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Distinct isoforms of the Drosophila Brd4 homologue are present at enhancers, promoters and insulator sites.

Kellner WA, Van Bortle K, Li L, Ramos E, Takenaka N, Corces VG - Nucleic Acids Res. (2013)

Bottom Line: Correlations between the distribution of Fs(1)h-S and various forms of acetylated histones H3 and H4 suggest a preference for binding to H3K9acS10ph.Surprisingly, Fs(1)h-L is located at sites in the genome where multiple insulator proteins are also present.The results suggest that Fs(1)h-S may be responsible for the classical role assigned to this protein, whereas Fs(1)h-L may have a new and unexpected role in chromatin architecture by working in conjunction with insulator proteins to mediate intra- or inter-chromosome interactions.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology, Emory University, Atlanta, GA 30322, USA and Department of Biostatistics and Bioinformatics, Emory University, Atlanta, GA 30322, USA.

ABSTRACT
Brd4 is a double bromodomain protein that has been shown to interact with acetylated histones to regulate transcription by recruiting Positive Transcription Elongation Factor b to the promoter region. Brd4 is also involved in gene bookmarking during mitosis and is a therapeutic target for the treatment of acute myeloid leukemia. The Drosophila melanogaster Brd4 homologue is called Fs(1)h and, like its vertebrate counterpart, encodes different isoforms. We have used ChIP-seq to examine the genome-wide distribution of Fs(1)h isoforms. We are able to distinguish the Fs(1)h-L and Fs(1)h-S binding profiles and discriminate between the genomic locations of the two isoforms. Fs(1)h-S is present at enhancers and promoters and its amount parallels transcription levels. Correlations between the distribution of Fs(1)h-S and various forms of acetylated histones H3 and H4 suggest a preference for binding to H3K9acS10ph. Surprisingly, Fs(1)h-L is located at sites in the genome where multiple insulator proteins are also present. The results suggest that Fs(1)h-S may be responsible for the classical role assigned to this protein, whereas Fs(1)h-L may have a new and unexpected role in chromatin architecture by working in conjunction with insulator proteins to mediate intra- or inter-chromosome interactions.

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Fs(1)h is found at enhancers and promoters. ChIP-seq data for Fs(1)h-L&S, H3K4me3 and H3K4me1±1 kb from each peak summit was K-means clustered using Cluster 3.0 and viewed in Java Treeview. Promoter regions contain H3K4me3 but lack H3K4me1, whereas enhancer regions are marked by the presence of H3K4me1 and absence of H3K4me3. Fs(1)h-L&S is present at enhancers and promoters. In addition, a subset of sites indicated by question marks at the bottom of the heatmap is present in regions of the genome of unknown function.
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gkt722-F1: Fs(1)h is found at enhancers and promoters. ChIP-seq data for Fs(1)h-L&S, H3K4me3 and H3K4me1±1 kb from each peak summit was K-means clustered using Cluster 3.0 and viewed in Java Treeview. Promoter regions contain H3K4me3 but lack H3K4me1, whereas enhancer regions are marked by the presence of H3K4me1 and absence of H3K4me3. Fs(1)h-L&S is present at enhancers and promoters. In addition, a subset of sites indicated by question marks at the bottom of the heatmap is present in regions of the genome of unknown function.

Mentions: Fs(1)h is found at promoters, enhancers and other sites of unknown function. Brd4 has been found to play a critical role in transcription by releasing RNAPII from the promoter proximal pause. Current results suggest that this function is carried out by recognition of acetylated lysines in histones H3 and H4 tails via the tandem double bromodomains. To analyze the role of the Drosophila Brd4 homologue Fs(1)h in nuclear biology, we determined its genome-wide distribution by ChIP-seq using an antibody that recognizes both protein isoforms, Fs(1)h-S and Fs(1)h-L (3); we will use the term Fs(1)h-L&S to indicate situations in which the two isoforms cannot be distinguished experimentally. We predicted we would find enrichment of Fs(1)h-L&S at active enhancers and promoters in light of previous reports describing the presence of Brd4 at the FOSL1 enhancer and promoter in mammalian cells (12). To test this possibility, we compared the distribution of Fs(1)h-L&S with that of H3K4me3 and H3K4me1 obtained by ChIP-seq (16). Peaks of Fs(1)h-L&S identified by MACS in two biological replicates (n = 8423) were used as anchors to generate heatmaps of H3K4me3, which is correlated with active promoters, and H3K4me1, which is correlated with enhancers (16). Although we cannot be sure that all H3K4me1 enriched regions act as enhancers, this histone modification best defines this class of regulatory elements. The heatmaps were then K-means clustered using Cluster 3.0, and Fs(1)h-L&S was found at clusters enriched with H3K4me1 and H3K4me3 (Figure 1). In addition, Fs(1)h-L&S occurs in two clusters of unknown identity that are not correlated with enrichment of either H3K4me1 or H3K4me3. The cluster with the strongest Fs(1)h-L&S signal falls into this category, suggesting that one or both Fs(1)h isoforms might have a role different from that previously studied in transcription activation (Figure 1).Figure 1.


Distinct isoforms of the Drosophila Brd4 homologue are present at enhancers, promoters and insulator sites.

