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The NSL complex regulates housekeeping genes in Drosophila.

Lam KC, Mühlpfordt F, Vaquerizas JM, Raja SJ, Holz H, Luscombe NM, Manke T, Akhtar A - PLoS Genet. (2012)

Bottom Line: The observed Pol II reduction coincides with compromised binding of TBP and TFIIB to target promoters, indicating that the NSL complex is required for optimal recruitment of the pre-initiation complex on target genes.Moreover, genes that undergo the most dramatic loss of Pol II upon NSL knockdowns tend to be enriched in DNA Replication-related Element (DRE).Taken together, our findings show that the MOF-containing NSL complex acts as a major regulator of housekeeping genes in flies by modulating initiation of Pol II transcription.

View Article: PubMed Central - PubMed

Affiliation: Max-Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany.

ABSTRACT
MOF is the major histone H4 lysine 16-specific (H4K16) acetyltransferase in mammals and Drosophila. In flies, it is involved in the regulation of X-chromosomal and autosomal genes as part of the MSL and the NSL complexes, respectively. While the function of the MSL complex as a dosage compensation regulator is fairly well understood, the role of the NSL complex in gene regulation is still poorly characterized. Here we report a comprehensive ChIP-seq analysis of four NSL complex members (NSL1, NSL3, MBD-R2, and MCRS2) throughout the Drosophila melanogaster genome. Strikingly, the majority (85.5%) of NSL-bound genes are constitutively expressed across different cell types. We find that an increased abundance of the histone modifications H4K16ac, H3K4me2, H3K4me3, and H3K9ac in gene promoter regions is characteristic of NSL-targeted genes. Furthermore, we show that these genes have a well-defined nucleosome free region and broad transcription initiation patterns. Finally, by performing ChIP-seq analyses of RNA polymerase II (Pol II) in NSL1- and NSL3-depleted cells, we demonstrate that both NSL proteins are required for efficient recruitment of Pol II to NSL target gene promoters. The observed Pol II reduction coincides with compromised binding of TBP and TFIIB to target promoters, indicating that the NSL complex is required for optimal recruitment of the pre-initiation complex on target genes. Moreover, genes that undergo the most dramatic loss of Pol II upon NSL knockdowns tend to be enriched in DNA Replication-related Element (DRE). Taken together, our findings show that the MOF-containing NSL complex acts as a major regulator of housekeeping genes in flies by modulating initiation of Pol II transcription.

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NSL-bound genes display a specific nucleosome organization at their TSS.(A) The TSSs of constitutively active genes, either NSL-bound or –non-bound, were analyzed regarding their reported transcription initiation patterns [35]. NSL-bound TSSs mostly belong to genes with weak and broad transcription initiation peaks (40% and 11.4%) whereas NSL-non-bound TSSs mainly belong to genes with narrow transcription initiation peaks (19.3%). (B) Boxplots of the sum of overlapping nucleosome reads in the regions 200 bp upstream and 200 bp downstream of the TSSs of constitutively expressed NSL-bound genes (red), constitutively expressed NSL-non-bound genes (gray), and tissue-specific genes (white). Genes were stratified based on their gene expression quartile (see Materials and Methods) which demonstrates that the depletion of nucleosomes immediately upstream of the TSS that we observed for NSL-bound housekeeping genes (left side) is independent of expression levels (p-values for −200 bp region <2.2e-16; Wilcoxon test).
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pgen-1002736-g003: NSL-bound genes display a specific nucleosome organization at their TSS.(A) The TSSs of constitutively active genes, either NSL-bound or –non-bound, were analyzed regarding their reported transcription initiation patterns [35]. NSL-bound TSSs mostly belong to genes with weak and broad transcription initiation peaks (40% and 11.4%) whereas NSL-non-bound TSSs mainly belong to genes with narrow transcription initiation peaks (19.3%). (B) Boxplots of the sum of overlapping nucleosome reads in the regions 200 bp upstream and 200 bp downstream of the TSSs of constitutively expressed NSL-bound genes (red), constitutively expressed NSL-non-bound genes (gray), and tissue-specific genes (white). Genes were stratified based on their gene expression quartile (see Materials and Methods) which demonstrates that the depletion of nucleosomes immediately upstream of the TSS that we observed for NSL-bound housekeeping genes (left side) is independent of expression levels (p-values for −200 bp region <2.2e-16; Wilcoxon test).

Mentions: In addition to expression-based definitions of housekeeping genes, we wanted to test further correlations of NSL binding with characteristics of constitutively expressed genes. Earlier studies have revealed two basic types of Drosophila promoters based on the pattern of the transcriptional initiation: broad and peaked [33]–[36]. While broad promoters preferably belong to housekeeping genes, peaked promoters are associated with tissue-specific expression. Based on data from [35], we found that NSL-bound TSSs are predominantly associated with dispersed transcription initiation patterns (Figure 3A).


The NSL complex regulates housekeeping genes in Drosophila.

