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The insulator protein SU(HW) fine-tunes nuclear lamina interactions of the Drosophila genome.

van Bemmel JG, Pagie L, Braunschweig U, Brugman W, Meuleman W, Kerkhoven RM, van Steensel B - PLoS ONE (2010)

Bottom Line: Specific interactions of the genome with the nuclear lamina (NL) are thought to assist chromosome folding inside the nucleus and to contribute to the regulation of gene expression.By knockdown and overexpression studies we demonstrate that SU(HW) weakens genome - NL interactions through a local antagonistic effect, but we did not obtain evidence that it is essential for border formation.Our results provide insights into the evolution of LAD organization and identify SU(HW) as a fine-tuner of genome - NL interactions.

View Article: PubMed Central - PubMed

Affiliation: Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, The Netherlands.

ABSTRACT
Specific interactions of the genome with the nuclear lamina (NL) are thought to assist chromosome folding inside the nucleus and to contribute to the regulation of gene expression. High-resolution mapping has recently identified hundreds of large, sharply defined lamina-associated domains (LADs) in the human genome, and suggested that the insulator protein CTCF may help to demarcate these domains. Here, we report the detailed structure of LADs in Drosophila cells, and investigate the putative roles of five insulator proteins in LAD organization. We found that the Drosophila genome is also organized in discrete LADs, which are about five times smaller than human LADs but contain on average a similar number of genes. Systematic comparison to new and published insulator binding maps shows that only SU(HW) binds preferentially at LAD borders and at specific positions inside LADs, while GAF, CTCF, BEAF-32 and DWG are mostly absent from these regions. By knockdown and overexpression studies we demonstrate that SU(HW) weakens genome - NL interactions through a local antagonistic effect, but we did not obtain evidence that it is essential for border formation. Our results provide insights into the evolution of LAD organization and identify SU(HW) as a fine-tuner of genome - NL interactions.

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Lamina associated domains in the Drosophila genome.(A) Genome – NL interaction maps in Drosophila Kc cells and human Lung Fibroblasts along a 4 Mb region at respectively chromosome 2L and chromosome 18. Human data are from [8]. Y-axes depict the log2 transformed Dam-LAM over Dam-only methylation ratio, smoothed by a running median of respectively 15 and 5 probes. Rectangles below each map represent calculated LAD positions for Drosophila (red) and human (blue). Grey rectangles at the bottom represent genes at the + and - strand. (B) Distribution of LAD sizes in Drosophila (red) and human cells (blue). Dashed lines mark the median LAD sizes. (C) Histogram of the number of genes per LAD. (D–F) Profiles across aligned LAD borders (824 borders, left and mirrored right borders combined). Running window median (red line) and a random subset of 2001 single genes (black dots in E and F). The region around each border from which data was taken ranges from the center of the inter-LAD region to the center of the LAD; this ensures that each data point is used only once. X-axis depicts the position relative to the nearest LAD border; positive coordinates inside, negative coordinates outside LADs. (D) Median gene coverage. (E) mRNA levels in A-values, (log2(Cy5)+log2(Cy3))/2 (F) Median RpII18 occupancy on entire genes as determined by DamID [data from30].
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pone-0015013-g001: Lamina associated domains in the Drosophila genome.(A) Genome – NL interaction maps in Drosophila Kc cells and human Lung Fibroblasts along a 4 Mb region at respectively chromosome 2L and chromosome 18. Human data are from [8]. Y-axes depict the log2 transformed Dam-LAM over Dam-only methylation ratio, smoothed by a running median of respectively 15 and 5 probes. Rectangles below each map represent calculated LAD positions for Drosophila (red) and human (blue). Grey rectangles at the bottom represent genes at the + and - strand. (B) Distribution of LAD sizes in Drosophila (red) and human cells (blue). Dashed lines mark the median LAD sizes. (C) Histogram of the number of genes per LAD. (D–F) Profiles across aligned LAD borders (824 borders, left and mirrored right borders combined). Running window median (red line) and a random subset of 2001 single genes (black dots in E and F). The region around each border from which data was taken ranges from the center of the inter-LAD region to the center of the LAD; this ensures that each data point is used only once. X-axis depicts the position relative to the nearest LAD border; positive coordinates inside, negative coordinates outside LADs. (D) Median gene coverage. (E) mRNA levels in A-values, (log2(Cy5)+log2(Cy3))/2 (F) Median RpII18 occupancy on entire genes as determined by DamID [data from30].

Mentions: We averaged the data of two independent DamID experiments, which highly correlated with each other (Pearson correlation of 0.77) and with the previously published low resolution data (Pearson correlation of 0.74). The resulting profile (Fig. 1a, Fig. S1) shows that the genome in Kc cells is associated with the NL through large continuous domains, alternating with regions of low association. A domain detection algorithm, previously developed for the analysis of human NL interaction data [8] identified a total of 412 Drosophila Lamina Associated Domains (LADs) (Table S1). These LADs vary in size between 7 and 700 kb, with a median size of ∼90 kb (red line in Fig. 1b). In total they cover 40% of the genome (data not shown).


