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Co-transcriptional splicing regulates 3′ end cleavage during mammalian erythropoiesis
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Abstract
Pre-mRNA processing steps are tightly coordinated with transcription in many organisms. To determine how co-transcriptional splicing is integrated with transcription elongation and 3' end formation in mammalian cells, we performed long-read sequencing of individual nascent RNAs and precision run-on sequencing (PRO-seq) during mouse erythropoiesis. Splicing was not accompanied by transcriptional pausing and was detected when RNA polymerase II (Pol II) was within 75-300 nucleotides of 3' splice sites (3'SSs), often during transcription of the downstream exon. Interestingly, several hundred introns displayed abundant splicing intermediates, suggesting that splicing delays can take place between the two catalytic steps. Overall, splicing efficiencies were correlated among introns within the same transcript, and intron retention was associated with inefficient 3' end cleavage. Remarkably, a thalassemia patient-derived mutation introducing a cryptic 3'SS improved both splicing and 3' end cleavage of individual β-globin transcripts, demonstrating functional coupling between the two co-transcriptional processes as a determinant of productive gene output.
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“Pro-seq was conducted largely according to published protocols with slight modifications (Reimer et al., 2021).”
From Mapping information-rich genotype-phenotype landscapes with genome-scale Perturb-seq (2022) · cites this paper as Reimer et al., 2021
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Metadata
- Authors
- Reimer, K. A., Mimoso, C. A., Adelman, K., & Neugebauer, K. M.
- Affiliations
- Yale University (US)
- Harvard University (US)
- Corresponding author
- Neugebauer, Karla M.
- Venue
- Molecular Cell
- Publisher
- Elsevier BV
- Published
- 2021-03
- Volume
- 81
- Issue
- 5
- Pages
- 998-1012.e7
- ISSN
- 1097-2765 (ISSN-L)
- PMC
- PMC8038867
- OpenAlex
- W3121080183
- Cited by
- 180
- References
- 102
- Citations by year
- 2026: 21 · 2025: 26 · 2024: 41 · 2023: 31 · 2022: 34 · 2021: 22
- FWCI
- 10.52
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Molecular Cell (publishedVersion)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Funders
- National Institutes of Health
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Health Sciences › Medicine › Genetics (clinical) › Hemoglobinopathies and Related Disorders
- Keywords
- co-transcriptional splicing, 3' end cleavage, erythropoiesis, pre-mRNA processing, transcription elongation, RNA polymerase II, 3' splice site, splicing intermediates, intron retention, splicing efficiency, thalassemia, beta-globin, cryptic splice site, nascent RNA
- MeSH terms
- Animals, Base Sequence, Cell Differentiation, Erythropoiesis, Exons, Humans, Introns, Leukocytes, Mutation, RNA Polymerase II, RNA Splicing, beta-Thalassemia, Spliceosomes, RNA Splice Sites, Erythroid Cells, Cell Line, Tumor, Mice, beta-Globins, RNA Cleavage, Transcription Elongation, Genetic
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