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| Status |
Public on May 15, 2024 |
| Title |
Dynamic Roles for the Paf1 Complex in Regulating Transcription Elongation and Co-Transcriptional Processes [RNA-seq] |
| Organisms |
Schizosaccharomyces pombe; Saccharomyces cerevisiae |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Eukaryotes employ a set of conserved transcription elongation factors to modulate the behavior of RNA polymerase II (RNAPII). Disruptions of one such factor, the Paf1 complex (Paf1C), generate subunit-specific phenotypes, including distinct changes to co-transcriptional histone modifications. How individual Paf1C subunits impact transcription and coupled processes remains ambiguous. By comparing conditional depletion and steady-state deletion of Paf1C subunits, we determine direct and indirect contributions of Paf1C to gene expression in Saccharomyces cerevisiae. Through nascent transcript sequencing, RNAPII profiling, and mechanistic modeling of transcription elongation dynamics, we find evidence for unique roles of Paf1C subunits in regulating RNAPII processivity, elongation rate, mRNA stability, transcript splicing, and repression of antisense transcripts. Through genetic suppression, we attribute increased antisense transcription, but not other defects, of a PAF1 mutant to loss of H3 K36 methylation. This work comprehensively analyzes both the immediate and extended roles of Paf1C subunits in transcription elongation and transcript regulation.
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| Overall design |
4-thiouracil sequencing of Paf1C mutants, Paf1C-rapid depletion alleles, and genetic interrogation of H3K36me contributions to Paf1C-dependent phenotypes.
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| Contributor(s) |
Francette A, Arndt K |
| Citation(s) |
38712269 |
| Submission date |
Feb 08, 2024 |
| Last update date |
May 16, 2024 |
| Contact name |
Karen Arndt |
| E-mail(s) |
arndt@pitt.edu
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| Organization name |
University of Pittsburgh
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| Department |
Biological Sciences
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| Lab |
A316 Langley Hall
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| Street address |
4249 Fifth Ave
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| City |
Pittsburgh |
| State/province |
PA |
| ZIP/Postal code |
15260 |
| Country |
USA |
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| Platforms (1) |
| GPL28173 |
Illumina NextSeq 500 (Saccharomyces cerevisiae; Schizosaccharomyces pombe) |
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| Samples (12)
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| GSM8070524 |
ctr9D, Total, Rep2, Paf1CD |
| GSM8070525 |
leo1D, Total, Rep1, Paf1CD |
| GSM8070526 |
leo1D, Total, Rep2, Paf1CD |
| GSM8070527 |
paf1D, Total, Rep1, Paf1CD |
| GSM8070528 |
paf1D, Total, Rep2, Paf1CD |
| GSM8070529 |
rtf1D, Total, Rep1, Paf1CD |
| GSM8070530 |
rtf1D, Total, Rep2, Paf1CD |
| GSM8070531 |
Wt, Total, Rep1, Paf1CD |
| GSM8070532 |
Wt, Total, Rep2, Paf1CD |
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| Relations |
| BioProject |
PRJNA1074747 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE255362_RAW.tar |
254.3 Mb |
(http)(custom) |
TAR (of BW) |
SRA Run Selector |
| Raw data are available in SRA |
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