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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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SU(HW) distribution relative to LADs is sequence driven and linked to CP190 binding.(A) Profiles of sequence motifs across aligned LAD borders. X-axis depicts the position relative to the nearest LAD border; positive coordinates inside LADs and negative coordinates outside LADs. Colored lines show the median frequency within a running window of 10 kb for sequence motifs, grey lines for DamID identified peaks. (B) Profiles of CP190 peaks [28] across aligned LAD borders; all Cp190 peaks (1st panel), CP190 peaks without SU(HW) binding, defined as peaks with an average log2(SU(HW)binding ratio) <1.0 (2nd panel), CP190 peaks with SU(HW) binding, defined as CP190 peaks with an average log2(SU(HW)binding ratio) >1.5 (3rd panel).
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pone-0015013-g003: SU(HW) distribution relative to LADs is sequence driven and linked to CP190 binding.(A) Profiles of sequence motifs across aligned LAD borders. X-axis depicts the position relative to the nearest LAD border; positive coordinates inside LADs and negative coordinates outside LADs. Colored lines show the median frequency within a running window of 10 kb for sequence motifs, grey lines for DamID identified peaks. (B) Profiles of CP190 peaks [28] across aligned LAD borders; all Cp190 peaks (1st panel), CP190 peaks without SU(HW) binding, defined as peaks with an average log2(SU(HW)binding ratio) <1.0 (2nd panel), CP190 peaks with SU(HW) binding, defined as CP190 peaks with an average log2(SU(HW)binding ratio) >1.5 (3rd panel).

Mentions: The observed enrichment of SU(HW) and the paucity of the other four insulator proteins in LADs could be dictated by the genomic distribution of the corresponding DNA binding motifs, which is likely since the presence of a SU(HW) DNA binding motif is known to be highly predictive for SU(HW) binding [38]. Alternatively, the patterns could be driven by respectively cooperative or exclusive interactions with other chromatin components in LADs. To discriminate between these two mechanisms we compared the occurrence of protein binding peaks to the distribution of the corresponding sequence motifs for CTCF, GAF and SU(HW) (respectively grey and colored lines in Fig. 3a). This revealed that the distributions of these three insulator proteins and their cognate motifs are highly similar when aligned to LADs and LAD borders. The motifs of CTCF and GAF are depleted in LADs and not specifically enriched in border regions. In contrast, the motif of SU(HW) is enriched within LADs as well as in border regions. Importantly, the SU(HW) motif shows the same prominent enrichment inside LADs at ∼40 kb from LAD borders as was observed for SU(HW) binding. Thus, the enrichments of SU(HW) at LAD borders and at the +40 kb position are to a large extent “hard-coded” in the sequence of the Drosophila genome.


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)

SU(HW) distribution relative to LADs is sequence driven and linked to CP190 binding.(A) Profiles of sequence motifs across aligned LAD borders. X-axis depicts the position relative to the nearest LAD border; positive coordinates inside LADs and negative coordinates outside LADs. Colored lines show the median frequency within a running window of 10 kb for sequence motifs, grey lines for DamID identified peaks. (B) Profiles of CP190 peaks [28] across aligned LAD borders; all Cp190 peaks (1st panel), CP190 peaks without SU(HW) binding, defined as peaks with an average log2(SU(HW)binding ratio) <1.0 (2nd panel), CP190 peaks with SU(HW) binding, defined as CP190 peaks with an average log2(SU(HW)binding ratio) >1.5 (3rd panel).
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Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2991331&req=5

pone-0015013-g003: SU(HW) distribution relative to LADs is sequence driven and linked to CP190 binding.(A) Profiles of sequence motifs across aligned LAD borders. X-axis depicts the position relative to the nearest LAD border; positive coordinates inside LADs and negative coordinates outside LADs. Colored lines show the median frequency within a running window of 10 kb for sequence motifs, grey lines for DamID identified peaks. (B) Profiles of CP190 peaks [28] across aligned LAD borders; all Cp190 peaks (1st panel), CP190 peaks without SU(HW) binding, defined as peaks with an average log2(SU(HW)binding ratio) <1.0 (2nd panel), CP190 peaks with SU(HW) binding, defined as CP190 peaks with an average log2(SU(HW)binding ratio) >1.5 (3rd panel).
Mentions: The observed enrichment of SU(HW) and the paucity of the other four insulator proteins in LADs could be dictated by the genomic distribution of the corresponding DNA binding motifs, which is likely since the presence of a SU(HW) DNA binding motif is known to be highly predictive for SU(HW) binding [38]. Alternatively, the patterns could be driven by respectively cooperative or exclusive interactions with other chromatin components in LADs. To discriminate between these two mechanisms we compared the occurrence of protein binding peaks to the distribution of the corresponding sequence motifs for CTCF, GAF and SU(HW) (respectively grey and colored lines in Fig. 3a). This revealed that the distributions of these three insulator proteins and their cognate motifs are highly similar when aligned to LADs and LAD borders. The motifs of CTCF and GAF are depleted in LADs and not specifically enriched in border regions. In contrast, the motif of SU(HW) is enriched within LADs as well as in border regions. Importantly, the SU(HW) motif shows the same prominent enrichment inside LADs at ∼40 kb from LAD borders as was observed for SU(HW) binding. Thus, the enrichments of SU(HW) at LAD borders and at the +40 kb position are to a large extent “hard-coded” in the sequence of the Drosophila genome.

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