Topological domains in mammalian genomes identified by analysis of chromatin interactions
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...Megabase-scale TADs appear to be constant between mammalian cell types and conserved across species (Dixon et al., 2012; Nora et al., 2012)....
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...More recently, technologies for genome-wide mapping of chromatin architecture have been described, but comprehensive detection comes at the expense of resolution for mammalian genomes (Hi-C) (Dixon et al., 2012; Lieberman-Aiden et al., 2009) or is restricted to only interactions mediated by a preselected protein of interest (ChIA-PET) (Handoko et al....
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...(A), (B), (D), and (E) Hi-C data (adapted from Dixon et al., 2012) displayed for (A) and (D) 10 Mb and (B) and (E) 1 Mb regions around (A) and (B) Sox2 and (D) and (E)Olig1-Olig2 for mouse E14 ES cells (top) and mouse cortex (bottom)....
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...in (Dixon et al., 2012) and (H) subdomain boundaries called in the present work...
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...At the subcompartment level, chromatin is further organized into megabasesized topologically associating domains (TADs) that represent spatial neighborhoods of high-frequency chromatin interactions (Dixon et al., 2012; Hou et al., 2012; Nora et al., 2012; Sexton et al., 2012)....
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"Topological domains in mammalian ge..." refers background in this paper
...mESC H3K36me3, H3K79me2, Oct4, Sox2, Nanog Figure 4, Supplemental Figure 20-22 GSE11724 Marson, A. et al. Connecting microRNA genes to the core transcriptional regulatory circuitry of embryonic stem cells. Cell 134, 521-33 (2008).(42) mESC H3K9me3 Figure 2, 4 GSE18371 Bilodeau, S....
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...mESC H3K36me3, H3K79me2, Oct4, Sox2, Nanog Figure 4, Supplemental Figure 20-22 GSE11724 Marson, A. et al. Connecting microRNA genes to the core transcriptional regulatory circuitry of embryonic stem cells. Cell 134, 521-33 (2008).(42) mESC H3K9me3 Figure 2, 4 GSE18371 Bilodeau, S., Kagey, M.H., Frampton, G.M., Rahl, P.B. & Young, R.A. SetDB1 contributes to repression of genes encoding developmental regulators and maintenance of ES cell state. Genes Dev 23, 2484-9 (2009).(43) mESC Jarid2, Jarid1a, Suz12, Ezh2 Supplemental Figure 20-22 GSE18776 Peng, J....
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...mESC H3K36me3, H3K79me2, Oct4, Sox2, Nanog Figure 4, Supplemental Figure 20-22 GSE11724 Marson, A. et al. Connecting microRNA genes to the core transcriptional regulatory circuitry of embryonic stem cells. Cell 134, 521-33 (2008).(42) mESC H3K9me3 Figure 2, 4 GSE18371 Bilodeau, S., Kagey, M.H., Frampton, G.M., Rahl, P.B. & Young, R.A. SetDB1 contributes to repression of genes encoding developmental regulators and maintenance of ES cell state. Genes Dev 23, 2484-9 (2009).(43) mESC Jarid2, Jarid1a, Suz12, Ezh2 Supplemental Figure 20-22 GSE18776 Peng, J.C. et al. Jarid2/Jumonji coordinates control of PRC2 enzymatic activity and target gene occupancy in pluripotent cells. Cell 139, 1290-302 (2009).(44) mESC PolII Serine 5, PolII Serine 2, NelfA, Ctr9, Spt5 Supplemental Figure 20-22 GSE20530 Rahl, P....
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