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Drosophila MSL complex globally acetylates H4K16 on the male X chromosome for dosage compensation.

Gelbart ME, Larschan E, Peng S, Park PJ, Kuroda MI - Nat. Struct. Mol. Biol. (2009)

Bottom Line: However, it has been puzzling that approximately 25% of transcribed genes on the X chromosome do not stably recruit MSL complex.The distribution of H4K16ac is much broader than that of the MSL complex, and our results favor the idea that chromosome-wide H4K16ac reflects transient association of the MSL complex, occurring through spreading or chromosomal looping.Our results parallel those of localized Polycomb repressive complex and its more broadly distributed chromatin mark, trimethylated histone H3 Lys27 (H3K27me3), suggesting a common principle for the establishment of active and silenced chromatin domains.

View Article: PubMed Central - PubMed

Affiliation: Division of Genetics, Department of Medicine, Brigham & Women's Hospital, Boston, Massachusetts, USA.

ABSTRACT
The Drosophila melanogaster male-specific lethal (MSL) complex binds the single male X chromosome to upregulate gene expression to equal that from the two female X chromosomes. However, it has been puzzling that approximately 25% of transcribed genes on the X chromosome do not stably recruit MSL complex. Here we find that almost all active genes on the X chromosome are associated with robust H4 Lys16 acetylation (H4K16ac), the histone modification catalyzed by the MSL complex. The distribution of H4K16ac is much broader than that of the MSL complex, and our results favor the idea that chromosome-wide H4K16ac reflects transient association of the MSL complex, occurring through spreading or chromosomal looping. Our results parallel those of localized Polycomb repressive complex and its more broadly distributed chromatin mark, trimethylated histone H3 Lys27 (H3K27me3), suggesting a common principle for the establishment of active and silenced chromatin domains.

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Global H4K16ac on the male X in vivo. (a) H4K16ac is enriched along the majority of the X chromosome relative to 2L in male larvae. The distribution of log ratios at all probes on the X (red) and 2L (blue) is plotted for H4K16ac in male larvae. (b) As in SL2 cells, transcribed genes show the highest levels of H4K16ac in male larvae. The distribution of log ratios at all probes on the X chromosome, classified according to probes present in transcribed genes (TG, red), untranscribed genes (UTG, blue) and intergenic regions (IGR, orange), is shown. (c) MOF is required for H4K16ac in male larvae at sites on the X that lack detectable MSL3-TAP binding, as determined by ChIP-chip11. mof mutant male larvae (blue, purple) and their wild-type brothers (red, yellow) were generated from mof+ mothers. Known MSL targets (the roX2 CES (chromatin entry site) and CG13316 3′ end) and autosomal genes served as positive and negative controls, respectively. We assayed four genes on the X that lack detectable MSL binding11 but are enriched by H4K16ac in male larval ChIP-chip experiments (CG15570, CG13021, CG32523 and CG4949). Genes were classified as transcribed (gene names in red) or untranscribed (gene names in black) based on Affymetrix analysis in SL2 cells5. The H4K16ac ChIP signals were quantified as percent IP normalized to input and H3 levels. The ChIP signals for the two mof1 and the two mof2 genotypes were then normalized to Pka from mof1/Y; [mof+]/+ and mof2/Y; [mof+]/+ males respectively, and the replicates were averaged (see Supplementary Methods). The error bars represent the range from two independent experiments.
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Figure 4: Global H4K16ac on the male X in vivo. (a) H4K16ac is enriched along the majority of the X chromosome relative to 2L in male larvae. The distribution of log ratios at all probes on the X (red) and 2L (blue) is plotted for H4K16ac in male larvae. (b) As in SL2 cells, transcribed genes show the highest levels of H4K16ac in male larvae. The distribution of log ratios at all probes on the X chromosome, classified according to probes present in transcribed genes (TG, red), untranscribed genes (UTG, blue) and intergenic regions (IGR, orange), is shown. (c) MOF is required for H4K16ac in male larvae at sites on the X that lack detectable MSL3-TAP binding, as determined by ChIP-chip11. mof mutant male larvae (blue, purple) and their wild-type brothers (red, yellow) were generated from mof+ mothers. Known MSL targets (the roX2 CES (chromatin entry site) and CG13316 3′ end) and autosomal genes served as positive and negative controls, respectively. We assayed four genes on the X that lack detectable MSL binding11 but are enriched by H4K16ac in male larval ChIP-chip experiments (CG15570, CG13021, CG32523 and CG4949). Genes were classified as transcribed (gene names in red) or untranscribed (gene names in black) based on Affymetrix analysis in SL2 cells5. The H4K16ac ChIP signals were quantified as percent IP normalized to input and H3 levels. The ChIP signals for the two mof1 and the two mof2 genotypes were then normalized to Pka from mof1/Y; [mof+]/+ and mof2/Y; [mof+]/+ males respectively, and the replicates were averaged (see Supplementary Methods). The error bars represent the range from two independent experiments.

