GSE169465
G+C content of transcribed sequence modulates DSIF-assisted DNA occupancy by RNA polymerase II [RNA-seq]
The DSIF complex, which is composed of the Supt4h and Supt5h transcription elongation proteins, clamps RNA polymerase II (RNAPII) onto DNA templates—facilitating polymerase processivity. Lowering of DSIF components can differentially decrease expression of certain neurodegenerative disease-gene alleles containing nucleotide repeat expansions, suggesting that DSIF assists RNAPII progression through these alleles. To identify sequence features that globally affect the actions of DSIF in neuronal cells, we used ultra—deep ChIP-seq analyses  together with RNA-seq to investigate and quantify the genome-wide consequences  of reducing DSIF on template occupancy and transcription by RNAPII.  Our ChIP-seq analysis yielded an average of 378 million reads per sample, facilitating  precision in  identification of read end-points. The results indicate that DSIF is differentially utilized throughout the human genome by RNAPII in its occupancy of human DNA and that the G+C_composition of the template segment being transcribed determines the extent to which the polymerase relies on DSIF for template occupancy.  Additional analysis by us of previously published data obtained. We following knockdown of  the Supt5h component of DSIF  in  murine fibroblasts  showed similar effects.  We further observed  that DSIF reduction resulted in  progressively decreased RNAPII occupancy of template during transcript elongation in genes of  high G+C content, but  had little effect on genes low in G+C content. Our discovery that DSIF dependency varies in different template regions according to G+C content and transcript length suggest a biochemical basis for selective effects of deficiency of DSIF components on genes containing expansions of G+C-rich nucleotide repeats. Overall design: Compare elongating RNAPII's DNA occupancy by ChIP-seq and RNA transcription by RNA-seq when Supt4 is present or absent in human neuronal progenitor cells