Abstract

S-adenosylmethionine (SAM) is the methyl donor for nearly all cellular methylation events. Cells regulate intracellular SAM levels through intron detention of MAT2A, the only SAM synthetase expressed in most cells. The N6-adenosine methyltransferase METTL16 promotes splicing of the MAT2A detained intron by an unknown mechanism. Using an unbiased CRISPR knock-out screen, we identified CFIm25 (NUDT21) as a regulator of MAT2A intron detention and intracellular SAM levels. CFIm25 is a component of the cleavage factor Im (CFIm) complex that regulates poly(A) site selection, but we show it promotes MAT2A splicing independent of poly(A) site selection. CFIm25-mediated MAT2A splicing induction requires the RS domains of its binding partners, CFIm68 and CFIm59 as well as binding sites in the detained intron and 3´ UTR. These studies uncover mechanisms that regulate MAT2A intron detention and reveal a previously undescribed role for CFIm in splicing and SAM metabolism.

Data availability

Raw and unedited CRISPR screen data is deposited on GEO (GSE172217). Raw and unedited Poly(A)-ClickSeq data is deposited on GEO (GSE158591). Analysis of Poly(A)-ClickSeq is found in Supplementary File 2.

The following data sets were generated
The following previously published data sets were used

Article and author information

Author details

  1. Anna M Scarborough

    Microbiology, University of Texas Southwestern Medical Center, Dallas, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0003-3621-234X
  2. Juliana N Flaherty

    Microbiology, University of Texas Southwestern Medical Center, Irving, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-9745-6762
  3. Olga V Hunter

    Microbiology, University of Texas Southwestern Medical Center, Dallas, United States
    Competing interests
    The authors declare that no competing interests exist.
  4. Kuanqing Liu

    Biochemistry, University of Texas Southwestern Medical Center, Dallas, United States
    Competing interests
    The authors declare that no competing interests exist.
  5. Ashwani Kumar

    Eugine McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, United States
    Competing interests
    The authors declare that no competing interests exist.
  6. Chao Xing

    Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-1838-0502
  7. Benjamin P Tu

    Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-5545-9183
  8. Nicholas K Conrad

    Microbiology, University of Texas Southwestern Medical Center, Dallas, United States
    For correspondence
    nicholas.conrad@utsouthwestern.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-8562-0895

Funding

Welch Foundation (I-1915-20170325)

  • Nicholas K Conrad

National Institute of General Medical Sciences (R01 GM127311)

  • Nicholas K Conrad

National Institute of General Medical Sciences (R01 GM127311-S1)

  • Juliana N Flaherty

National Institute of General Medical Sciences (T32 GM007062)

  • Anna M Scarborough

National Institute of General Medical Sciences (R35 GM136370)

  • Benjamin P Tu

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Eric J Wagner, University of Texas Medical Branch at Galveston, United States

Version history

  1. Received: November 16, 2020
  2. Accepted: May 3, 2021
  3. Accepted Manuscript published: May 5, 2021 (version 1)
  4. Version of Record published: May 21, 2021 (version 2)

Copyright

© 2021, Scarborough et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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  1. Anna M Scarborough
  2. Juliana N Flaherty
  3. Olga V Hunter
  4. Kuanqing Liu
  5. Ashwani Kumar
  6. Chao Xing
  7. Benjamin P Tu
  8. Nicholas K Conrad
(2021)
SAM homeostasis is regulated by CFIm-mediated splicing of MAT2A
eLife 10:e64930.
https://doi.org/10.7554/eLife.64930

Share this article

https://doi.org/10.7554/eLife.64930

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