 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Aug 15, 2011 |
| Title |
Transcriptional activity regulates alternative cleavage and polyadenylation |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
Genes containing multiple polyadenylation (polyA) sites express mRNA isoforms with variable 3’ untranslated regions (3’UTRs). We found that short and long 3’UTR isoforms were relatively more abundant when genes were highly and lowly expressed, respectively, in human and mouse cells. Consistently, upregulated and downregulated genes were more likely to have shortened and lengthened 3’UTRs, respectively, when genes changed expression under different cell conditions or in response to extracellular stimuli. Using nuclear run-on assays, we found that RNA polymerase II (Pol II) was more likely to pause at the polyA site of highly expressed genes than that of lowly expressed ones. Moreover, in line with the difference in polyA site usage, highly expressed genes tend to have higher H3K4me3 and H3K36me3 levels but a lower density of nucleosome around promoter-proximal polyA sites relative to distal ones. Taken together, our results indicate that the efficiency of 3’ end processing is generally coupled to transcriptional activity, leading to modulation of polyA site choice by transcription and thus connecting transcriptional control with post-transcriptional regulation via pre-mRNA processing.
|
| |
|
| Overall design |
Nascent RNA sequencing of C2C12 cell
|
| |
|
| Contributor(s) |
Ji Z, Luo W, Li W, Hoque M, Pan Z, Zhao Y, Tian B |
| Citation(s) |
21952137 |
| Submission date |
Jan 10, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Zhe Ji |
| E-mail(s) |
zhe.ji@northwestern.edu
|
| Organization name |
Northwestern University
|
| Street address |
303 E Superior St, Lurie 6-107
|
| City |
Chicago |
| State/province |
ILLINOIS |
| ZIP/Postal code |
60611 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL9250 |
Illumina Genome Analyzer II (Mus musculus) |
|
| Samples (1) |
| GSM651870 |
Nascent RNA sequencing of C2C12 cell |
|
| Relations |
| SRA |
SRP005283 |
| BioProject |
PRJNA136695 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE26512_RAW.tar |
44.7 Mb |
(http)(custom) |
TAR (of BED) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
