Journal
NATURE CHEMICAL BIOLOGY
Volume 13, Issue 5, Pages 501-+Publisher
NATURE PUBLISHING GROUP
DOI: 10.1038/NCHEMBIO.2317
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Funding
- National Science Foundation [1349248]
- Harvard Medical School Center of Excellence in Systems Pharmacology NIH [P50 GM107618]
- Giovanni Armenise-Harvard Foundation
- [R01 MH101528-01]
- [NHGRI: R01 HG007173]
- Direct For Biological Sciences
- Div Of Molecular and Cellular Bioscience [1349248] Funding Source: National Science Foundation
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Pharmacological perturbation is a powerful tool for understanding mRNA synthesis, but identification of the specific steps of this multi-step process that are targeted by small molecules remains challenging. Here we applied strand-specific total RNA sequencing (RNA-seq) to identify and distinguish specific pharmacological effects on transcription and pre-mRNA processing in human cells. We found unexpectedly that the natural product isoginkgetin, previously described as a splicing inhibitor, inhibits transcription elongation. Compared to well-characterized elongation inhibitors that target CDK9, isoginkgetin caused RNA polymerase accumulation within a broader promoter-proximal band, indicating that elongation inhibition by isoginkgetin occurs after release from promoter-proximal pause. RNA-seq distinguished isoginkgetin and CDK9 inhibitors from topoisomerase I inhibition, which alters elongation across gene bodies. We were able to detect these and other specific defects in mRNA synthesis at low sequencing depth using simple metagene-based metrics. These metrics now enable total-RNA-seq-based screening for high-throughput identification of pharmacological effects on individual stages of mRNA synthesis.
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