Skip to main content
bioRxiv
  • Home
  • About
  • Submit
  • ALERTS / RSS
Advanced Search
New Results

pre-mRNA spatial distributions suggest that splicing can occur post-transcriptionally

Allison Coté, Chris Coté, Sareh Bayatpour, Heather L. Drexler, Katherine A. Alexander, Fei Chen, Asmamaw T. Wassie, View ORCID ProfileEdward S. Boyden, Shelley Berger, L. Stirling Churchman, Arjun Raj
doi: https://doi.org/10.1101/2020.04.06.028092
Allison Coté
1Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Chris Coté
1Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Sareh Bayatpour
1Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Heather L. Drexler
2Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Katherine A. Alexander
3Department of Cell and Developmental Biology, Penn Institute of Epigenetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Fei Chen
4Broad Institute of MIT and Harvard, Cambridge, MA 02142
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Asmamaw T. Wassie
5Departments of Biological Engineering and Brain and Cognitive Sciences, Media Lab and McGovern Institute, Massachusetts Institute of Technology, Cambridge, MA 02139
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Edward S. Boyden
5Departments of Biological Engineering and Brain and Cognitive Sciences, Media Lab and McGovern Institute, Massachusetts Institute of Technology, Cambridge, MA 02139
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Edward S. Boyden
Shelley Berger
3Department of Cell and Developmental Biology, Penn Institute of Epigenetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
L. Stirling Churchman
2Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA 02115
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Arjun Raj
1Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • For correspondence: arjunrajlab@gmail.com
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Supplementary material
  • Data/Code
  • Preview PDF
Loading

Abstract

Splicing is the molecular process by which introns are removed from pre-mRNA and exons are joined together to form the sequence of the mature mRNA. While the biochemical steps of splicing have been largely worked out, the ordering and spatial distribution of these steps, especially in relation to the transcriptional process itself, remain controversial. Here, we use single molecule RNA FISH together with expansion microscopy to measure the spatial distribution of nascent and partially spliced transcripts in mammalian cells, allowing us to infer the order in which an intron is transcribed and spliced out of the pre-mRNA. We show that 4 out of 4 genes we interrogated exhibit clear post-transcriptional splicing of at least one intron, and that introns can be spliced in any order. Expansion microscopy further revealed the presence of a transcription site proximal zone in which the motion of RNA is slower than in the nucleoplasm. Full length pre-mRNA undergo continuous splicing as they move through this zone after transcription. Upon leaving this zone, some genes’ transcripts localize to speckles during the process of splicing while others appear to traffic freely through the nucleus without localizing to any other nuclear compartment. Our results suggest a model in which transcription and splicing are largely independent, and the existence of a slow moving zone around the transcription site allows for the unification of co-transcriptional and post-transcriptional models of splicing.

Competing Interest Statement

AR receives royalties related to Stellaris RNA FISH products from LGC/Biosearch Technologies.

Footnotes

  • https://www.dropbox.com/sh/sqr9zk2icptemfa/AABHRHroWbcowgPr_4VS2x9ba?dl=0

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
Back to top
PreviousNext
Posted June 29, 2021.
Download PDF

Supplementary Material

Data/Code
Email

Thank you for your interest in spreading the word about bioRxiv.

NOTE: Your email address is requested solely to identify you as the sender of this article.

Enter multiple addresses on separate lines or separate them with commas.
pre-mRNA spatial distributions suggest that splicing can occur post-transcriptionally
(Your Name) has forwarded a page to you from bioRxiv
(Your Name) thought you would like to see this page from the bioRxiv website.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
pre-mRNA spatial distributions suggest that splicing can occur post-transcriptionally
Allison Coté, Chris Coté, Sareh Bayatpour, Heather L. Drexler, Katherine A. Alexander, Fei Chen, Asmamaw T. Wassie, Edward S. Boyden, Shelley Berger, L. Stirling Churchman, Arjun Raj
bioRxiv 2020.04.06.028092; doi: https://doi.org/10.1101/2020.04.06.028092
Digg logo Reddit logo Twitter logo Facebook logo Google logo LinkedIn logo Mendeley logo
Citation Tools
pre-mRNA spatial distributions suggest that splicing can occur post-transcriptionally
Allison Coté, Chris Coté, Sareh Bayatpour, Heather L. Drexler, Katherine A. Alexander, Fei Chen, Asmamaw T. Wassie, Edward S. Boyden, Shelley Berger, L. Stirling Churchman, Arjun Raj
bioRxiv 2020.04.06.028092; doi: https://doi.org/10.1101/2020.04.06.028092

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
  • Tweet Widget
  • Facebook Like
  • Google Plus One

Subject Area

  • Cell Biology
Subject Areas
All Articles
  • Animal Behavior and Cognition (3686)
  • Biochemistry (7774)
  • Bioengineering (5668)
  • Bioinformatics (21245)
  • Biophysics (10563)
  • Cancer Biology (8162)
  • Cell Biology (11915)
  • Clinical Trials (138)
  • Developmental Biology (6738)
  • Ecology (10388)
  • Epidemiology (2065)
  • Evolutionary Biology (13843)
  • Genetics (9694)
  • Genomics (13056)
  • Immunology (8123)
  • Microbiology (19956)
  • Molecular Biology (7833)
  • Neuroscience (42973)
  • Paleontology (318)
  • Pathology (1276)
  • Pharmacology and Toxicology (2256)
  • Physiology (3350)
  • Plant Biology (7208)
  • Scientific Communication and Education (1309)
  • Synthetic Biology (1999)
  • Systems Biology (5528)
  • Zoology (1126)