.

K. C. Lam, The NSL complex-mediated nucleosome landscape is required to maintain transcription fidelity and suppression of transcription noise, Genes Dev, vol.33, pp.1-14, 2019.

M. F. Wangler, Model organisms facilitate rare disease diagnosis and therapeutic research, Genetics, vol.207, pp.9-27, 2017.

T. Horn, T. Sandmann, and M. Boutros, Design and evaluation of genome-wide libraries for RNA interference screens, Genome Biol, vol.11, p.61, 2010.

J. Zhang, T. D. Chung, and K. R. Oldenburg, A simple statistical parameter for use in evaluation and validation of high throughput screening assays, J. Biomol. Screen, vol.4, pp.67-73, 1999.

K. Van-bortle, Insulator function and topological domain border strength scale with architectural protein occupancy, Genome Biol, vol.15, p.82, 2014.

C. Xu and V. G. Corces, Towards a predictive model of chromatin 3D organization, Semin. Cell Dev. Biol, vol.57, pp.24-30, 2016.

E. Spencer, J. Jiang, and Z. J. Chen, Signal-induced ubiquitination of I?B? by the F-box protein Slimb/?-TrCP, Genes Dev, vol.13, pp.284-294, 1999.

D. M. Virshup and S. Shenolikar, From promiscuity to precision: protein phosphatases get a makeover, Mol. Cell, vol.33, pp.537-545, 2009.

D. Szklarczyk, STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets, Nucleic Acids Res, vol.47, pp.607-613, 2018.

T. Kockmann, The BET protein FSH functionally interacts with ASH1 to orchestrate global gene activity in Drosophila, Genome Biol, vol.14, p.18, 2013.

H. Kwak and J. Lis, Control of transcriptional elongation, Annu Rev. Genet, vol.47, pp.483-508, 2013.

R. Di-micco, Control of embryonic stem cell identity by BRD4-dependent transcriptional elongation of super-enhancer-associated pluripotency genes, Cell Rep, vol.9, pp.234-247, 2014.

J. Lovén, Selective inhibition of tumor oncogenes by disruption of superenhancers, Cell, vol.153, pp.320-334, 2013.

B. R. Sabari, Coactivator condensation at super-enhancers links phase separation and gene control, Science, vol.361, p.3958, 2018.

A. Chatterjee, MOF acetyl transferase regulates transcription and respiration in mitochondria, Cell, vol.167, issue.e723, pp.722-738, 2016.

P. Filippakopoulos, Selective inhibition of BET bromodomains, Nature, vol.468, pp.1067-1073, 2010.

E. Nicodeme, Suppression of inflammation by a synthetic histone mimic, Nature, vol.468, pp.1119-1123, 2010.

G. E. Winter, BET bromodomain proteins function as master transcription elongation factors independent of CDK9 recruitment, Mol. Cell, vol.67, p.19, 2017.

C. Tagwerker, 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, vol.5, pp.737-748, 2006.

Y. Cai, Subunit composition and substrate specificity of a MOFcontaining histone acetyltransferase distinct from the male-specific lethal (MSL) complex, J. Biol. Chem, vol.285, pp.4268-4272, 2010.

P. Filippakopoulos, Histone recognition and large-scale structural analysis of the human bromodomain family, Cell, vol.149, pp.214-231, 2012.

F. Vollmuth, W. Blankenfeldt, and M. Geyer, Structures of the dual bromodomains of the P-TEFb-activating protein Brd4 at atomic resolution, J. Biol. Chem, vol.284, pp.36547-36556, 2009.

J. Morinière, Cooperative binding of two acetylation marks on a histone tail by a single bromodomain, Nature, vol.461, pp.664-668, 2009.

T. Umehara, Structural basis for acetylated histone H4 recognition by the human BRD2 bromodomain, J. Biol. Chem, vol.285, pp.7610-7618, 2010.

T. Conrad, The MOF chromobarrel domain controls genome-wide H4K16 acetylation and spreading of the MSL complex, Dev. Cell, vol.22, pp.610-624, 2012.

E. R. Smith, 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, vol.25, pp.9175-9188, 2005.
URL : https://hal.archives-ouvertes.fr/hal-02154288

A. S. Bhagwat, BET bromodomain inhibition releases the mediator complex from select cis-regulatory elements, Cell Rep, vol.15, pp.519-530, 2016.

M. Gonzales-cope, S. Sidoli, N. V. Bhanu, K. Won, and B. A. Garcia, Histone H4 acetylation and the epigenetic reader Brd4 are critical regulators of pluripotency in embryonic stem cells, BMC Genomics, vol.17, p.95, 2016.

T. Xiao, Histone H2B ubiquitylation is associated with elongating RNA polymerase II, Mol. Cell Biol, vol.25, pp.637-651, 2005.

