Molecular Cell
Volume 65, Issue 4, 16 February 2017, Pages 685-698.e8
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Article
Paf1 Has Distinct Roles in Transcription Elongation and Differential Transcript Fate

https://doi.org/10.1016/j.molcel.2017.01.006Get rights and content
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Highlights

  • Strand-specific maps of Paf1 on Pol2 using TEF-seq

  • Paf1 influences transcription elongation at all genes

  • Paf1 is dynamically enriched/depleted on Pol2, independent of its role in elongation

  • Paf1 enrichment promotes nuclear export of the encoded transcripts

Summary

RNA polymerase II (Pol2) movement through chromatin and the co-transcriptional processing and fate of nascent transcripts is coordinated by transcription elongation factors (TEFs) such as polymerase-associated factor 1 (Paf1), but it is not known whether TEFs have gene-specific functions. Using strand-specific nucleotide resolution techniques, we show that levels of Paf1 on Pol2 vary between genes, are controlled dynamically by environmental factors via promoters, and reflect levels of processing and export factors on the encoded transcript. High levels of Paf1 on Pol2 promote transcript nuclear export, whereas low levels reflect nuclear retention. Strains lacking Paf1 show marked elongation defects, although low levels of Paf1 on Pol2 are sufficient for transcription elongation. Our findings support distinct Paf1 functions: a core general function in transcription elongation, satisfied by the lowest Paf1 levels, and a regulatory function in determining differential transcript fate by varying the level of Paf1 on Pol2.

Keywords

Paf1
differential mRNP nuclear export
transcription elongation
TEF-seq
NET-seq
lncRNA
mRNA
RNA polymerase II
nucleosome
Saccharomyces cerevisiae

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