Cited by 186RNA Research and SplicingRNA and protein synthesis mechanismsHemoglobinopathies and Related Disorders

Co-transcriptional splicing regulates 3′ end cleavage during mammalian erythropoiesis

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Reimer, Kirsten A., Mimoso, Claudia A., Adelman, Karen, Neugebauer, Karla M.·2021·Molecular Cell

Published version of a preprint

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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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)
OpenAlex
W3121080183
Cited by
180
References
102
Citations by year
2026: 21 · 2025: 26 · 2024: 41 · 2023: 31 · 2022: 34 · 2021: 22 · 2020: 5
FWCI
10.52
Type
journal article
Language
en
Open access
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 › 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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