The activation potential of MOF is constrained for dosage compensation
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ABSTRACT:
ORGANISM(S): Drosophila melanogaster
PROVIDER: GSE20695 | GEO | 2010/06/26
SECONDARY ACCESSION(S): PRJNA125011
REPOSITORIES: GEO
Similar Datasets
Project description:The H4K16 acetyltransferase MOF plays a crucial role in dosage compensation in Drosophila, but has additional, global functions. We compared the molecular context and effect of MOF in male and female flies combining chromosome-wide mapping and transcriptome studies with analyses of defined reporter loci in transgenic flies. MOF distributes dynamically between two complexes, the Dosage Compensation Complex and a complex containing MBD-R2, a global facilitator of transcription. These different targeting principles define the distribution of MOF between the X chromosome and autosomes and at transcription units with 5’ or 3’ enrichment. The male X chromosome differs from all other chromosomes in that H4K16 acetylation levels do not correlate with transcription output. The reconstitution of this phenomenon at a model locus revealed that the activation potential of MOF is constraint in male cells in the context of the DCC to arrive at the two-fold activation of transcription characteristic of dosage compensation. ChIP-chip profiling of MBD-R2, MOF and MSL1 in adult male and female flies, and SL2 cells, incl. at least 3 biological replicates
2010-06-26 | E-GEOD-20695 | biostudies-arrayexpress
Project description:The H4K16 acetyltransferase MOF plays a crucial role in dosage compensation in Drosophila, but has additional, global functions in gene control. We compared the molecular context and effect of MOF activity in male and female flies combining chromosome-wide mapping and transcriptome studies with analyses of defined reporter loci in transgenic flies. MOF distributes dynamically between two types of complexes, the Dosage Compensation Complex (DCC) and complexes containing MBD-R2, a global facilitator of transcription. These different targeting principles define the distribution of MOF between the X chromosome and autosomes and at transcription units with 5’ or 3’ enrichment. The male X chromosome differs from all other chromosomes in that H4K16 acetylation levels do not correlate with transcription output. The reconstitution of this phenomenon at a model locus revealed that the activation potential of MOF is constrained in male cells in the context of the DCC to arrive at the two-fold activation of transcription characteristic of dosage compensation.
2010-06-26 | GSE20744 | GEO
Project description:Drosophila dosage compensation is an epigenetic phenomenon in which the transcription of most genes on X-chromosome is enhanced by approximately two folds in males to equalize that in females. In this study, we provide evidence that transcriptional repressors, such as HP1 and linker histone H1, are globally reduced on male X chromosome. We further investigated the role of HP1 and linker H1 on X chromosome dosage compensation using flies with overexpression of HP1 and H1, we demonstrate that these repressors surpress H4K16 acetylation, presence of the elongating RNA Pol II and the transcription of the genes on male X chromosomes. To understand how H1 and HP1 are regulated on male X chromosome, we next explored the relationship between MOF and the two repressors of chromatin. We show that the hyperacetylation of H4K16 induced by MOF resulted in the loss of H1 and HP1 on chromatin and global chromatin decondensation. Our biochemical analysis further shows that the presence of acetylation on histone H4 at lysine 16 directly inhibits the interaction between histone H4 and linker H1. This study therefore provides novel clues on understanding the dynamic regulation of chromatin regulators on male X chromosome dosage compensation.
2017-11-01 | GSE29537 | GEO
Project description:We replaced the endogenous histones of Drosophila melanogaster with either histones containing an H3K9R mutation or histones containing an H4K16R mutation to interrogate established genome-wide correlations between chromatin state, transcription, and DNA replication timing. We performed total RNA-seq in H4K16R males and females to investigate the role of H4K16 in dosage compensation of the male X chromosome. We found that H4K16 directly promotes hyper-expression of the male X chromosome in Drosophila. To generate replication timing profiles, we performed Repli-seq in HWT males and females, H4K16R males and females, and H3K9R females. We found that H3K9 promotes late replication of the pericentromeric heterochromatin and H4K16 promotes early replication of the male X chromosome.
2018-09-21 | GSE114925 | GEO
Project description:Drosophila X chromosomes are subject to dosage compensation in males and are known to have a specialized chromatin structure in the male soma. We are interested in how specific chromatin structure change contributes to X chromosome hyperactivity and dosage compensation. We have conducted a global analysis of localize two dosage compensation complex dependent histone marks H4AcK16 and H3PS10 and one dosage compensation complex independent histone mark H3diMeK4 in the genome, especially on X chromosome by ChIP-chip approach in both male and female adult flies. We also probed general genomewide chromatin structure by deep DNA sequencing of sheared ChIP input DNA from male and female adult flies.