M. A. Dawson, Inhibition of BET recruitment to chromatin as an effective treatment for MLL-fusion leukaemia, Nature, vol.478, pp.529-533, 2011.

S. Baldi and P. B. Becker, The variant histone H2A. V of Drosophila-three roles, two guises, Chromosoma, vol.122, pp.245-258, 2013.

C. M. Weber, S. Ramachandran, and S. Henikoff, Nucleosomes are contextspecific, H2A. Z-modulated barriers to RNA polymerase, Mol. Cell, vol.53, pp.819-830, 2014.

A. Dey, F. Chitsaz, A. Abbasi, T. Misteli, and K. Ozato, The double bromodomain protein Brd4 binds to acetylated chromatin during interphase and mitosis, Proc. Natl Acad. Sci. USA, vol.100, pp.8758-8763, 2003.

J. Roe, F. Mercan, K. Rivera, D. J. Pappin, and C. R. Vakoc, BET bromodomain inhibition suppresses the function of hematopoietic transcription factors in acute myeloid leukemia, Mol. Cell, vol.58, pp.1028-1039, 2015.

J. Sakamaki, Bromodomain protein BRD4 is a transcriptional repressor of autophagy and lysosomal function, Mol. Cell, vol.66, p.519, 2017.

A. Zippo, Histone crosstalk between H3S10ph and H4K16ac generates a histone code that mediates transcription elongation, Cell, vol.138, pp.1122-1136, 2009.

J. E. Delmore, BET bromodomain inhibition as a therapeutic strategy to target c-Myc, Cell, vol.146, pp.904-917, 2011.

M. Muhar, SLAM-seq defines direct gene-regulatory functions of the BRD4-MYC axis, Science, vol.360, pp.800-805, 2018.

R. A. Cairns and T. W. Mak, The current state of cancer metabolism, Nat. Rev. Cancer, vol.16, pp.613-614, 2016.

D. G. Valerio, Histone acetyltransferase activity of MOF is required for MLL-AF9 leukemogenesis, Cancer Res, vol.77, pp.1753-1762, 2017.

T. Arbogast, Mouse models of 17q21. 31 microdeletion and microduplication syndromes highlight the importance of Kansl1 for cognition, PLoS Genet, vol.13, p.1006886, 2017.
URL : https://hal.archives-ouvertes.fr/tel-01325216

M. F. Basilicata, De novo mutations in MSL3 cause an X-linked syndrome marked by impaired histone H4 lysine 16 acetylation, Nat. Genet, vol.50, p.1442, 2018.
URL : https://hal.archives-ouvertes.fr/hal-02058702

J. Nichols and K. Jones, Derivation of mouse embryonic stem (ES) cell lines using small-molecule inhibitors of Erk and Gsk3 signaling (2i), p.94086, 2017.

C. A. Worby, N. Simonson-leff, and J. E. Dixon, RNA interference of gene expression (RNAi) in cultured Drosophila cells, Sci. Signal, vol.95, p.1, 2001.

O. Pelz, M. Gilsdorf, and M. Boutros, Web cellHTS2: a web-application for the analysis of high-throughput screening data, BMC Bioinform, vol.11, p.185, 2010.

Y. Liao, G. K. Smyth, and W. Shi, The Subread aligner: fast, accurate and scalable read mapping by seed-and-vote, Nucleic Acids Res, vol.41, pp.108-108, 2013.

S. Anders, P. T. Pyl, and W. Huber, HTSeq-a Python framework to work with high-throughput sequencing data, Bioinformatics, vol.31, pp.166-169, 2015.

M. I. Love, W. Huber, and S. Anders, Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2, Genome Biol, vol.15, p.550, 2014.

A. Dobin, STAR: ultrafast universal RNA-seq aligner, Bioinformatics, vol.29, pp.15-21, 2013.

Y. Liao, G. K. Smyth, and W. Shi, featureCounts: an efficient general purpose program for assigning sequence reads to genomic features, Bioinformatics, vol.30, pp.923-930, 2013.

M. Manzo, Isoform-specific localization of DNMT3A regulates DNA methylation fidelity at bivalent CpG islands, EMBO J, vol.36, pp.3421-3434, 2017.

B. Langmead and S. L. Salzberg, Fast gapped-read alignment with Bowtie 2, Nat. methods, vol.9, pp.357-359, 2012.

F. Ramírez, deepTools2: a next generation web server for deepsequencing data analysis, Nucleic Acids Res, vol.44, pp.160-165, 2016.

J. Feng, T. Liu, B. Qin, Y. Zhang, and X. S. Liu, Identifying ChIP-seq enrichment using MACS, Nat. Protoc, vol.7, pp.1728-1740, 2012.

K. M. Johansen, Polytene chromosome squash methods for studying transcription and epigenetic chromatin modification in Drosophila using antibodies, Methods, vol.48, pp.387-397, 2009.