Journal: Nature Communications

Article Title: Variation of C-terminal domain governs RNA polymerase II genomic locations and alternative splicing in eukaryotic transcription

doi: 10.1038/s41467-024-52391-6

Figure Lengend Snippet: a Phase diagram of wild-type GST-hCTD. Black-filled circles indicate conditions where liquid-liquid phase separation is observed with DIC microscope. Phase diagram of GST-yCTD ( b ), GST-T4E yCTD ( c ), GST-T4E-spaced yCTD ( d ) and GST-S7E-spaced yCTD ( e ). f ChIP-Seq analyses of genomic binding of RPB1_52xCTD and RPB1_26xCTD. The heatmaps and profiles are generated using deepTools2 suite . The heatmaps show bigWig scores over genomic intervals. The rows (genes) are sorted based on the mean score per region in the descending order. The profile above shows average signal over all the genes. The genome is binned to the size of 50 bp. The genes are scaled (either stretched or shrunken) to fit into 2000-bp window between TSS and TES. Also, a window 2 kb upstream from TSS and 2 kb downstream of TES are shown. g ChIP-Seq analyses of genomic binding of RPB1_26xCTD T4E (all), 26xCTD T4E (spaced) and 26xCTD S7E (spaced). h ChIP-Seq example illustrating the association of different RPB1 CTD constructs along with the active transcribing genes. i Boxplot of the pausing index in 26xCTD and 52xCTD (19,630 protein-coding genes). Shown is one representative paired biological replicate: CTD_26x vs CTD_52x. Boxplots represent median (50%) with interquartile range (25–75%), whiskers show minimal and maximal values, outliers not shown. Statistical comparison was performed using two-sided paired Wilcoxon test. ns not significant. Source data are provided as a Source Data file.

Article Snippet: Ten microliters of each sample were applied to slide glass and covered with 22 mm coverslip DIC images were acquired with Nikon eclipse Ni Compound Microscope with 60× objective.

Techniques: Microscopy, ChIP-sequencing, Binding Assay, Generated, Construct, Comparison