Limits...
Cohesin-mediated interactions organize chromosomal domain architecture.

Sofueva S, Yaffe E, Chan WC, Georgopoulou D, Vietri Rudan M, Mira-Bontenbal H, Pollard SM, Schroth GP, Tanay A, Hadjur S - EMBO J. (2013)

Bottom Line: Post-mitotic nuclei deficient for functional cohesin exhibit global architectural changes associated with loss of cohesin/CTCF contacts and relaxation of topological domains.Transcriptional analysis shows that this cohesin-dependent perturbation of domain organization leads to widespread gene deregulation of both cohesin-bound and non-bound genes.Our data thereby support a role for cohesin in the global organization of domain structure and suggest that domains function to stabilize the transcriptional programmes within them.

View Article: PubMed Central - PubMed

Affiliation: Research Department of Cancer Biology, Cancer Institute, University College London, London, UK.

ABSTRACT
To ensure proper gene regulation within constrained nuclear space, chromosomes facilitate access to transcribed regions, while compactly packaging all other information. Recent studies revealed that chromosomes are organized into megabase-scale domains that demarcate active and inactive genetic elements, suggesting that compartmentalization is important for genome function. Here, we show that very specific long-range interactions are anchored by cohesin/CTCF sites, but not cohesin-only or CTCF-only sites, to form a hierarchy of chromosomal loops. These loops demarcate topological domains and form intricate internal structures within them. Post-mitotic nuclei deficient for functional cohesin exhibit global architectural changes associated with loss of cohesin/CTCF contacts and relaxation of topological domains. Transcriptional analysis shows that this cohesin-dependent perturbation of domain organization leads to widespread gene deregulation of both cohesin-bound and non-bound genes. Our data thereby support a role for cohesin in the global organization of domain structure and suggest that domains function to stabilize the transcriptional programmes within them.

Show MeSH
Large-scale transcriptional deregulation in cohesin-deficient cells. (A) Scatter plot comparison between the transcription level of genes in control cells (x axis) and cohesin-deficient cells (y axis). Genes were classified into 770 upregulated genes (z-score>2, red), 992 downregulated genes (z-score<2, blue) and minimal-change genes (grey). (B) Distribution of 1762 deregulated genes according to cohesin/CTCF occupancy at the TSS (<1 Kb), near the TSS (<10 Kb) and away from TSS (>10 Kb). (C) Enrichment of the number of deregulated genes in the groups defined in (B), over a background composed of all genes. Deregulated genes with cohesin/CTCF at the TSS are enriched by 44%. (D) Pearson correlation of the transcriptional response to cohesin knockout of gene pairs, which are 100–200 Kb apart and have no separating cohesin/CTCF site (red). The correlation for pairs of genes which are separated by at least one site is shown as a control (grey). (E) 4C-Seq viewpoints positioned (from left to right) at a cohesin/CTCF site 15 Kb upstream of the Deptor TSS, 830 bp from the Deptor TSS or 1.4 Kb upstream of the Col14a1 TSS. Shown are the 4C-Seq profiles during a time course of Rad21 deletion for each viewpoint, which reveal a progressive loss of cohesin–cohesin contacts with decreasing cohesin protein levels. Shown is the % drop in Rad21 protein levels at each time point based on a quantitative western blot analysis. (F) 4C-Seq viewpoints positioned 580 bp from the TSS of the downregulated Olfml3 gene (right bait) as well as at a Rad21/CTCF binding site 300 Kb away. These sites interact according to the Hi-C data and this interaction is specifically lost in Rad21-deficient cells. (G) 4C-Seq viewpoints positioned 3.1 Kb from the TSS of the upregulated Igfbp5 gene (right bait) and a cohesin/CTCF site 10 Kb away from the TSS. The latter preferentially interacts with the cohesin/CTCF site at the other edge of this large domain. This interaction is lost in the mutant. The ChIP-Seq tracks for Rad21, CTCF and TSS locations and change in expression are also shown.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4489921&req=5

