Cohesin-based chromatin interactions enable regulated gene expression within preexisting architectural compartments
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Cites background from "Cohesin-based chromatin interaction..."
...at the CD3 and GATA3 loci (41, 42) (Table S2A-B)....
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...Previous studies have established that CTCF is bound at the anchor sites of chromosome loop structures, but not every CTCF-bound site in the genome is involved in looping interactions, and the CTCF-bound sites that are detected at the boundaries at looping interactions tend to be co-bound by cohesin (8, 9, 11, 24, 40, 42, 63-66)....
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...To define a second control set of non-boundary CTCF sites (“control set 2”), we used previous evidence that the CTCF-bound sites that are detected at the boundaries at looping interactions tend to be co-bound by cohesin (8, 9, 11, 24, 40, 42, 63-66)....
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References
43,862 citations
"Cohesin-based chromatin interaction..." refers background or methods in this paper
...Trimmed reads were aligned independently to the mouse reference genome assembly (NCBI37/mm9) using BWA (Li and Durbin 2009)....
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...There was a highly significant overlap of 502 differential interactions between replicates (P < 10 15, odds ratio of 5.25 for 224 increased interactions and 9.96 for...
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...Rather, cohesin enables discrete gene expression states by promoting cohesin-based interac- tions within a preexisting architectural framework....
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20,335 citations
"Cohesin-based chromatin interaction..." refers methods in this paper
...Raw reads for each condition and replicate were independently aligned to mouse transcript sequences (cDNA sequences from Ensembl version 66, NCBI37/mm9) (Flicek et al. 2013) using Bowtie version 0.12.8 (Langmead et al. 2009) with default pa- rameters....
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...8 (Langmead et al. 2009) with default parameters....
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18,346 citations
"Cohesin-based chromatin interaction..." refers background in this paper
...3D), indicating that most are direct targets of cohesin-mediated regulation....
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13,356 citations
"Cohesin-based chromatin interaction..." refers background or methods in this paper
...We used the Bioconductor R package DESeq version 1.6.1 (Anders and Huber 2010) to determine significantly differentially expressed genes in cohesin-deficient thymocytes versus control cells (FDR = 0.05)....
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...1 (Anders and Huber 2010) to determine significantly differentially expressed genes in cohesin-deficient thymocytes versus control cells (FDR = 0....
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9,620 citations
"Cohesin-based chromatin interaction..." refers methods in this paper
...…compart- Genome Research 2067 www.genome.org Cohesin-based chromatin interactions Cohesin binding predicts perturbed long-range interactions in cohesin-deficient thymocytes We applied the HOMER pipeline (Heinz et al. 2010) to our Hi-C data (see Methods, section on Hi-C data analysis, for details)....
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...We applied the HOMER pipeline (Heinz et al. 2010) to our Hi-C data (see Methods, section on Hi-C data analysis, for details)....
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