A Posttranscriptional Role for the Yeast Paf1-RNA Polymerase II Complex Is Revealed by Identification of Primary Targets
ABSTRACT The yeast Paf1 complex (Paf1C: Paf1, Cdc73, Ctr9, Rtf1, and Leo1) is associated with RNA Polymerase II (Pol II) at promoters and coding regions of transcriptionally active genes, but transcript abundance for only a small subset of genes is altered by loss of Paf1. By using conditional and null alleles of PAF1 and microarrays, we determined the identity of both primary and secondary targets of the Paf1C. Neither primary nor secondary Paf1C target promoters were responsive to loss of Paf1. Instead, Paf1 loss altered poly(A) site utilization of primary target genes SDA1 and MAK21, resulting in increased abundance of 3'-extended mRNAs. The 3'-extended MAK21 RNA is sensitive to nonsense-mediated decay (NMD), as revealed by its increased abundance in the absence of Upf1. Therefore, although the Paf1C is associated with Pol II at initiation and during elongation, these critical Paf1-dependent changes in transcript abundance are due to alterations in posttranscriptional processing.
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ABSTRACT: Cmr1 (Changed mutation rate) is a histone interacting, WD40 domain containing protein, with a previously identified role in the DNA damage repair pathway. Recent interest in Cmr1 has suggested roles in additional cellular processes. The current study was carried out to determine whether Cmr1 is involved in Pol II mediated transcription. Results presented herein provide the first evidence that Cmr1 is recruited to the coding regions of Pol II transcribed genes. It is recruited to the 5’ open reading frame in a manner dependent on Ser5 phosphorylation of the Pol II carboxyl terminal domain by the kinase Kin28. Strong evidence is provided that a primary function of Cmr1 is to coordinate recruitment and retention of the multifunctional elongation factor Paf1. Cmr1 was observed to occupy the coding region of the inducible genes ARG1 and HIS4 at significant levels, but not that of the constitutively expressed genes ADH1 and PMA1, suggesting that it regulates a subset of the multiple functions identified for Paf1. Additionally, it is important for efficient recruitment of the histone chaperone complex FACT and of the mRNA processing factor Rna14, both of which are consistent with previously identified roles for Paf1.06/2014, Degree: MSc
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ABSTRACT: The proteasome is a large self-compartmentalized protease complex that recognizes, unfolds, and destroys ubiquitylated substrates. Proteasome activities are required for a host of cellular functions, and it has become clear in recent years that one set of critical actions of the proteasome occur on chromatin. In this review, we discuss some of the ways in which proteasomes directly regulate the structure and function of chromatin and chromatin regulatory proteins, and how this influences gene transcription. We discuss lingering controversies in the field, the relative importance of proteolytic versus non-proteolytic proteasome activities in this process, and highlight areas that require further investigation. Our intention is to show that proteasomes are involved in major steps controlling the expression of the genetic information, that proteasomes use both proteolytic mechanisms and ATP-dependent protein remodeling to accomplish this task, and that much is yet to be learned about the full spectrum of ways that proteasomes influence the genome.12/2014; 4(4):1026-1044. DOI:10.3390/biom4041026