The insulator protein SU(HW) fine-tunes nuclear lamina interactions of the Drosophila genome.

van Bemmel JG, Pagie L, Braunschweig U, Brugman W, Meuleman W, Kerkhoven RM, van Steensel B - PLoS ONE (2010)

Lamina associated domains in the Drosophila genome.(A) Genome – NL interaction maps in Drosophila Kc cells and human Lung Fibroblasts along a 4 Mb region at respectively chromosome 2L and chromosome 18. Human data are from [8]. Y-axes depict the log2 transformed Dam-LAM over Dam-only methylation ratio, smoothed by a running median of respectively 15 and 5 probes. Rectangles below each map represent calculated LAD positions for Drosophila (red) and human (blue). Grey rectangles at the bottom represent genes at the + and - strand. (B) Distribution of LAD sizes in Drosophila (red) and human cells (blue). Dashed lines mark the median LAD sizes. (C) Histogram of the number of genes per LAD. (D–F) Profiles across aligned LAD borders (824 borders, left and mirrored right borders combined). Running window median (red line) and a random subset of 2001 single genes (black dots in E and F). The region around each border from which data was taken ranges from the center of the inter-LAD region to the center of the LAD; this ensures that each data point is used only once. X-axis depicts the position relative to the nearest LAD border; positive coordinates inside, negative coordinates outside LADs. (D) Median gene coverage. (E) mRNA levels in A-values, (log2(Cy5)+log2(Cy3))/2 (F) Median RpII18 occupancy on entire genes as determined by DamID [data from30].
© Copyright Policy
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC2991331&req=5

pone-0015013-g001: Lamina associated domains in the Drosophila genome.(A) Genome – NL interaction maps in Drosophila Kc cells and human Lung Fibroblasts along a 4 Mb region at respectively chromosome 2L and chromosome 18. Human data are from [8]. Y-axes depict the log2 transformed Dam-LAM over Dam-only methylation ratio, smoothed by a running median of respectively 15 and 5 probes. Rectangles below each map represent calculated LAD positions for Drosophila (red) and human (blue). Grey rectangles at the bottom represent genes at the + and - strand. (B) Distribution of LAD sizes in Drosophila (red) and human cells (blue). Dashed lines mark the median LAD sizes. (C) Histogram of the number of genes per LAD. (D–F) Profiles across aligned LAD borders (824 borders, left and mirrored right borders combined). Running window median (red line) and a random subset of 2001 single genes (black dots in E and F). The region around each border from which data was taken ranges from the center of the inter-LAD region to the center of the LAD; this ensures that each data point is used only once. X-axis depicts the position relative to the nearest LAD border; positive coordinates inside, negative coordinates outside LADs. (D) Median gene coverage. (E) mRNA levels in A-values, (log2(Cy5)+log2(Cy3))/2 (F) Median RpII18 occupancy on entire genes as determined by DamID [data from30].
Mentions: We averaged the data of two independent DamID experiments, which highly correlated with each other (Pearson correlation of 0.77) and with the previously published low resolution data (Pearson correlation of 0.74). The resulting profile (Fig. 1a, Fig. S1) shows that the genome in Kc cells is associated with the NL through large continuous domains, alternating with regions of low association. A domain detection algorithm, previously developed for the analysis of human NL interaction data [8] identified a total of 412 Drosophila Lamina Associated Domains (LADs) (Table S1). These LADs vary in size between 7 and 700 kb, with a median size of ∼90 kb (red line in Fig. 1b). In total they cover 40% of the genome (data not shown).

Bottom Line: Specific interactions of the genome with the nuclear lamina (NL) are thought to assist chromosome folding inside the nucleus and to contribute to the regulation of gene expression.By knockdown and overexpression studies we demonstrate that SU(HW) weakens genome - NL interactions through a local antagonistic effect, but we did not obtain evidence that it is essential for border formation.Our results provide insights into the evolution of LAD organization and identify SU(HW) as a fine-tuner of genome - NL interactions.

View Article: PubMed Central - PubMed

Affiliation: Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, The Netherlands.

ABSTRACT
Specific interactions of the genome with the nuclear lamina (NL) are thought to assist chromosome folding inside the nucleus and to contribute to the regulation of gene expression. High-resolution mapping has recently identified hundreds of large, sharply defined lamina-associated domains (LADs) in the human genome, and suggested that the insulator protein CTCF may help to demarcate these domains. Here, we report the detailed structure of LADs in Drosophila cells, and investigate the putative roles of five insulator proteins in LAD organization. We found that the Drosophila genome is also organized in discrete LADs, which are about five times smaller than human LADs but contain on average a similar number of genes. Systematic comparison to new and published insulator binding maps shows that only SU(HW) binds preferentially at LAD borders and at specific positions inside LADs, while GAF, CTCF, BEAF-32 and DWG are mostly absent from these regions. By knockdown and overexpression studies we demonstrate that SU(HW) weakens genome - NL interactions through a local antagonistic effect, but we did not obtain evidence that it is essential for border formation. Our results provide insights into the evolution of LAD organization and identify SU(HW) as a fine-tuner of genome - NL interactions.

Show MeSH
Related in: MedlinePlus