SAM homeostasis is regulated by CFIm-mediated splicing of MAT2A
- University of Texas Southwestern Medical Center, United States
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.
-
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.
Article and author information
Author details
Anna M Scarborough
Juliana N Flaherty
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
- Eric J Wagner, University of Texas Medical Branch at Galveston, United States
Version history
- Received: November 16, 2020
- Accepted: May 3, 2021
- Accepted Manuscript published: May 5, 2021 (version 1)
- 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.
Metrics
-
- 2,055
- views
-
- 317
- downloads
-
- 22
- citations
Views, downloads and citations are aggregated across all versions of this paper published by eLife.
Download links
A two-part list of links to download the article, or parts of the article, in various formats.
Downloads (link to download the article as PDF)
Open citations (links to open the citations from this article in various online reference manager services)
Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)
SAM homeostasis is regulated by CFIm-mediated splicing of MAT2A
eLife 10:e64930.
https://doi.org/10.7554/eLife.64930
Further reading
-
- Chromosomes and Gene Expression
- Immunology and Inflammation
Ikaros is a transcriptional factor required for conventional T cell development, differentiation, and anergy. While the related factors Helios and Eos have defined roles in regulatory T cells (Treg), a role for Ikaros has not been established. To determine the function of Ikaros in the Treg lineage, we generated mice with Treg-specific deletion of the Ikaros gene (Ikzf1). We find that Ikaros cooperates with Foxp3 to establish a major portion of the Treg epigenome and transcriptome. Ikaros-deficient Treg exhibit Th1-like gene expression with abnormal production of IL-2, IFNg, TNFa, and factors involved in Wnt and Notch signaling. While Ikzf1-Treg-cko mice do not develop spontaneous autoimmunity, Ikaros-deficient Treg are unable to control conventional T cell-mediated immune pathology in response to TCR and inflammatory stimuli in models of IBD and organ transplantation. These studies establish Ikaros as a core factor required in Treg for tolerance and the control of inflammatory immune responses.
-
- Cell Biology
- Chromosomes and Gene Expression
Heat stress is a major threat to global crop production, and understanding its impact on plant fertility is crucial for developing climate-resilient crops. Despite the known negative effects of heat stress on plant reproduction, the underlying molecular mechanisms remain poorly understood. Here, we investigated the impact of elevated temperature on centromere structure and chromosome segregation during meiosis in Arabidopsis thaliana. Consistent with previous studies, heat stress leads to a decline in fertility and micronuclei formation in pollen mother cells. Our results reveal that elevated temperature causes a decrease in the amount of centromeric histone and the kinetochore protein BMF1 at meiotic centromeres with increasing temperature. Furthermore, we show that heat stress increases the duration of meiotic divisions and prolongs the activity of the spindle assembly checkpoint during meiosis I, indicating an impaired efficiency of the kinetochore attachments to spindle microtubules. Our analysis of mutants with reduced levels of centromeric histone suggests that weakened centromeres sensitize plants to elevated temperature, resulting in meiotic defects and reduced fertility even at moderate temperatures. These results indicate that the structure and functionality of meiotic centromeres in Arabidopsis are highly sensitive to heat stress, and suggest that centromeres and kinetochores may represent a critical bottleneck in plant adaptation to increasing temperatures.
