The Paf1 Complex Broadly Impacts the Transcriptome ofSaccharomyces cerevisiae

Abstract

The Polymerase Associated Factor 1 complex (Paf1C) is a multifunctional regulator of eukaryotic gene expression important for the coordination of transcription with chromatin modification and post-transcriptional processes. In this study, we investigated the extent to which the functions of Paf1C combine to regulate the Saccharomyces cerevisiae transcriptome. While previous studies focused on the roles of Paf1C in controlling mRNA levels, here, we took advantage of a genetic background that enriches for unstable transcripts, and demonstrate that deletion of PAF1 affects all classes of Pol II transcripts including multiple classes of noncoding RNAs (ncRNAs). By conducting a de novo differential expression analysis independent of gene annotations, we found that Paf1 positively and negatively regulates antisense transcription at multiple loci. Comparisons with nascent transcript data revealed that many, but not all, changes in RNA levels detected by our analysis are due to changes in transcription instead of post-transcriptional events. To investigate the mechanisms by which Paf1 regulates protein-coding genes, we focused on genes involved in iron and phosphate homeostasis, which were differentially affected by PAF1 deletion. Our results indicate that Paf1 stimulates phosphate gene expression through a mechanism that is independent of any individual Paf1C-dependent histone modification. In contrast, the inhibition of iron gene expression by Paf1 correlates with a defect in H3 K36 trimethylation. Finally, we showed that one iron regulon gene, FET4, is coordinately controlled by Paf1 and transcription of upstream noncoding DNA. Together, these data identify roles for Paf1C in controlling both coding and noncoding regions of the yeast genome.

Altered rRNA processing disrupts nuclear RNA homeostasis via competition for the poly(A)-binding protein Nab2

“…For transcript quantification, all libraries were quantified against the same transcriptome using Salmon (version 0.12.0) ( 61 ). The custom transcriptome was prepared using a bed file that contained coordinates for pervasive transcripts, ribosomal RNAs, and mRNAs to obtain transcript fasta sequences using bedtools getfasta command (version 2.29.2) against the UCSC sacCer3 genome ( 62 , 63 ). For RPKM estimation, all libraries were aligned to the UCSC sacCer3 genome.…”

New mechanisms of DELLA protein regulation and activity in Arabidopsis

“…Tables 1 and 2). The identification of misregulated phosphate response genes is in agreement with previous studies showing that both GA and Paf1c are involved in the control of phosphate homeostasis (Jiang et al, 2007;Zhang et al, 2019;Ellison et al, 2019). However, to the best of our knowledge, neither GA nor Paf1c have been previously related to glucosinolates.…”

Non-coding RNAs as cell wall regulators inSaccharomyces cerevisiae

“…Expression of ECM3 is also posi vely regulated by the Paf1 complex, which associates with RNA Polymerase II during transcrip onal elonga on and plays a crucial role in the co-transcrip onal establishment of histone modifica ons, of which ubiqui na on of histone H2B lysine 123 and methyla on of histone H3 lysine 4 are required for ECM3 expression (Raupach et al 2016). The Paf1 complex has recently been implicated in broadly affec ng transcrip on of non-coding RNAs (Ellison et al 2019). Interes ngly, both inac va on of the Paf1 complex and abroga on of EUC1 transcrip on reduce methyla on of histone H3 lysine 4 in the 5' region of ECM3's ORF.…”