fig04: Large-scale transcriptional deregulation in cohesin-deficient cells. (A) Scatter plot comparison between the transcription level of genes in control cells (x axis) and cohesin-deficient cells (y axis). Genes were classified into 770 upregulated genes (z-score>2, red), 992 downregulated genes (z-score<2, blue) and minimal-change genes (grey). (B) Distribution of 1762 deregulated genes according to cohesin/CTCF occupancy at the TSS (<1 Kb), near the TSS (<10 Kb) and away from TSS (>10 Kb). (C) Enrichment of the number of deregulated genes in the groups defined in (B), over a background composed of all genes. Deregulated genes with cohesin/CTCF at the TSS are enriched by 44%. (D) Pearson correlation of the transcriptional response to cohesin knockout of gene pairs, which are 100–200 Kb apart and have no separating cohesin/CTCF site (red). The correlation for pairs of genes which are separated by at least one site is shown as a control (grey). (E) 4C-Seq viewpoints positioned (from left to right) at a cohesin/CTCF site 15 Kb upstream of the Deptor TSS, 830 bp from the Deptor TSS or 1.4 Kb upstream of the Col14a1 TSS. Shown are the 4C-Seq profiles during a time course of Rad21 deletion for each viewpoint, which reveal a progressive loss of cohesin–cohesin contacts with decreasing cohesin protein levels. Shown is the % drop in Rad21 protein levels at each time point based on a quantitative western blot analysis. (F) 4C-Seq viewpoints positioned 580 bp from the TSS of the downregulated Olfml3 gene (right bait) as well as at a Rad21/CTCF binding site 300 Kb away. These sites interact according to the Hi-C data and this interaction is specifically lost in Rad21-deficient cells. (G) 4C-Seq viewpoints positioned 3.1 Kb from the TSS of the upregulated Igfbp5 gene (right bait) and a cohesin/CTCF site 10 Kb away from the TSS. The latter preferentially interacts with the cohesin/CTCF site at the other edge of this large domain. This interaction is lost in the mutant. The ChIP-Seq tracks for Rad21, CTCF and TSS locations and change in expression are also shown.

Mentions: We used RNA-seq to determine whether the global domain perturbation we observe in cohesin-deficient ASTs has an effect on the transcriptional status of these cells. Genome-wide analysis (Figure 4A) showed remarkably widespread differences in expression between Rad21Lox/Lox and Rad21Δ/Δ ASTs with extensive upregulation and downregulation of hundreds of genes. Such extensive transcriptional changes can be indicative of an indirect activation of a general cellular programme (e.g., stress response and differentiation); however, a comprehensive analysis of the genes deregulated as a result of Rad21 deficiency did not reveal a significant overlap with known transcriptional modules nor an enrichment for particular functional categories (Supplementary Table S1), suggesting that ASTs respond to cohesin deficiency in a way that is unlikely to be controlled by common secondary signalling and transcriptional regulators.


Cohesin-mediated interactions organize chromosomal domain architecture.

Sofueva S, Yaffe E, Chan WC, Georgopoulou D, Vietri Rudan M, Mira-Bontenbal H, Pollard SM, Schroth GP, Tanay A, Hadjur S - EMBO J. (2013)

Large-scale transcriptional deregulation in cohesin-deficient cells. (A) Scatter plot comparison between the transcription level of genes in control cells (x axis) and cohesin-deficient cells (y axis). Genes were classified into 770 upregulated genes (z-score>2, red), 992 downregulated genes (z-score<2, blue) and minimal-change genes (grey). (B) Distribution of 1762 deregulated genes according to cohesin/CTCF occupancy at the TSS (<1 Kb), near the TSS (<10 Kb) and away from TSS (>10 Kb). (C) Enrichment of the number of deregulated genes in the groups defined in (B), over a background composed of all genes. Deregulated genes with cohesin/CTCF at the TSS are enriched by 44%. (D) Pearson correlation of the transcriptional response to cohesin knockout of gene pairs, which are 100–200 Kb apart and have no separating cohesin/CTCF site (red). The correlation for pairs of genes which are separated by at least one site is shown as a control (grey). (E) 4C-Seq viewpoints positioned (from left to right) at a cohesin/CTCF site 15 Kb upstream of the Deptor TSS, 830 bp from the Deptor TSS or 1.4 Kb upstream of the Col14a1 TSS. Shown are the 4C-Seq profiles during a time course of Rad21 deletion for each viewpoint, which reveal a progressive loss of cohesin–cohesin contacts with decreasing cohesin protein levels. Shown is the % drop in Rad21 protein levels at each time point based on a quantitative western blot analysis. (F) 4C-Seq viewpoints positioned 580 bp from the TSS of the downregulated Olfml3 gene (right bait) as well as at a Rad21/CTCF binding site 300 Kb away. These sites interact according to the Hi-C data and this interaction is specifically lost in Rad21-deficient cells. (G) 4C-Seq viewpoints positioned 3.1 Kb from the TSS of the upregulated Igfbp5 gene (right bait) and a cohesin/CTCF site 10 Kb away from the TSS. The latter preferentially interacts with the cohesin/CTCF site at the other edge of this large domain. This interaction is lost in the mutant. The ChIP-Seq tracks for Rad21, CTCF and TSS locations and change in expression are also shown.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4489921&req=5

