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| Status |
Public on Jun 28, 2019 |
| Title |
Paf1C regulates RNA polymerase II progression by modulating elongation rate |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Other
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| Summary |
Elongation factor Paf1C regulates several stages of the RNA polymerase II (Pol II) transcription cycle, although it is unclear how it modulates Pol II distribution and progression in mammalian cells. We found that conditional ablation of Paf1 resulted in the accumulation of unphosphorylated and Ser5 phosphorylated Pol II around promoter proximal regions and within the first 20-30 kb of gene bodies, respectively. Paf1 ablation did not impact the recruitment of other key elongation factors, namely, Spt5, Spt6, and the FACT complex, suggesting that Paf1 function may be mechanistically distinguishable from each of these factors. Moreover, loss of Paf1 triggered an increase in TSS-proximal nucleosome occupancy, which could impose a considerable barrier to Pol II elongation past TSS-proximal regions. Remarkably, accumulation of Ser5P in the first 20-30 kb coincided with reductions in histone H2B ubiquitylation within this region. Furthermore, we show that nascent RNA species accumulate within this window, suggesting a mechanism whereby Paf1 loss leads to aberrant, prematurely terminated transcripts and diminution of full-length transcripts. Importantly, we found that loss of Paf1 results in Pol II elongation rate defects with significant rate compression. Our findings suggest that Paf1C is critical for modulating Pol II elongation rates by functioning beyond the pause-release step as an "accelerator" over specific early gene body regions.
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| Overall design |
ChIP-seq, Pro-seq, ssRNA-seq, MNase-seq and ATAC-seq after conditional knockout Paf1 or siRNA-mediated knockdown of Paf1 in mouse C2C12 myoblast cells
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| Contributor(s) |
Hou L, Wang Y, Liu Y, Zhang N, Shamovsky I, Nudler E, Tian B, Dynlacht BD |
| Citation(s) |
31249142 |
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| Submission date |
Jun 22, 2018 |
| Last update date |
Jun 30, 2019 |
| Contact name |
Liming H ou |
| E-mail(s) |
mnhouliming@gmail.com
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| Organization name |
NYU Langone Health
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| Street address |
522 1st Av.
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| City |
New York |
| ZIP/Postal code |
10016 |
| Country |
USA |
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| Platforms (2) |
| GPL17021 |
Illumina HiSeq 2500 (Mus musculus) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
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| Samples (66)
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| GSM3212316 |
-dox_Pol2_ChIPSeq |
