A CTCF-independent role for cohesin in tissue-specific transcription - PubMed (original) (raw)

A CTCF-independent role for cohesin in tissue-specific transcription

Dominic Schmidt et al. Genome Res. 2010 May.

Abstract

The cohesin protein complex holds sister chromatids in dividing cells together and is essential for chromosome segregation. Recently, cohesin has been implicated in mediating transcriptional insulation, via its interactions with CTCF. Here, we show in different cell types that cohesin functionally behaves as a tissue-specific transcriptional regulator, independent of CTCF binding. By performing matched genome-wide binding assays (ChIP-seq) in human breast cancer cells (MCF-7), we discovered thousands of genomic sites that share cohesin and estrogen receptor alpha (ER) yet lack CTCF binding. By use of human hepatocellular carcinoma cells (HepG2), we found that liver-specific transcription factors colocalize with cohesin independently of CTCF at liver-specific targets that are distinct from those found in breast cancer cells. Furthermore, estrogen-regulated genes are preferentially bound by both ER and cohesin, and functionally, the silencing of cohesin caused aberrant re-entry of breast cancer cells into cell cycle after hormone treatment. We combined chromosomal interaction data in MCF-7 cells with our cohesin binding data to show that cohesin is highly enriched at ER-bound regions that capture inter-chromosomal loop anchors. Together, our data show that cohesin cobinds across the genome with transcription factors independently of CTCF, plays a functional role in estrogen-regulated transcription, and may help to mediate tissue-specific transcriptional responses via long-range chromosomal interactions.

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Figures

Figure 1.

Figure 1.

Identification of CTCF-independent cohesin binding events in the human genome. (A) Genomic binding of the cohesin subunits RAD21 and STAG1 as well as CTCF shows colocalization at the H19/IGF2 locus in MCF-7 cells. (B) Illustrative CTCF-independent binding events are shown at a 120-kb region on chromosome 15 in MCF-7 cells; this genomic track is centered around a single shared cohesin-CTCF site. (C) Distribution of cohesin-, CTCF-, and cohesin–non-CTCF-binding (CNC) events in the human genome: 5′, 3′, start, end, exon, intron, and intergenic regions of Ensembl genes are shown. The number of sites was normalized and displayed as fold-enrichment relative to genome background. (D) CTCF consensus DNA motif de novo derived from the MCF-7 CTCF binding events. The occurrence of the CTCF consensus within the CTCF, STAG1, RAD21, CNC events and random genomic regions are presented. (E) Estrogen response elements enriched within the CNC events.

Figure 2.

Figure 2.

Estrogen receptor, cohesin, and CTCF binding at known estrogen receptor target genes. The genomic binding profiles for cohesin (RAD21 and STAG1), estrogen receptor alpha (ER), and CTCF at four known ER target genes demonstrate extensive co-occupancy of ER and cohesin in the absence of CTCF.

Figure 3.

Figure 3.

Cohesin binding with CTCF is cell-type invariant, whereas cohesin binding with tissue-specific TFs is cell-type specific. (A) The CTCF binding events on chromosome 1 in MCF-7 cells strongly correspond with both CTCF binding in HepG2 cells and cohesin in both tissues but are not generally shared with tissue-specific master regulators. (B) In contrast, a subset of the ER binding events bound by cohesin in MCF-7 cells independently of CTCF are shown. Showing the tissue specificity of these binding events, in HepG2 cells, these regions are rarely found to be bound by cohesin. (C) Similarly, a subset of the CEBPA binding events that are bound by cohesin in HepG2 cells independently of CTCF do not show cohesin binding in MCF-7 cells.

Figure 4.

Figure 4.

Cohesin binding can be independent of CTCF. (A) Cohesin (STAG1 and RAD21) enrichment at cohesin-CTCF sites is reduced upon CTCF removal by RNAi knockdown (CTCF k.d.). (B) Cohesin enrichment at ER-CNCs is largely unaffected by CTCF knockdown. (C) Cohesin binding increases upon estrogen treatment at sites not shared with CTCF (Kolmogorov-Smirnov, _P_-value < 10−9 [STAG1]; _P_-value < 10−15 [RAD21]).

Figure 5.

Figure 5.

Correlation of estrogen receptor and cohesin binding events with estrogen gene regulation. (A) Estrogen binding alone enriches for functional targets. The genes that have an ER binding event are 1.4 times more likely to have changed their gene expression than expected by random chance (Fisher's exact test, _P_-value = 10−18). (B) Genes bound by both ER and cohesin (but not CTCF) are 2.2 times more likely to have altered gene expression upon estrogen treatment than by random chance, further enriching functional targets (Fisher's exact test, _P_-value = 10−41).

Figure 6.

Figure 6.

Cohesin is functionally required for correct estrogen-induced cell cycle progression. (A) Following RNAi-mediated knockdown of RAD21 and CTCF, cell cycle distributions after vehicle or estrogen treatment were assessed by propidium iodide staining followed by flow cytometry. (B) The percentage of cells in G0/G1 (black bars) and S/G2/M (gray bars) phases were quantitated after 24 h of vehicle or estrogen treatment (mean of n = 2; error bars, ±SD; *, _t_-test _P_-value ≤ 0.001). In vehicle-treated cells, suppression of CTCF caused a doubling of the cells in S/G2/M phases, compared with mock treatment. After 24 h of estrogen treatment, the removal of the cohesin subunit RAD21 caused a decrease in the number of cells that have transitioned to S/G2/M, indicating reduced cell-cycle progression. Removal of CTCF again enhanced entry into S/G2/M, but not with statistical significance.

Figure 7.

Figure 7.

Cohesin preferentially associates with estrogen receptor–mediated through-space chromatin interactions. (A) Genomic binding of cohesin (RAD21 and STAG1), estrogen receptor alpha, and CTCF are shown as genomic enrichment tracks above the genome annotation of the known ER target gene XBP1, and ChIA-PET interaction data (Fullwood et al. 2009) are shown as purple sequencing tracks beneath the genome annotation. (B, 1) ER binding events were divided into loop anchors and noninteracting binding events. Association of CTCF (2), STAG1 (3), and RAD21 (4) with ER-interacting binding events (loop anchors, solid lines) and ER noninteracting binding events (dashed lines) are shown.

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