2010-01-11 | GSE15593 | GEO
Project description:Drosophila X chromosomes are subject to dosage compensation in males and are known to have a specialized chromatin structure in the male soma. We are interested in how specific chromatin structure change contributes to X chromosome hyperactivity and dosage compensation. We have conducted a global analysis of localize two dosage compensation complex dependent histone marks H4AcK16 and H3PS10 and one dosage compensation complex independent histone mark H3diMeK4 in the genome, especially on X chromosome by ChIP-chip approach in both male and female adult flies. We also probed general genomewide chromatin structure by deep DNA sequencing of sheared ChIP input DNA from male and female adult flies. Chromatin immunoprecipitations were performed in 5-7 day aged adult male and female flies with three histone modification antibodies. ChIP enriched DNA and input DNA was labeled by Cy3 or Cy5 dye separately and hybridized simultaneously to the Drosophila FlyGEM arrays. At least two biological replicates were performed for each antibody and sex. DNA-seq (NIDDK-Drosophila-Illumina-DNASeq) were performed on ChIP-input sheared DNA to check the general chromatin structure of different chromosome.
2010-01-11 | E-GEOD-15593 | biostudies-arrayexpress
Project description:Many animal species employ a chromosome-based mechanism of sex determination, which has led to coordinate evolution of dosage compensation systems. Dosage compensation not only corrects the imbalance in the number of X-chromosomes between the sexes, but is also hypothesized to correct dosage imbalance within cells due to mono-allelic X expression and bi-allelic autosomal expression, by upregulating X-linked genes (termed M-bM-^@M-^XOhnoM-bM-^@M-^Ys hypothesisM-bM-^@M-^Y). To identify molecular mechanisms of X upregulation in mammals we established genome-wide profiles for the initiation and elongation forms of RNA polymerase II (PolII), PolII-S5p (phosphorylated at serine 5) and PolII-S2p (phosphorylated at serine 2), and for histone modifications in mouse cell lines and tissues. We found that in addition to being enriched in PolII-S5p but not in PolII-S2p, X-linked promoters were also enriched in two epigenetic marks, H4K16ac and H2AZ, dependent on expression levels. To address the function of the H4K16 acetyltransferase MOF occupancy profiles were established and knockdowns of MOF and MSL1 were done in mouse ES cells. Our results support a conserved role for the MSL complex to enhance transcription initiation of X-linked genes. Comparison of the profiles of RNA PolII, the H4K16ac acetyltransferase MOF and histone active marks on the X versus autosomes in mouse
2013-03-05 | E-GEOD-44835 | biostudies-arrayexpress
Project description:In this study we focus on the MYST-type acetyltransferase MOF (males-absent-on-the-first, KAT8), which is the effector enzyme of two transcription regulator complexes in Dro-sophila. As part of the male-specific-lethal dosage compensation complex (MSL-DCC, or DCC for short), the enzyme is targeted to transcribed genes on the X chromosome, where it acetylates H4K16 to unfold the chromatin fiber to boost transcription (15-17). In the context of the NSL complex (16) MOF has been reported to acetylate different combina-tions of histone H4 lysines 5, 8, 12 and 16 at promoters in different cells, illustrating the potential of complex subunits to modulate substrate specificity (18-21). Defining the substrate selectivity of KATs in vivo poses several challenges (1). The intrin-sic substrate selectivity of enzymes may be modulated by its molecular environment, be it the complex assembly or the chromatin context. Redundant activities of different en-zymes, indirect effects and the action of lysine deacetylases (KDACs) may occlude the consequences of loss-of-function manipulation. Furthermore, the specificity of the anti-bodies that are commonly used to detect distinct acetylated lysines in histones may be compromised due to low-level off-target effects, interference of modifications next to acetylated lysines, and the tendency of Kac-antibodies to react with relaxed selectivity with oligo-acetylated histone tails (22-25). A more reliable strategy involves the detection of modified histone peptides by mass spectrometry, which unequivocally detects individ-ual modifications and defined combinations of modifications and has a much better dy-namic range than traditional Western blotting (26-30). In a complementary approach one may determine the intrinsic substrate selectivity of defined recombinant enzymes and KAT complexes in biochemical assays (31). We re-cently reconstituted a recombinant MOF-containing core DCC (here termed ‘4-MSL’, since it contains the subunits MOF, MSL1, MSL2 and MSL3 (32)) and now