Histone H1 regulates non-coding RNA turnover on chromatin in a m6A-dependent manner

Slow RNAPII Transcription Elongation Rate, Low Levels of RNAPII Pausing, and Elevated Histone H1 Content at Promoters Associate with Higher m6A Deposition on Nascent mRNAs

“…To relate different parameters of the transcriptional cycle with the RNAPII elongation speed, we first integrated genome-wide datasets of RNAPII occupancy (RNAPII ChIP-seq) and chromatin-enriched RNA production (CheRNA-seq) recently generated by us in both cell types [ 9 ] ( Figure 2 A,B). We found that higher elongation rates correlated with higher RNAPII promoter densities and mRNA output on chromatin at each cell type ( Figure 2 C,D), although only slow-transcribed genes were significantly different from the other two speed categories (Wilcoxon, p -value = 1.76 × 10 −77 and p -value = 9.97 × 10 −89 , for medium and fast rate genes RNAPII levels; and p -value = 2.54 × 10 −131 and p -value = 6.04 × 10 −174 , for medium and fast rate genes CheRNA levels in WT cells, respectively).…”

“…CheRNA data was downloaded from Fernández-Justel et al [ 9 ]. Reads were aligned to the mm10 reference genome and to the Luciferase coding sequence used as spike-in with Tophat2 [ 19 ] using standard parameters.…”

“…RNAPII ChIP data was downloaded from Fernández-Justel et al [ 9 ]. Reads were aligned to the mouse mm10 and human hg19 reference genomes (since 1/20th of human chromatin was added prior immunoprecipitation as spike-in, see [ 9 ] for details) using the bwa mem algorithm, and merged with the reference mouse transcriptome of 26,021 genes. Two types of intersections were performed.…”

“…The datasets of DRB-TTseq and MNase-seq experiments generated in this work were deposited in GEO: GSE213270. Datasets from CheRNA, RNAPII-ChIP, and MeChRIP sequencing experiments in WT and H1-TKO mESCs were generated in our laboratory and deposited in GSE166426 [ 9 ]. H3K4me3, H3K27me3, and H3K9me3 ChIP-seq data in WT and H1-TKO mESCs were downloaded from GSE75426 [ 22 ].…”

“…Here, we set out to examine this by determining transcription elongation rates in mouse embryonic stem cells (mESCs). We analyzed in parallel mESCs triple knock-out for three of the genes encoding for the linker histone H1 (H1-TKO; [ 8 ]), since we recently showed that histone H1 depletion reduces m6A levels at nascent coding and non-coding RNAs [ 9 ]. In particular, we aimed to address two questions: (i) whether the transcription elongation rate is predictive of m6A deposition levels on nascent RNAs and (ii) whether it is modulated by promoter chromatin structure.…”