| GSM3212319 |
+dox_Pro-seq_rep1 |
| GSM3212320 |
-dox_Pro-seq_rep1 |
| GSM3212321 |
+dox_DRB_5min_Pro-seq_rep1 |
| GSM3212322 |
-dox_DRB_5min_Pro-seq_rep1 |
| GSM3212323 |
+dox_DRB_15min_Pro-seq_rep1 |
| GSM3212324 |
-dox_DRB_15min_Pro-seq_rep1 |
| GSM3212325 |
+dox_DRB_30min_Pro-seq_rep1 |
| GSM3212326 |
-dox_DRB_30min_Pro-seq_rep1 |
| GSM3212327 |
+dox_Pro-seq_rep2 |
| GSM3212328 |
-dox_Pro-seq_rep2 |
| GSM3212329 |
+dox_DRB_5min_Pro-seq_rep2 |
| GSM3212330 |
-dox_DRB_5min_Pro-seq_rep2 |
| GSM3212331 |
+dox_DRB_15min_Pro-seq_rep2 |
| GSM3212332 |
-dox_DRB_15min_Pro-seq_rep2 |
| GSM3212333 |
+dox_DRB_30min_Pro-seq_rep2 |
| GSM3212334 |
-dox_DRB_30min_Pro-seq_rep2 |
| GSM3212335 |
siNS_MNase-seq |
| GSM3212336 |
siPaf1_MNase-seq |
| GSM3212337 |
+dox_MNase-seq_rep1 |
| GSM3212338 |
-dox_MNase-seq_rep1 |
| GSM3212339 |
rescue_Mnase-seq_rep1 |
| GSM3212340 |
+dox_MNase-seq_rep2 |
| GSM3212341 |
-dox_MNase-seq_rep2 |
| GSM3212342 |
rescue_Mnase-seq_rep2 |
| GSM3212343 |
siNS_ATAC-seq_rep1 |
| GSM3212344 |
siPaf1_ATAC-seq_rep1 |
| GSM3212345 |
siNS_ATAC-seq_rep2 |
| GSM3212346 |
siPaf1_ATAC-seq_rep2 |
| GSM3212347 |
+dox_input DNA_H2Bub_ChIPSeq |
| GSM3212348 |
+dox_H2Bub_ChIPSeq |
| GSM3212349 |
-dox_input DNA_H2Bub_ChIPSeq |
| GSM3212350 |
-dox_H2Bub_ChIPSeq |
| GSM3212351 |
siNS_input DNA_H2Bub_ChIPSeq |
| GSM3212353 |
siNS_H2Bub_ChIPSeq |
| GSM3212354 |
siPaf1_input DNA_H2Bub_ChIPSeq |
| GSM3212356 |
siPaf1_H2Bub_ChIPSeq |
| GSM3212357 |
+dox_ssRNA-seq_rep1 |
| GSM3212358 |
-dox_ssRNA-seq_rep1 |
| GSM3212360 |
+dox_ssRNA-seq_rep2 |
| GSM3212361 |
-dox_ssRNA-seq_rep2 |
| GSM3212383 |
siNS_input DNA_ChIPSeq (Spt6) |
| GSM3212384 |
siNS_Spt6_ChIPSeq |
| GSM3212385 |
siPaf1_input DNA_ChIPSeq (Spt6) |
| GSM3212386 |
siPaf1_Spt6_ChIPSeq |
| GSM3897597 |
+dox_input DNA_ChIPSeq (Spt5,Spt16,Ser2P-rep1,Ser5P-rep1) |
| GSM3897598 |
-dox_4d_input DNA_ChIPSeq (Spt5,Spt16,Ser2P-rep1,Ser5P-rep1) |
| GSM3897599 |
+dox_Spt5_ChIPSeq |
| GSM3897600 |
-dox_4d_Spt5_ChIPSeq |
| GSM3897601 |
+dox_Ser2P_rep1_ChIPSeq |
| GSM3897602 |
-dox_4d_Ser2P_rep1_ChIPSeq |
| GSM3897603 |
+dox_Ser5P_rep1_ChIPSeq |
| GSM3897604 |
-dox_4d_Ser5P_rep1_ChIPSeq |
| GSM3897605 |
+dox_Spt16_ChIPSeq |
| GSM3897606 |
-dox_4d_Spt16_ChIPSeq |
| GSM3897607 |
+dox_Spt6_ChIPSeq |
| GSM3897608 |
-dox_4d_Spt6_ChIPSeq |
| GSM3897609 |
+dox_Ser2P_rep2_ChIPSeq |
| GSM3897610 |
-dox_4d_Ser2P_rep2_ChIPSeq |
| GSM3897611 |
+dox_Ser5P_rep2_ChIPSeq |
| GSM3897612 |
-dox_4d_Ser5P_rep2_ChIPSeq |
| GSM3897613 |
+dox_input DNA_ChIPSeq (Spt6,Ser2P-rep2,Ser5P-rep2) |
| GSM3897614 |
-dox_4d_input DNA_ChIPSeq (Spt6,Ser2P-rep2,Ser5P-rep2) |
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| Relations |
| BioProject |
PRJNA477543 |
| SRA |
SRP151141 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE116169_RAW.tar |
12.7 Gb |
(http)(custom) |
TAR (of BIGWIG) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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