fig04: Large-scale transcriptional deregulation in cohesin-deficient cells. (A) Scatter plot comparison between the transcription level of genes in control cells (x axis) and cohesin-deficient cells (y axis). Genes were classified into 770 upregulated genes (z-score>2, red), 992 downregulated genes (z-score<2, blue) and minimal-change genes (grey). (B) Distribution of 1762 deregulated genes according to cohesin/CTCF occupancy at the TSS (<1 Kb), near the TSS (<10 Kb) and away from TSS (>10 Kb). (C) Enrichment of the number of deregulated genes in the groups defined in (B), over a background composed of all genes. Deregulated genes with cohesin/CTCF at the TSS are enriched by 44%. (D) Pearson correlation of the transcriptional response to cohesin knockout of gene pairs, which are 100–200 Kb apart and have no separating cohesin/CTCF site (red). The correlation for pairs of genes which are separated by at least one site is shown as a control (grey). (E) 4C-Seq viewpoints positioned (from left to right) at a cohesin/CTCF site 15 Kb upstream of the Deptor TSS, 830 bp from the Deptor TSS or 1.4 Kb upstream of the Col14a1 TSS. Shown are the 4C-Seq profiles during a time course of Rad21 deletion for each viewpoint, which reveal a progressive loss of cohesin–cohesin contacts with decreasing cohesin protein levels. Shown is the % drop in Rad21 protein levels at each time point based on a quantitative western blot analysis. (F) 4C-Seq viewpoints positioned 580 bp from the TSS of the downregulated Olfml3 gene (right bait) as well as at a Rad21/CTCF binding site 300 Kb away. These sites interact according to the Hi-C data and this interaction is specifically lost in Rad21-deficient cells. (G) 4C-Seq viewpoints positioned 3.1 Kb from the TSS of the upregulated Igfbp5 gene (right bait) and a cohesin/CTCF site 10 Kb away from the TSS. The latter preferentially interacts with the cohesin/CTCF site at the other edge of this large domain. This interaction is lost in the mutant. The ChIP-Seq tracks for Rad21, CTCF and TSS locations and change in expression are also shown.
Mentions: We used RNA-seq to determine whether the global domain perturbation we observe in cohesin-deficient ASTs has an effect on the transcriptional status of these cells. Genome-wide analysis (Figure 4A) showed remarkably widespread differences in expression between Rad21Lox/Lox and Rad21Δ/Δ ASTs with extensive upregulation and downregulation of hundreds of genes. Such extensive transcriptional changes can be indicative of an indirect activation of a general cellular programme (e.g., stress response and differentiation); however, a comprehensive analysis of the genes deregulated as a result of Rad21 deficiency did not reveal a significant overlap with known transcriptional modules nor an enrichment for particular functional categories (Supplementary Table S1), suggesting that ASTs respond to cohesin deficiency in a way that is unlikely to be controlled by common secondary signalling and transcriptional regulators.

Bottom Line: Post-mitotic nuclei deficient for functional cohesin exhibit global architectural changes associated with loss of cohesin/CTCF contacts and relaxation of topological domains.Transcriptional analysis shows that this cohesin-dependent perturbation of domain organization leads to widespread gene deregulation of both cohesin-bound and non-bound genes.Our data thereby support a role for cohesin in the global organization of domain structure and suggest that domains function to stabilize the transcriptional programmes within them.

View Article: PubMed Central - PubMed

Affiliation: Research Department of Cancer Biology, Cancer Institute, University College London, London, UK.

ABSTRACT
To ensure proper gene regulation within constrained nuclear space, chromosomes facilitate access to transcribed regions, while compactly packaging all other information. Recent studies revealed that chromosomes are organized into megabase-scale domains that demarcate active and inactive genetic elements, suggesting that compartmentalization is important for genome function. Here, we show that very specific long-range interactions are anchored by cohesin/CTCF sites, but not cohesin-only or CTCF-only sites, to form a hierarchy of chromosomal loops. These loops demarcate topological domains and form intricate internal structures within them. Post-mitotic nuclei deficient for functional cohesin exhibit global architectural changes associated with loss of cohesin/CTCF contacts and relaxation of topological domains. Transcriptional analysis shows that this cohesin-dependent perturbation of domain organization leads to widespread gene deregulation of both cohesin-bound and non-bound genes. Our data thereby support a role for cohesin in the global organization of domain structure and suggest that domains function to stabilize the transcriptional programmes within them.

Show MeSH