Fig. 6
From: Regulation of CHD2 expression by the Chaserr long noncoding RNA gene is essential for viability
Changes in Pol2 occupancy in Chaserr–/– mEFs and RNA binding by CHD2. a Correlation between changes in gene expression levels and changes in Pol2 occupancy at the promoter region (±300 bases around TSS). Color indicates point density. b As in a, but for changes in Pol2 occupancy at gene body regions (defined from 1 kb downstream of the TSS to the TTS). c Pol2 pausing index (see the “Methods” section) in our WT mEF Pol2 ChIP-seq data (left) and ENCODE mEF data (right) for genes with the indicated changes in gene expression in Chaserr−/− mEFs (adjusted P < 0.05). Boxplots show the 5th, 25th, 50th, 75th, and 95th percentiles. d Changes in Pol2 pausing index as a function of changes in gene expression between Chaserr−/− and WT mEFs. Color indicates point density. e Normalized RIP-seq read counts within gene bodies in CHD2 and IgG RIP libraries (average of two replicates). Red dots correspond to genes with adjusted P < 0.05 (DESeq2 analysis). f Changes in gene expression of genes significantly associated with CHD2 (from e) and other genes expressed in mEFs in the indicated RNA-seq-based comparison. Boxplots show the 5th, 25th, 50th, 75th, and 95th percentiles. g RIP-seq read coverage in the Chaserr locus. h Fractions of reads mapping to the indicated regions in the indicated RIP-seq library. Source data are provided as a Source Data file
