Human histone H1 variants impact splicing outcome by controlling RNA polymerase II elongation rate [PRO-seq]

Histones shape chromatin structure and the epigenetic landscape. H1, the most diverse histone in the human genome, has 11 variants. Due to high structural similarity between the H1s, their unique functions in transferring information from the chromatin to mRNA processing machineries, have remained elusive. Here, we generated human cell lines lacking up to five H1 subtypes, allowing us to characterize the genomic binding profiles of six H1 variants. Most H1s bind to specific sites, and binding depends on multiple factors including GC content. The highly expressed H1.2 has a high affinity for exons, whereas H1.3 binds intronic sequences. Although H1s have a minor effect on global gene expression levels, they are major splicing regulators, especially of exon skipping and intron retention events, through their effects on the elongation rate of RNA polymerase II. Thus, H1 variants determine splicing fate by modulating the RNA polymerase II elongation rate. Determine the H1-mediated RNA polymerase II elongation rate and its influence on alternative splicing by conducting and analyzing precision nuclear run-on (PRO-seq) experiments in both WT and H1 knockout cells, then integrate this information with our RNA-seq results