Sub1 and RPA Associate with RNA Polymerase II at Different Stages of Transcription

Abstract

Summary Single stranded DNA binding proteins play many roles in nucleic acid metabolism, but their importance during transcription remains unclear. Quantitative proteomic analysis of RNA polymerase II (RNApII) pre-initiation complexes (PICs) identified Sub1 and the Replication Protein A complex (RPA), both of which bind single-stranded DNA (ssDNA). Sub1, homolog of mammalian coactivator PC4, exhibits strong genetic interactions with factors necessary for promoter melting. Sub1 localizes near the transcription bubble in vitro and binds to promoters in vivo dependent upon PIC assembly. In contrast, RPA localizes to transcribed regions of active genes, strongly correlated with transcribing RNApII but independently of replication. RFA1 interacts genetically with transcription elongation factor genes. Interestingly, RPA levels increase at active promoters in cells carrying a Sub1 deletion or ssDNA binding mutant, suggesting competition for a common binding site. We propose that Sub1 and RPA interact with the non-template strand of RNApII complexes during initiation and elongation, respectively.

Determination of Protein Interactome of Transcription Factor Sox2 in Embryonic Stem Cells Engineered for Inducible Expression of Four Reprogramming Factors

“…A recent study in yeast reported the RPa complex composed of RPa1, -2, and -3, which we demonstrate associates with Sox2 (Fig. 6), plays an important role during transcriptional elongation (34). Additionally, another report demonstrated that the DNA repair XPC nucleotide excision repair complex, composed of Xpc, Rad23b, and Cetn2, is necessary for Sox2 and Oct4 to activate the expression of the Nanog promoter (35).…”

Preferential Repair of DNA Double-strand Break at the Active Gene in Vivo

“…We hypothesize that RNA polymerase II promotes the recruitment of the repair factors to the DSB site at the active gene (and hence stimulates DSB repair), analogous to the fact that RNA polymerase II facilitates the recruitment of TC-NER-specific factor Rad26p to the DNA lesion at the active gene to promote NER (25). In support of this hypothesis, a recent study (57) implicated the interaction of RNA polymerase II with RPA (replication protein A complex), which is involved in DSB repair. Further, the INO80 chromatin remodeling complex that promotes DSB repair is recruited to the gene in a transcription-dependent manner (58,59).…”

Dismantling Promoter-driven RNA Polymerase II Transcription Complexes in Vitro by the Termination Factor Rat1

“…Recent studies have shown that two proteins linked to termination are enriched in pre-initiation complexes assembled in vitro (33,34). One is Sub1, which is thought to repress the termination activity of cleavage factor IA (35), and thus unlikely to promote release in our assay.…”