Lam KC, Mühlpfordt F, Vaquerizas JM, Raja SJ, Holz H, Luscombe NM, Manke T, Akhtar A - PLoS Genet. (2012)

NSL-bound genes display a specific nucleosome organization at their TSS.(A) The TSSs of constitutively active genes, either NSL-bound or –non-bound, were analyzed regarding their reported transcription initiation patterns [35]. NSL-bound TSSs mostly belong to genes with weak and broad transcription initiation peaks (40% and 11.4%) whereas NSL-non-bound TSSs mainly belong to genes with narrow transcription initiation peaks (19.3%). (B) Boxplots of the sum of overlapping nucleosome reads in the regions 200 bp upstream and 200 bp downstream of the TSSs of constitutively expressed NSL-bound genes (red), constitutively expressed NSL-non-bound genes (gray), and tissue-specific genes (white). Genes were stratified based on their gene expression quartile (see Materials and Methods) which demonstrates that the depletion of nucleosomes immediately upstream of the TSS that we observed for NSL-bound housekeeping genes (left side) is independent of expression levels (p-values for −200 bp region <2.2e-16; Wilcoxon test).
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC3375229&req=5

pgen-1002736-g003: NSL-bound genes display a specific nucleosome organization at their TSS.(A) The TSSs of constitutively active genes, either NSL-bound or –non-bound, were analyzed regarding their reported transcription initiation patterns [35]. NSL-bound TSSs mostly belong to genes with weak and broad transcription initiation peaks (40% and 11.4%) whereas NSL-non-bound TSSs mainly belong to genes with narrow transcription initiation peaks (19.3%). (B) Boxplots of the sum of overlapping nucleosome reads in the regions 200 bp upstream and 200 bp downstream of the TSSs of constitutively expressed NSL-bound genes (red), constitutively expressed NSL-non-bound genes (gray), and tissue-specific genes (white). Genes were stratified based on their gene expression quartile (see Materials and Methods) which demonstrates that the depletion of nucleosomes immediately upstream of the TSS that we observed for NSL-bound housekeeping genes (left side) is independent of expression levels (p-values for −200 bp region <2.2e-16; Wilcoxon test).
Mentions: In addition to expression-based definitions of housekeeping genes, we wanted to test further correlations of NSL binding with characteristics of constitutively expressed genes. Earlier studies have revealed two basic types of Drosophila promoters based on the pattern of the transcriptional initiation: broad and peaked [33]–[36]. While broad promoters preferably belong to housekeeping genes, peaked promoters are associated with tissue-specific expression. Based on data from [35], we found that NSL-bound TSSs are predominantly associated with dispersed transcription initiation patterns (Figure 3A).

Bottom Line: The observed Pol II reduction coincides with compromised binding of TBP and TFIIB to target promoters, indicating that the NSL complex is required for optimal recruitment of the pre-initiation complex on target genes.Moreover, genes that undergo the most dramatic loss of Pol II upon NSL knockdowns tend to be enriched in DNA Replication-related Element (DRE).Taken together, our findings show that the MOF-containing NSL complex acts as a major regulator of housekeeping genes in flies by modulating initiation of Pol II transcription.

View Article: PubMed Central - PubMed

Affiliation: Max-Planck Institute of Immunobiology and Epigenetics, Freiburg im Breisgau, Germany.

ABSTRACT
MOF is the major histone H4 lysine 16-specific (H4K16) acetyltransferase in mammals and Drosophila. In flies, it is involved in the regulation of X-chromosomal and autosomal genes as part of the MSL and the NSL complexes, respectively. While the function of the MSL complex as a dosage compensation regulator is fairly well understood, the role of the NSL complex in gene regulation is still poorly characterized. Here we report a comprehensive ChIP-seq analysis of four NSL complex members (NSL1, NSL3, MBD-R2, and MCRS2) throughout the Drosophila melanogaster genome. Strikingly, the majority (85.5%) of NSL-bound genes are constitutively expressed across different cell types. We find that an increased abundance of the histone modifications H4K16ac, H3K4me2, H3K4me3, and H3K9ac in gene promoter regions is characteristic of NSL-targeted genes. Furthermore, we show that these genes have a well-defined nucleosome free region and broad transcription initiation patterns. Finally, by performing ChIP-seq analyses of RNA polymerase II (Pol II) in NSL1- and NSL3-depleted cells, we demonstrate that both NSL proteins are required for efficient recruitment of Pol II to NSL target gene promoters. The observed Pol II reduction coincides with compromised binding of TBP and TFIIB to target promoters, indicating that the NSL complex is required for optimal recruitment of the pre-initiation complex on target genes. Moreover, genes that undergo the most dramatic loss of Pol II upon NSL knockdowns tend to be enriched in DNA Replication-related Element (DRE). Taken together, our findings show that the MOF-containing NSL complex acts as a major regulator of housekeeping genes in flies by modulating initiation of Pol II transcription.

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