Fig. 3
From: Highly structured homolog pairing reflects functional organization of the Drosophila genome
Pairing in PnM cells is correlated with active genomic regions and can be disrupted by RNAi. a 1.5 Mb region of 2 L: Pairing scores (PS) and cis scores (CS) shown in a genome browser as compared to chromatin types identified in Kc167 cells45 and with SNVs in PnM cells. b Normalized distributions of PS within regions of different chromatin types. Dashed line shows the threshold between tight and loose pairing. *p < 1−10, Mood’s test against yellow chromatin. c Distribution of PS values relative to the eigenvector shows that pairing is correlated with compartmentalization, A-type compartments being almost exclusively tightly paired, Spearman’s correlation coefficient (rs) = 0.706, p < 10−10. d Distribution of PS values relative to gene expression in PnM cells shows that expressed genes are almost exclusively tightly paired, Spearman’s correlation coefficient (rs) = 0.397, p < 10−10. e Levels of pairing (quantified and displayed as in Fig. 1d, in PnM cells after Slmb and TopII knockdown showed a reduction as compared to the control (mock) at all loci (*P < = 0.05, unpaired t-test) except for the AACAC satellite repeat and, in the case of TopII knockdown, at BX-C (ns, non-significant; error bars, s.d for three biological replicates; for N > 100 nuclei/replicate). Source data are provided as a Source Data file. f After Slmb and TopII knockdown, the aggregated pairing score (APS) values were reduced by 0.203% and 0.201%, respectively, as compared to untreated sample (p < 0.001) and 0.141% and 0.139%, respectively, as compared to mock (p < 0.001). The 0.062% reduction in mock as compared to untreated samples was also significant (p < 0.001). p-values determined using bootstrapping (Methods)