Mentions: In order to determine if chromosome-wide acetylation of H4 Lys16 is a general property of the male X, we performed ChIP-chip analysis of H4K16ac in third instar male larvae. As observed in SL2 cells, H4K16ac is more broadly associated with the male X chromosome than MSL complex, assayed previously11, and exhibits a significant baseline shift relative to 2L (Figs. 1a and 4a and Supplementary Figs. 2b and 5a). In contrast, this was not observed in female larvae or “female” Kc cells, which do not express MSL complex (Supplementary Fig. 6a). Further characterization of H4K16ac on the X in male larvae revealed similar properties as were observed in SL2 cells. Active genes show the highest levels of H4K16ac enrichment (Fig. 4b and Supplementary Fig. 5b), and H4K16ac is biased towards the middle and 3′ ends of these genes (Supplementary Fig. 5c).


Drosophila MSL complex globally acetylates H4K16 on the male X chromosome for dosage compensation.

Gelbart ME, Larschan E, Peng S, Park PJ, Kuroda MI - Nat. Struct. Mol. Biol. (2009)

Global H4K16ac on the male X in vivo. (a) H4K16ac is enriched along the majority of the X chromosome relative to 2L in male larvae. The distribution of log ratios at all probes on the X (red) and 2L (blue) is plotted for H4K16ac in male larvae. (b) As in SL2 cells, transcribed genes show the highest levels of H4K16ac in male larvae. The distribution of log ratios at all probes on the X chromosome, classified according to probes present in transcribed genes (TG, red), untranscribed genes (UTG, blue) and intergenic regions (IGR, orange), is shown. (c) MOF is required for H4K16ac in male larvae at sites on the X that lack detectable MSL3-TAP binding, as determined by ChIP-chip11. mof mutant male larvae (blue, purple) and their wild-type brothers (red, yellow) were generated from mof+ mothers. Known MSL targets (the roX2 CES (chromatin entry site) and CG13316 3′ end) and autosomal genes served as positive and negative controls, respectively. We assayed four genes on the X that lack detectable MSL binding11 but are enriched by H4K16ac in male larval ChIP-chip experiments (CG15570, CG13021, CG32523 and CG4949). Genes were classified as transcribed (gene names in red) or untranscribed (gene names in black) based on Affymetrix analysis in SL2 cells5. The H4K16ac ChIP signals were quantified as percent IP normalized to input and H3 levels. The ChIP signals for the two mof1 and the two mof2 genotypes were then normalized to Pka from mof1/Y; [mof+]/+ and mof2/Y; [mof+]/+ males respectively, and the replicates were averaged (see Supplementary Methods). The error bars represent the range from two independent experiments.
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Figure 4: Global H4K16ac on the male X in vivo. (a) H4K16ac is enriched along the majority of the X chromosome relative to 2L in male larvae. The distribution of log ratios at all probes on the X (red) and 2L (blue) is plotted for H4K16ac in male larvae. (b) As in SL2 cells, transcribed genes show the highest levels of H4K16ac in male larvae. The distribution of log ratios at all probes on the X chromosome, classified according to probes present in transcribed genes (TG, red), untranscribed genes (UTG, blue) and intergenic regions (IGR, orange), is shown. (c) MOF is required for H4K16ac in male larvae at sites on the X that lack detectable MSL3-TAP binding, as determined by ChIP-chip11. mof mutant male larvae (blue, purple) and their wild-type brothers (red, yellow) were