report on a study of its substrate selectivity on recombinant nucleosome arrays. Pilot experiments using traditional Western blotting of diagnostic antibodies suggested that, in addition to the expected H4K16 acetylation, H4K12 was modified. Since this finding disagrees with the prevailing view that the DCC selectively acetylates H4K16, we applied the targeted mass spectrometry described in (26) to our in vitro reactions, focusing on acetylation of the H4 N-terminus. We compared the acetylation reaction of the 4-MSL complex with another MYST enzyme, dTip60 (KAT5), in the context of a trimeric complex, akin to the yeast piccolo NuA4 complex, which is thought to have a more relaxed lysine selectivity on the H4 N-terminus (33-35). We found that during short reaction times, the 4-MSL complex acetylated H4K16 with excellent selectivity, while the dTip60piccolo complex preferentially modified H4K12. To our surprise, we also observed that during longer incubations the 4-MSL complex progres-sively acetylated K12, K8 and K5, leading to a complex mixture of oligo-acetylated H4. Mathematical modeling suggests that MOF recognizes and acetylates H4K16 with high selectivity, but remains bound to the substrate and continues to acetylate more N-terminal H4 lysines in a processive manner. Because the MSL-DCC in vivo contains long, non-coding roX RNA (15,36-38), we ex-plored whether RNA affected the specificity of the reaction. We observed that the addi-tion of RNA to the HAT reaction improves the specificity of the reaction and suppresses the generation of oligo-acetylated forms, possibly by reducing the dwell time of the en-zyme on the nucleosome substrate. The comparison of MOF and dTip60 activities in the context of recombinant HAT com-plexes revealed significant differences in activity and specificity. Our study describes a powerful experimental approach and conceptual framework for the analysis of physiolog-ically relevant components that modulate intrinsic activities.
2024-02-13 | PXD046636 | Pride
Project description:We have performed a comparison of global patterns of gene expression between two bird species, the chicken and zebra finch, especially with regard to sex bias of autosomal vs. Z chromosome genes, dosage compensation and evolution of sex bias. Both species appear to lack a Z chromosome-wide mechanism of dosage compensation, because both have a similar pattern of significantly higher expression of Z genes in males relative to females. Unlike the chicken Z chromosome, which has female-specific expression of the non-coding RNA MHM (male hypermethylated), and acetylation of histone 4 lysine 16 (H4K16) near MHM, the zebra finch Z chromosome appears to lack the MHM sequence and acetylation of H4K16. The zebra finch also does not show the reduced male to female (M:F) ratio of gene expression near MHM similar to that found in the chicken. Although the M:F ratios of Z chromosome gene expression are similar across tissues and ages within each species, they differ between the two species. Z genes showing the greatest species difference in M:F ratio were concentrated near the MHM region of the chicken Z chromosome. The current study shows that the zebra finch differs from the chicken because it lacks a specialized region of greater dosage compensation along the Z chromosome, and shows dosage compensation for a different set of Z genes than the chicken. These patterns suggest that different avian taxa may have evolved specific compensatory mechanisms.
2010-02-11 | GSE20035 | GEO
Project description:Many animal species employ a chromosome-based mechanism of sex determination, which has led to coordinate evolution of dosage compensation systems. Dosage compensation not only corrects the imbalance in the number of X-chromosomes between the sexes, but is also hypothesized to correct dosage imbalance within cells due to mono-allelic X expression and bi-allelic autosomal expression, by upregulating X-linked genes (termed ‘Ohno’s hypothesis’). To identify molecular mechanisms of X upregulation in mammals we established genome-wide profiles for the initiation and elongation forms of RNA polymerase II (PolII), PolII-S5p (phosphorylated at serine 5) and PolII-S2p (phosphorylated at serine 2), and for histone modifications in mouse cell lines and tissues. We found that in addition to being enriched in PolII-S5p but not in PolII-S2p, X-linked promoters were also enriched in two epigenetic marks, H4K16ac and H2AZ, dependent on expression levels. To address the function of the H4K16 acetyltransferase MOF occupancy profiles were established and knockdowns of MOF and MSL1 were done in mouse ES cells. Our results support a conserved role for the MSL complex to enhance transcription initiation of X-linked genes.
2013-03-05 | GSE44835 | GEO