Kellner WA, Van Bortle K, Li L, Ramos E, Takenaka N, Corces VG - Nucleic Acids Res. (2013)

Fs(1)h is found at enhancers and promoters. ChIP-seq data for Fs(1)h-L&S, H3K4me3 and H3K4me1±1 kb from each peak summit was K-means clustered using Cluster 3.0 and viewed in Java Treeview. Promoter regions contain H3K4me3 but lack H3K4me1, whereas enhancer regions are marked by the presence of H3K4me1 and absence of H3K4me3. Fs(1)h-L&S is present at enhancers and promoters. In addition, a subset of sites indicated by question marks at the bottom of the heatmap is present in regions of the genome of unknown function.
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Related In: Results  -  Collection

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gkt722-F1: Fs(1)h is found at enhancers and promoters. ChIP-seq data for Fs(1)h-L&S, H3K4me3 and H3K4me1±1 kb from each peak summit was K-means clustered using Cluster 3.0 and viewed in Java Treeview. Promoter regions contain H3K4me3 but lack H3K4me1, whereas enhancer regions are marked by the presence of H3K4me1 and absence of H3K4me3. Fs(1)h-L&S is present at enhancers and promoters. In addition, a subset of sites indicated by question marks at the bottom of the heatmap is present in regions of the genome of unknown function.
Mentions: Fs(1)h is found at promoters, enhancers and other sites of unknown function. Brd4 has been found to play a critical role in transcription by releasing RNAPII from the promoter proximal pause. Current results suggest that this function is carried out by recognition of acetylated lysines in histones H3 and H4 tails via the tandem double bromodomains. To analyze the role of the Drosophila Brd4 homologue Fs(1)h in nuclear biology, we determined its genome-wide distribution by ChIP-seq using an antibody that recognizes both protein isoforms, Fs(1)h-S and Fs(1)h-L (3); we will use the term Fs(1)h-L&S to indicate situations in which the two isoforms cannot be distinguished experimentally. We predicted we would find enrichment of Fs(1)h-L&S at active enhancers and promoters in light of previous reports describing the presence of Brd4 at the FOSL1 enhancer and promoter in mammalian cells (12). To test this possibility, we compared the distribution of Fs(1)h-L&S with that of H3K4me3 and H3K4me1 obtained by ChIP-seq (16). Peaks of Fs(1)h-L&S identified by MACS in two biological replicates (n = 8423) were used as anchors to generate heatmaps of H3K4me3, which is correlated with active promoters, and H3K4me1, which is correlated with enhancers (16). Although we cannot be sure that all H3K4me1 enriched regions act as enhancers, this histone modification best defines this class of regulatory elements. The heatmaps were then K-means clustered using Cluster 3.0, and Fs(1)h-L&S was found at clusters enriched with H3K4me1 and H3K4me3 (Figure 1). In addition, Fs(1)h-L&S occurs in two clusters of unknown identity that are not correlated with enrichment of either H3K4me1 or H3K4me3. The cluster with the strongest Fs(1)h-L&S signal falls into this category, suggesting that one or both Fs(1)h isoforms might have a role different from that previously studied in transcription activation (Figure 1).Figure 1.

Bottom Line: Correlations between the distribution of Fs(1)h-S and various forms of acetylated histones H3 and H4 suggest a preference for binding to H3K9acS10ph.Surprisingly, Fs(1)h-L is located at sites in the genome where multiple insulator proteins are also present.The results suggest that Fs(1)h-S may be responsible for the classical role assigned to this protein, whereas Fs(1)h-L may have a new and unexpected role in chromatin architecture by working in conjunction with insulator proteins to mediate intra- or inter-chromosome interactions.

View Article: PubMed Central - PubMed

Affiliation: Department of Biology, Emory University, Atlanta, GA 30322, USA and Department of Biostatistics and Bioinformatics, Emory University, Atlanta, GA 30322, USA.

ABSTRACT
Brd4 is a double bromodomain protein that has been shown to interact with acetylated histones to regulate transcription by recruiting Positive Transcription Elongation Factor b to the promoter region. Brd4 is also involved in gene bookmarking during mitosis and is a therapeutic target for the treatment of acute myeloid leukemia. The Drosophila melanogaster Brd4 homologue is called Fs(1)h and, like its vertebrate counterpart, encodes different isoforms. We have used ChIP-seq to examine the genome-wide distribution of Fs(1)h isoforms. We are able to distinguish the Fs(1)h-L and Fs(1)h-S binding profiles and discriminate between the genomic locations of the two isoforms. Fs(1)h-S is present at enhancers and promoters and its amount parallels transcription levels. Correlations between the distribution of Fs(1)h-S and various forms of acetylated histones H3 and H4 suggest a preference for binding to H3K9acS10ph. Surprisingly, Fs(1)h-L is located at sites in the genome where multiple insulator proteins are also present. The results suggest that Fs(1)h-S may be responsible for the classical role assigned to this protein, whereas Fs(1)h-L may have a new and unexpected role in chromatin architecture by working in conjunction with insulator proteins to mediate intra- or inter-chromosome interactions.

Show MeSH
Related in: MedlinePlus