|
| Status |
Public on May 13, 2021 |
| Title |
Dynamic imaging of nascent RNA reveals general principles of transcription dynamics and pervasive recursive splicing |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
Other
|
| Summary |
The coupled activities of RNA polymerase and the spliceosome are responsible for the abundance and isoform composition of mRNA in human cells. However, the dynamics of these megadalton enzymatic complexes working in concert on endogenous genes have not been described. Here, we establish a quasi-genome-scale platform for observing synthesis and processing kinetics of single nascent RNA molecules in real time. We find that all observed genes show transcriptional bursting. We also observe large kinetic variation in intron removal for single introns in single cells which is inconsistent with deterministic splice site selection. Transcriptome-wide footprinting of the U2AF complex further reveals widespread splice site selection within introns. We propose and validate a unified theoretical model for transcription and splicing based on pervasive stochastic recursive splicing.
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| |
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| Overall design |
Refer to individual Series
|
| |
|
| Contributor(s) |
Wan Y, Anastasakis DG, Hafner M, Larson DR |
| Citation(s) |
33979654 |
| |
| Submission date |
Jul 16, 2019 |
| Last update date |
Jun 15, 2021 |
| Contact name |
Daniel R Larson |
| E-mail(s) |
[email protected]
|
| Organization name |
NIH
|
| Street address |
41 Medlar Dr.
|
| City |
Bethesda |
| ZIP/Postal code |
20892 |
| Country |
USA |
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| Platforms (4)
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| Samples (23)
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| GSM3945682 |
Sample_F2 |
| GSM3945683 |
Sample_Input_A1 |
| GSM3945684 |
Sample_Input_A2 |
| GSM3945685 |
Sample_Input_F1 |
| GSM3945686 |
Sample_Input_F2 |
| GSM3945687 |
Primer extension sequencing (RAB7A) |
| GSM3945688 |
U2AF complex PARCLIP (nuclear fraction) |
| GSM3945689 |
U2AF complex PARCLIP (whole cell) |
| GSM5381363 |
HBECs_1 (Nanopore) |
| GSM5381364 |
HBECs_2 (Nanopore) |
| GSM5381365 |
HEK_siCtrl_A |
| GSM5381366 |
HEK_siCtrl_B |
| GSM5381367 |
HEK_siDBR1_A |
| GSM5381368 |
HEK_siDBR1_B |
| GSM5381369 |
HBECs, pulse chase Nascent RNA-seq, rep_A_10min |
| GSM5381370 |
HBECs, pulse chase Nascent RNA-seq, rep_A_20min |
| GSM5381371 |
HBECs, pulse chase Nascent RNA-seq, rep_A_40min |
| GSM5381372 |
HBECs, pulse chase Nascent RNA-seq, rep_B_5min |
| GSM5381373 |
HBECs, pulse chase Nascent RNA-seq, rep_B_10min |
| GSM5381374 |
HBECs, pulse chase Nascent RNA-seq, rep_B_20min |
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| This SuperSeries is composed of the following SubSeries:
|
| GSE134392 |
Dynamic imaging of nascent RNA reveals general principles of transcription dynamics and pervasive recursive splicing [nascent RNA profiling] |
| GSE134393 |
Dynamic imaging of nascent RNA reveals general principles of transcription dynamics and pervasive recursive splicing [primer extension] |
| GSE134394 |
Dynamic imaging of nascent RNA reveals general principles of transcription dynamics and pervasive recursive splicing [PARCLIP] |
| GSE178180 |
Dynamic imaging of nascent RNA reveals general principles of transcription dynamics and pervasive recursive splicing [Nanopore] |
| GSE178181 |
Dynamic imaging of nascent RNA reveals general principles of transcription dynamics and pervasive recursive splicing [Lariat seq] |
| GSE178182 |
Dynamic imaging of nascent RNA reveals general principles of transcription dynamics and pervasive recursive splicing [pulse_chase_nascent RNA] |
|
| Relations |
| BioProject |
PRJNA555160 |
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