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Fig. 5 | Epigenetics & Chromatin

Fig. 5

From: Crosstalk between chromatin structure, cohesin activity and transcription

Fig. 5

Histone depletion has a moderate effect on cohesin binding and distribution. a Cohesin distribution at chromosome I in wild-type and t::HHF2 cells synchronized in G1 and released into fresh medium until G2-metaphase, as determined by ChIP-on-chip analysis against Scc1-HA. b Cohesin distribution at the ribosomal DNA locus in wild-type and t::HHF2 cells. c Number of IGRs classified according to the orientation of the flanking genes that overlap with cohesins (by at least 1 bp) in wild-type and t::HHF2 cells. d Relative amount of cohesins in t::HHF2 cells relative to wild-type cells at the indicated genomic regions. The total amount of cohesins at each region was calculated considering the sum of positive signals (relative to the untagged strain) with a p < 0.05. The ratio between the mutant and the wild-type at each region was normalized to that obtained for the whole genome, which was taken as 1. The proportion of cohesins between mutant and wild-type cells at each genomic region relative to the genome average was statistically different according to a two-tailed Chi-square test (p < 0.001). e Cohesin enrichment in t::HHF2 cells relative to wild-type cells at different genomic regions, as determined by ChIP and qPCR analyses against HA-Scc1 in cells grown as in a. IGR and tRNA genes are indicated in Methods section. Cohesin enrichment was calculated as the ratio between immunoprecipitated DNA and input in t::HHF2 cells relative to the same value in the wild-type cells. The average and SEM from 3 to 4 independent experiments are shown. An untagged strain was used as an internal control to confirm the specific enrichment at each region. The amount of Scc1 relative to Pgk1 is shown on the left. No significant differences were observed between wild-type and mutant cells from four independent measurements. f Number of IGRs, ORF, tRNA, ARS and telomeres that overlap with cohesins (by at least 1 bp) in wild-type and t::HHF2 cells. g Probability that scc1-73 alters cohesin-associated nucleosomes if scc1-73-altered nucleosomes were randomly distributed, as determined by a hypergeometric test. The rate between the observed and expected frequencies of common nucleosomes is also shown. The number of nucleosomes in each case is indicated in parentheses. h Comparison of the percentages of altered nucleosomes by histone depletion (showing occupancy, fuzziness and position shift) in the regions with cohesins (9596 nucleosomes) relative to the whole genome (66,278 nucleosomes) in t::HHF2 cells. A hypergeometric test was used to determine the probability of obtaining the indicated percentages of altered nucleosomes at regions with cohesin if their distributions were random

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