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Architectural proteins CTCF and cohesin have distinct roles in modulating the higher order structure and expression of the CFTR locus.

Gosalia N, Neems D, Kerschner JL, Kosak ST, Harris A - Nucleic Acids Res. (2014)

Bottom Line: CTCF mediates the interactions between CTCF/cohesin binding sites, some of which have enhancer-blocking insulator activity.Cohesin shares this tethering role, but in addition stabilizes interactions between the promoter and cis-acting intronic elements including enhancers, which are also dependent on the forkhead box A1/A2 (FOXA1/A2) transcription factors (TFs).Disruption of the three-dimensional structure of the CFTR gene by depletion of CTCF or RAD21 increases gene expression, which is accompanied by alterations in histone modifications and TF occupancy across the locus, and causes internalization of the gene from the nuclear periphery.

View Article: PubMed Central - PubMed

Affiliation: Human Molecular Genetics Program, Lurie Children's Research Center, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA.

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Altered long-range interactions after CTCF and RAD21 depletion. (A) and (B) q3C interactions in cells treated with NC siRNA (gray) or siRNAs targeting CTCF and RAD21 (black), n = 3. The 3C bait (dotted line) is either at the CFTR promoter (A) or the −20.9 kb site (B). ∧ indicate sites that are statistically different after knockdown as determined by an unpaired, two-tailed Student's t-test, P-values listed in Supplementary Table S2. Other sites of interest are marked with arrows. Experimental details are in Figure 2 legend.
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Figure 3: Altered long-range interactions after CTCF and RAD21 depletion. (A) and (B) q3C interactions in cells treated with NC siRNA (gray) or siRNAs targeting CTCF and RAD21 (black), n = 3. The 3C bait (dotted line) is either at the CFTR promoter (A) or the −20.9 kb site (B). ∧ indicate sites that are statistically different after knockdown as determined by an unpaired, two-tailed Student's t-test, P-values listed in Supplementary Table S2. Other sites of interest are marked with arrows. Experimental details are in Figure 2 legend.

Mentions: To further delineate the function of CTCF and cohesin at the CFTR locus, both CTCF and RAD21 were targeted for simultaneous knockdown. Depletion of CTCF and RAD21 led to a loss of interactions across the locus between all the cis-regulatory elements and the two baits at the CFTR promoter and −20.9 kb as measured by q3C (Figure 3A and B). A significant decrease in associations was observed between the promoter and CTCF/cohesin binding sites I, II, IV and V (Figure 3A, marked by ∧). Moreover, a significant loss of interactions was also detected between the promoter and cis-regulatory elements within introns 10, 11 and 19, some of which are intestinal-selective enhancers (8). The most dramatic change in interactions with the −20.9 kb bait was at the +48.9 kb (IV) site, where a 50% loss in looping was detected (Figure 3B, marked by ∧).


Architectural proteins CTCF and cohesin have distinct roles in modulating the higher order structure and expression of the CFTR locus.

Gosalia N, Neems D, Kerschner JL, Kosak ST, Harris A - Nucleic Acids Res. (2014)

Altered long-range interactions after CTCF and RAD21 depletion. (A) and (B) q3C interactions in cells treated with NC siRNA (gray) or siRNAs targeting CTCF and RAD21 (black), n = 3. The 3C bait (dotted line) is either at the CFTR promoter (A) or the −20.9 kb site (B). ∧ indicate sites that are statistically different after knockdown as determined by an unpaired, two-tailed Student's t-test, P-values listed in Supplementary Table S2. Other sites of interest are marked with arrows. Experimental details are in Figure 2 legend.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC4150766&req=5

Figure 3: Altered long-range interactions after CTCF and RAD21 depletion. (A) and (B) q3C interactions in cells treated with NC siRNA (gray) or siRNAs targeting CTCF and RAD21 (black), n = 3. The 3C bait (dotted line) is either at the CFTR promoter (A) or the −20.9 kb site (B). ∧ indicate sites that are statistically different after knockdown as determined by an unpaired, two-tailed Student's t-test, P-values listed in Supplementary Table S2. Other sites of interest are marked with arrows. Experimental details are in Figure 2 legend.
Mentions: To further delineate the function of CTCF and cohesin at the CFTR locus, both CTCF and RAD21 were targeted for simultaneous knockdown. Depletion of CTCF and RAD21 led to a loss of interactions across the locus between all the cis-regulatory elements and the two baits at the CFTR promoter and −20.9 kb as measured by q3C (Figure 3A and B). A significant decrease in associations was observed between the promoter and CTCF/cohesin binding sites I, II, IV and V (Figure 3A, marked by ∧). Moreover, a significant loss of interactions was also detected between the promoter and cis-regulatory elements within introns 10, 11 and 19, some of which are intestinal-selective enhancers (8). The most dramatic change in interactions with the −20.9 kb bait was at the +48.9 kb (IV) site, where a 50% loss in looping was detected (Figure 3B, marked by ∧).

Bottom Line: CTCF mediates the interactions between CTCF/cohesin binding sites, some of which have enhancer-blocking insulator activity.Cohesin shares this tethering role, but in addition stabilizes interactions between the promoter and cis-acting intronic elements including enhancers, which are also dependent on the forkhead box A1/A2 (FOXA1/A2) transcription factors (TFs).Disruption of the three-dimensional structure of the CFTR gene by depletion of CTCF or RAD21 increases gene expression, which is accompanied by alterations in histone modifications and TF occupancy across the locus, and causes internalization of the gene from the nuclear periphery.

View Article: PubMed Central - PubMed

Affiliation: Human Molecular Genetics Program, Lurie Children's Research Center, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA.

Show MeSH
Related in: MedlinePlus