A Posttranscriptional Role for the Yeast Paf1-RNA Polymerase II Complex Is Revealed by Identification of Primary Targets

Department of Biochemistry and Molecular Genetics and Molecular Biology Program, University of Colorado, Denver, USA.
Molecular Cell (Impact Factor: 14.02). 11/2005; 20(2):213-23. DOI: 10.1016/j.molcel.2005.08.023
Source: PubMed


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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    • "It was suggested that Cdc73 might regulate mRNA processing by facilitating the recruitment of 3′ factors to transcribed loci. Other evidence of PAF involvement in 3′ processing comes from yeast, where PAF was shown to affect poly (A) tail length (Mueller et al., 2004) and poly (A) site selection (Penheiter et al., 2005). In addition, another study (Nagaike et al., 2011) found a role of PAF in mediating stimulation of 3′ processing by transcriptional activators, confirming its potential role in bridging polyadenylation to transcription (Fig. 3B). "
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    ABSTRACT: The 3' ends of most eukaryotic messenger RNAs must undergo a maturation step that includes an endonucleolytic cleavage followed by addition of a polyadenylate tail. While this reaction is catalyzed by the action of only two enzymes it is supported by an unexpectedly large number of proteins. This complexity reflects the necessity of coordinating this process with other nuclear events, and growing evidence indicates that even more factors than previously thought are necessary to connect 3' processing to additional cellular pathways. In this review we summarize the current understanding of the molecular machinery involved in this step of mRNA maturation, focusing on new core and auxiliary proteins that connect polyadenylation to splicing, DNA damage, transcription and cancer.
    Molecules and Cells 08/2014; 37(9). DOI:10.14348/molcells.2014.0177 · 2.09 Impact Factor
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    • "ticular , Paf1 interacts both genetically and physically with Spt16 ( Squazzo et al . , 2002 ) . Consistent with this , Spt16 recruitment is reduced in the absence of Paf1 ( Pruneski et al . , 2011 ) . Additionally , Paf1 is involved in regulating transcription termination and mRNA 3 ' processing ( Mueller et al . , 2004 ; Nagaike et al . , 2011 ; Penheiter et al . , 2005 ; Sheldon et al . , 2005 ) ."
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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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    • "The recruitment of the Bre1/Rad6 ubiquitin conjugase-ligase complex by PAF1C is essential for H2B monoubiquitylation (15,16), which is a prerequisite for the subsequent methylation of H3K4 and H3K79 by the Set1/COMPASS and Dot1 methyltransferases, respectively (15,17–20). Moreover, various studies have implicated PAF1C function in other diverse cellular processes, including the processing of mRNA and small nucleolar RNA during posttranscriptional events (12,21–23), mammalian embryonic development and survival in adults (24,25) and embryonic stem cell identity maintenance (26). Additional evidence implicates PAFC1 in immunological responses to disease states and cancer progression (27,28). "
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    ABSTRACT: The highly conserved Paf1 complex (PAF1C) plays critical roles in RNA polymerase II transcription elongation and in the regulation of histone modifications. It has also been implicated in other diverse cellular activities, including posttranscriptional events, embryonic development and cell survival and maintenance of embryonic stem cell identity. Here, we report the structure of the human Paf1/Leo1 subcomplex within PAF1C. The overall structure reveals that the Paf1 and Leo1 subunits form a tightly associated heterodimer through antiparallel beta-sheet interactions. Detailed biochemical experiments indicate that Leo1 binds to PAF1C through Paf1 and that the Ctr9 subunit is the key scaffold protein in assembling PAF1C. Furthermore, we show that the Paf1/Leo1 heterodimer is necessary for its binding to histone H3, the histone octamer, and nucleosome in vitro. Our results shed light on the PAF1C assembly process and substrate recognition during various PAF1C-coordinated histone modifications.
    Nucleic Acids Research 09/2013; 41(22). DOI:10.1093/nar/gkt819 · 9.11 Impact Factor
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