generated from mof+ mothers. Known MSL targets (the roX2 CES (chromatin entry site) and CG13316 3′ end) and autosomal genes served as positive and negative controls, respectively. We assayed four genes on the X that lack detectable MSL binding11 but are enriched by H4K16ac in male larval ChIP-chip experiments (CG15570, CG13021, CG32523 and CG4949). Genes were classified as transcribed (gene names in red) or untranscribed (gene names in black) based on Affymetrix analysis in SL2 cells5. The H4K16ac ChIP signals were quantified as percent IP normalized to input and H3 levels. The ChIP signals for the two mof1 and the two mof2 genotypes were then normalized to Pka from mof1/Y; [mof+]/+ and mof2/Y; [mof+]/+ males respectively, and the replicates were averaged (see Supplementary Methods). The error bars represent the range from two independent experiments.
Mentions: In order to determine if chromosome-wide acetylation of H4 Lys16 is a general property of the male X, we performed ChIP-chip analysis of H4K16ac in third instar male larvae. As observed in SL2 cells, H4K16ac is more broadly associated with the male X chromosome than MSL complex, assayed previously11, and exhibits a significant baseline shift relative to 2L (Figs. 1a and 4a and Supplementary Figs. 2b and 5a). In contrast, this was not observed in female larvae or “female” Kc cells, which do not express MSL complex (Supplementary Fig. 6a). Further characterization of H4K16ac on the X in male larvae revealed similar properties as were observed in SL2 cells. Active genes show the highest levels of H4K16ac enrichment (Fig. 4b and Supplementary Fig. 5b), and H4K16ac is biased towards the middle and 3′ ends of these genes (Supplementary Fig. 5c).

Bottom Line: However, it has been puzzling that approximately 25% of transcribed genes on the X chromosome do not stably recruit MSL complex.The distribution of H4K16ac is much broader than that of the MSL complex, and our results favor the idea that chromosome-wide H4K16ac reflects transient association of the MSL complex, occurring through spreading or chromosomal looping.Our results parallel those of localized Polycomb repressive complex and its more broadly distributed chromatin mark, trimethylated histone H3 Lys27 (H3K27me3), suggesting a common principle for the establishment of active and silenced chromatin domains.

View Article: PubMed Central - PubMed

Affiliation: Division of Genetics, Department of Medicine, Brigham & Women's Hospital, Boston, Massachusetts, USA.

ABSTRACT
The Drosophila melanogaster male-specific lethal (MSL) complex binds the single male X chromosome to upregulate gene expression to equal that from the two female X chromosomes. However, it has been puzzling that approximately 25% of transcribed genes on the X chromosome do not stably recruit MSL complex. Here we find that almost all active genes on the X chromosome are associated with robust H4 Lys16 acetylation (H4K16ac), the histone modification catalyzed by the MSL complex. The distribution of H4K16ac is much broader than that of the MSL complex, and our results favor the idea that chromosome-wide H4K16ac reflects transient association of the MSL complex, occurring through spreading or chromosomal looping. Our results parallel those of localized Polycomb repressive complex and its more broadly distributed chromatin mark, trimethylated histone H3 Lys27 (H3K27me3), suggesting a common principle for the establishment of active and silenced chromatin domains.

Show MeSH
Related in: MedlinePlus