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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 [ChIP-seq] |
| Organisms |
Saccharomyces cerevisiae; Kluyveromyces lactis |
| Experiment type |
Genome binding/occupancy 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 |
ChIP sequencing of RNAPII localization upon long and short term inactivaiton of the Paf1 complex
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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) |
| GPL34174 |
Illumina NextSeq 500 (Kluyveromyces lactis; Saccharomyces cerevisiae) |
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| Samples (16)
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| GSM8070508 |
Ctr9, Aux, INPUT, Rep2 |
| GSM8070509 |
Ctr9, Veh, antiFLAG, Rep1 |
| GSM8070510 |
Ctr9, Veh, antiFLAG, Rep2 |
| GSM8070511 |
Ctr9, Veh, INPUT, Rep1 |
| GSM8070512 |
Ctr9, Veh, INPUT, Rep2 |
| GSM8070513 |
ctr9D, antiFLAG, Rep1 |
| GSM8070514 |
ctr9D, antiFLAG, Rep2 |
| GSM8070515 |
ctr9D, INPUT, Rep1 |
| GSM8070516 |
ctr9D, INPUT, Rep2 |
| GSM8070517 |
Wt, antiFLAG, Rep1 |
| GSM8070518 |
Wt, antiFLAG, Rep2 |
| GSM8070519 |
Wt, INPUT, Rep1 |
| GSM8070520 |
Wt, INPUT, Rep2 |
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| Relations |
| BioProject |
PRJNA1074743 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE255361_RAW.tar |
455.2 Mb |
(http)(custom) |
TAR (of BW) |
SRA Run Selector |
| Raw data are available in SRA |
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