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The chromatin architectural proteins HMGD1 and H1 bind reciprocally and have opposite effects on chromatin structure and gene regulation.

Nalabothula N, McVicker G, Maiorano J, Martin R, Pritchard JK, Fondufe-Mittendorf YN - BMC Genomics (2014)

Bottom Line: In contrast, H1 is primarily associated with heterochromatic regions marked with repressive histone marks.We find that the ratio of HMGD1 to H1 binding is a better predictor of gene activity than either protein by itself, which suggests that reciprocal binding between these proteins is important for gene regulation.This study provides a framework to further study the interplay between chromatin architectural proteins and epigenetics in gene regulation.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY 40536, USA. y.fondufe-mittendorf@uky.edu.

ABSTRACT

Background: Chromatin architectural proteins interact with nucleosomes to modulate chromatin accessibility and higher-order chromatin structure. While these proteins are almost certainly important for gene regulation they have been studied far less than the core histone proteins.

Results: Here we describe the genomic distributions and functional roles of two chromatin architectural proteins: histone H1 and the high mobility group protein HMGD1 in Drosophila S2 cells. Using ChIP-seq, biochemical and gene specific approaches, we find that HMGD1 binds to highly accessible regulatory chromatin and active promoters. In contrast, H1 is primarily associated with heterochromatic regions marked with repressive histone marks. We find that the ratio of HMGD1 to H1 binding is a better predictor of gene activity than either protein by itself, which suggests that reciprocal binding between these proteins is important for gene regulation. Using knockdown experiments, we show that HMGD1 and H1 affect the occupancy of the other protein, change nucleosome repeat length and modulate gene expression.

Conclusion: Collectively, our data suggest that dynamic and mutually exclusive binding of H1 and HMGD1 to nucleosomes and their linker sequences may control the fluid chromatin structure that is required for transcriptional regulation. This study provides a framework to further study the interplay between chromatin architectural proteins and epigenetics in gene regulation.

Show MeSH
Density of HMGD1 and H1 across different chromosomes and genomic regions in S2 cells. (A) Density of midpoints from mapped HMGD1 and H1 ChIP-seq reads on each chromosome. (B) Density of HMGD1 and H1 ChIP-seq reads in different genomic regions: promoters (defined as 1 kb upstream and downstream of TSSs), exons, introns, and intergenic regions in the D. melanogaster genome. “Upstream” and “Downstream” regions are defined as 1 kb upstream and 1 kb downstream of the transcription start site, respectively.
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Figure 2: Density of HMGD1 and H1 across different chromosomes and genomic regions in S2 cells. (A) Density of midpoints from mapped HMGD1 and H1 ChIP-seq reads on each chromosome. (B) Density of HMGD1 and H1 ChIP-seq reads in different genomic regions: promoters (defined as 1 kb upstream and downstream of TSSs), exons, introns, and intergenic regions in the D. melanogaster genome. “Upstream” and “Downstream” regions are defined as 1 kb upstream and 1 kb downstream of the transcription start site, respectively.

Mentions: We examined the broad distribution of H1– and HMGD1-bound nucleosomes across chromosomes. After normalizing the total number of mapped reads in the H1 and HMGD1 datasets, we found that HMGD1-bound nucleosomes are consistently depleted on the heterochromatic chromosome arms compared to both H1 and total nucleosomes (Figure 2A and Additional file 1: Table S1). Interestingly, HMGD1 is highly abundant on the X chromosome compared to total nucleosomes. Potentially this could be related to dosage compensation in male flies (S2 cells are biologically male), which results in a doubling of gene expression on the X-chromosome (Meller and Kuroda 2002). These results are consistent with those from the chromatin fractionation experiments and indicate that HMGD1 is enriched in the euchromatic fraction of the genome.


The chromatin architectural proteins HMGD1 and H1 bind reciprocally and have opposite effects on chromatin structure and gene regulation.

Nalabothula N, McVicker G, Maiorano J, Martin R, Pritchard JK, Fondufe-Mittendorf YN - BMC Genomics (2014)

Density of HMGD1 and H1 across different chromosomes and genomic regions in S2 cells. (A) Density of midpoints from mapped HMGD1 and H1 ChIP-seq reads on each chromosome. (B) Density of HMGD1 and H1 ChIP-seq reads in different genomic regions: promoters (defined as 1 kb upstream and downstream of TSSs), exons, introns, and intergenic regions in the D. melanogaster genome. “Upstream” and “Downstream” regions are defined as 1 kb upstream and 1 kb downstream of the transcription start site, respectively.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC3928079&req=5

Figure 2: Density of HMGD1 and H1 across different chromosomes and genomic regions in S2 cells. (A) Density of midpoints from mapped HMGD1 and H1 ChIP-seq reads on each chromosome. (B) Density of HMGD1 and H1 ChIP-seq reads in different genomic regions: promoters (defined as 1 kb upstream and downstream of TSSs), exons, introns, and intergenic regions in the D. melanogaster genome. “Upstream” and “Downstream” regions are defined as 1 kb upstream and 1 kb downstream of the transcription start site, respectively.
Mentions: We examined the broad distribution of H1– and HMGD1-bound nucleosomes across chromosomes. After normalizing the total number of mapped reads in the H1 and HMGD1 datasets, we found that HMGD1-bound nucleosomes are consistently depleted on the heterochromatic chromosome arms compared to both H1 and total nucleosomes (Figure 2A and Additional file 1: Table S1). Interestingly, HMGD1 is highly abundant on the X chromosome compared to total nucleosomes. Potentially this could be related to dosage compensation in male flies (S2 cells are biologically male), which results in a doubling of gene expression on the X-chromosome (Meller and Kuroda 2002). These results are consistent with those from the chromatin fractionation experiments and indicate that HMGD1 is enriched in the euchromatic fraction of the genome.

Bottom Line: In contrast, H1 is primarily associated with heterochromatic regions marked with repressive histone marks.We find that the ratio of HMGD1 to H1 binding is a better predictor of gene activity than either protein by itself, which suggests that reciprocal binding between these proteins is important for gene regulation.This study provides a framework to further study the interplay between chromatin architectural proteins and epigenetics in gene regulation.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, KY 40536, USA. y.fondufe-mittendorf@uky.edu.

ABSTRACT

Background: Chromatin architectural proteins interact with nucleosomes to modulate chromatin accessibility and higher-order chromatin structure. While these proteins are almost certainly important for gene regulation they have been studied far less than the core histone proteins.

Results: Here we describe the genomic distributions and functional roles of two chromatin architectural proteins: histone H1 and the high mobility group protein HMGD1 in Drosophila S2 cells. Using ChIP-seq, biochemical and gene specific approaches, we find that HMGD1 binds to highly accessible regulatory chromatin and active promoters. In contrast, H1 is primarily associated with heterochromatic regions marked with repressive histone marks. We find that the ratio of HMGD1 to H1 binding is a better predictor of gene activity than either protein by itself, which suggests that reciprocal binding between these proteins is important for gene regulation. Using knockdown experiments, we show that HMGD1 and H1 affect the occupancy of the other protein, change nucleosome repeat length and modulate gene expression.

Conclusion: Collectively, our data suggest that dynamic and mutually exclusive binding of H1 and HMGD1 to nucleosomes and their linker sequences may control the fluid chromatin structure that is required for transcriptional regulation. This study provides a framework to further study the interplay between chromatin architectural proteins and epigenetics in gene regulation.

Show MeSH