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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.

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HMGD1 and H1 are correlated with gene expression. (A) Scatter plots of normalized HMGD1 and (B) H1 versus RNA-seq gene expression. Each data point represents a single gene. The HMGD1 rate is the log2 ratio of HMGD1 midpoints to total nucleosome midpoints from the promoter region -100 to +500 bp. The H1 rate is calculated similarly but for the region -550 to +50 bp. (C) Pearson correlations of RNA-seq gene expression with HMGD1 (red), H1 (blue), total nucleosome (black) or the HMGD1/H1 ratio (green). The correlations are computed for non-overlapping genomic regions corresponding roughly to the locations of well-positioned nucleosomes and the nucleosome depleted region (NDR). Vertical line segments represent 95% confidence intervals for the correlations.
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Figure 4: HMGD1 and H1 are correlated with gene expression. (A) Scatter plots of normalized HMGD1 and (B) H1 versus RNA-seq gene expression. Each data point represents a single gene. The HMGD1 rate is the log2 ratio of HMGD1 midpoints to total nucleosome midpoints from the promoter region -100 to +500 bp. The H1 rate is calculated similarly but for the region -550 to +50 bp. (C) Pearson correlations of RNA-seq gene expression with HMGD1 (red), H1 (blue), total nucleosome (black) or the HMGD1/H1 ratio (green). The correlations are computed for non-overlapping genomic regions corresponding roughly to the locations of well-positioned nucleosomes and the nucleosome depleted region (NDR). Vertical line segments represent 95% confidence intervals for the correlations.

Mentions: To quantify the relationship between gene expression, HMGD1, and H1, we calculated the Pearson correlation between gene expression and ChIP-seq read depth across promoter regions (Figure 4). HMGD1 showed a strong positive correlation (R = 0.71) and H1 had a negative correlation (R = -0.47) with gene expression (Figure 4A & B). We next divided promoters into several non-overlapping regions corresponding to the approximate locations of well-positioned nucleosomes and the nucleosome-depleted region (NDR) (Additional file 1: Figure S2). For each region we then calculated the correlation across all promoters. HMGD1 has a moderately strong positive correlation with gene expression both upstream and downstream of the promoter, with a maximum correlation at the +1 nucleosome (R = 0.50; P < 10-15) (Figure 4C). H1 has a negative correlation with gene expression, which is strongest at the nucleosome-depleted region immediately upstream of the TSS (R = -0.55; P < 10-15) (Figure 4C). These data suggest that while chromatin binding of HMGD1 is associated with transcription activation, H1 may be involved in gene silencing or repression.


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)

HMGD1 and H1 are correlated with gene expression. (A) Scatter plots of normalized HMGD1 and (B) H1 versus RNA-seq gene expression. Each data point represents a single gene. The HMGD1 rate is the log2 ratio of HMGD1 midpoints to total nucleosome midpoints from the promoter region -100 to +500 bp. The H1 rate is calculated similarly but for the region -550 to +50 bp. (C) Pearson correlations of RNA-seq gene expression with HMGD1 (red), H1 (blue), total nucleosome (black) or the HMGD1/H1 ratio (green). The correlations are computed for non-overlapping genomic regions corresponding roughly to the locations of well-positioned nucleosomes and the nucleosome depleted region (NDR). Vertical line segments represent 95% confidence intervals for the correlations.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 4: HMGD1 and H1 are correlated with gene expression. (A) Scatter plots of normalized HMGD1 and (B) H1 versus RNA-seq gene expression. Each data point represents a single gene. The HMGD1 rate is the log2 ratio of HMGD1 midpoints to total nucleosome midpoints from the promoter region -100 to +500 bp. The H1 rate is calculated similarly but for the region -550 to +50 bp. (C) Pearson correlations of RNA-seq gene expression with HMGD1 (red), H1 (blue), total nucleosome (black) or the HMGD1/H1 ratio (green). The correlations are computed for non-overlapping genomic regions corresponding roughly to the locations of well-positioned nucleosomes and the nucleosome depleted region (NDR). Vertical line segments represent 95% confidence intervals for the correlations.
Mentions: To quantify the relationship between gene expression, HMGD1, and H1, we calculated the Pearson correlation between gene expression and ChIP-seq read depth across promoter regions (Figure 4). HMGD1 showed a strong positive correlation (R = 0.71) and H1 had a negative correlation (R = -0.47) with gene expression (Figure 4A & B). We next divided promoters into several non-overlapping regions corresponding to the approximate locations of well-positioned nucleosomes and the nucleosome-depleted region (NDR) (Additional file 1: Figure S2). For each region we then calculated the correlation across all promoters. HMGD1 has a moderately strong positive correlation with gene expression both upstream and downstream of the promoter, with a maximum correlation at the +1 nucleosome (R = 0.50; P < 10-15) (Figure 4C). H1 has a negative correlation with gene expression, which is strongest at the nucleosome-depleted region immediately upstream of the TSS (R = -0.55; P < 10-15) (Figure 4C). These data suggest that while chromatin binding of HMGD1 is associated with transcription activation, H1 may be involved in gene silencing or repression.

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