Diverse Roles of RNA Polymerase II-associated Factor 1 Complex in Different Subpathways of Nucleotide Excision Repair

Abstract

Transcription-coupled repair (TCR) and global genomic repair (GGR) are two pathways of nucleotide excision repair (NER). In Saccharomyces cerevisiae, Rad26 is important but not absolutely required for TCR. Rpb4, a nonessential RNA polymerase II (Pol II) subunit that forms a subcomplex with Rpb7, and the Spt4-Spt5 complex, a transcription elongation factor, have been shown to suppress Rad26-independent TCR. The Pol II-associated factor 1 complex (Paf1C) has been shown to function in transcription elongation, 3-processing of mRNAs, and posttranslational modification of histones. Here we show that Paf1C plays a marginal role in facilitating Rad26-dependent TCR but significantly suppresses Rad26-independent TCR. The suppression of Rad26-independent TCR is achieved by cooperating with Spt4-Spt5. We propose a model that, in the absence of Rad26, a lesion is "locked" in the active center of a Pol II elongation complex, which is stabilized by the coordinated interactions of Rpb4-Rpb7, Spt4-Spt5, and Paf1C with each other and with the core Pol II. We also found that Paf1C facilitates GGR, especially in internucleosomal linker regions. The facilitation of GGR is achieved through enabling monoubiquitination of histone H2B lysine 123 by Bre1, which in turn permits di-and trimethylation of histone H3 lysine 79 by Dot1. To our best knowledge, among the NER-modulating factors documented so far, Paf1C appears to have the most diverse functions in different NER pathways or subpathways.

Ribosomopathies: Global process, tissue specific defects

“… 91 RNA Pol I transcription is initiated by an interaction between the upstream binding factor (UBF), and the species-specific promoter selectivity factor, SL1. Specifically, UBF interacts with TATA binding protein 92 and TAF1, 56,93 which are components of the SL1 complex, and PAF53. 94 UBF also interacts with pRb, which inhibits RNA Pol I activity.…”

The many roles of the conserved eukaryotic Paf1 complex in regulating transcription, histone modifications, and disease states

“…The repair of DNA damage by nucleotide excision repair (NER) occurs thorough two major pathways, global genome (GG-NER) repair and transcription coupled repair (TC-NER). Members of the Paf1C complex, histone modifiers and FACT have all been implicated to differing extents as participating in these NER pathways [138–140]. Additional studies will be needed to elucidate the contribution of the Paf1C to DNA damage repair pathways and determine if all of its roles require its histone modifications functions.…”

Transcription bypass of DNA lesions enhances cell survival but attenuates transcription coupled DNA repair

“…Previous studies have ruled out the roles of ubiquitination and degradation of Rpb1 ( 49 – 51 ) and back-tracking of RNAP II by TFIIS ( 52 ) in TCR. A number of transcription elongation factors, such as Spt4 ( 22 ), Spt5 ( 20 , 21 ) and PAFc ( 24 ), which stabilize and promote forward-tracking of the RNAP II elongation complex, have been shown to repress TCR. Here, we show that transcription bypass of lesions attenuates TCR, although the bypass may expose the lesions to DNA repair machinery.…”

“…In S. cerevisiae , the elongating RNAP II complex, which is stabilized by Spt5 and other associated transcription elongation factors, is intrinsically repressive to TCR ( 20 ). Rad26 appears to facilitate TCR by antagonizing the repression, as it becomes dispensable for TCR in the absence of Spt4 ( 21 , 22 ), Rpb4 ( 23 ), the RNAP II associated factor 1 complex (PAFc) ( 24 ) and certain domains of Spt5 ( 20 , 21 ).…”