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.
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.
NUDT21 regulates intron detention of the SAM synthetase MAT2A RNANCBI Gene Expression Omnibus, GSE158591.
CRISPR screen identifies NUDT21 as a regulator of intron detention of the SAM synthetase MAT2A RNANCBI Gene Expression Omnibus, GSE172217.
Genome-wide analysis of pre-mRNA 3' end processing reveals a decisive role of human cleavage factor I in the regulation of 3' UTR length: CLIPNCBI Gene Expression Omnibus, GSE37398.
- Nicholas K Conrad
- Nicholas K Conrad
- Juliana N Flaherty
- Anna M Scarborough
- Benjamin P Tu
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
- Eric J Wagner, University of Texas Medical Branch at Galveston, United States
- Received: November 16, 2020
- Accepted: May 3, 2021
- Accepted Manuscript published: May 5, 2021 (version 1)
© 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.