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The coiled-coil protein FLL2 is known to promote liquid–liquid phase separation in the polyadenylation complex, however, the role of FLL2 in polyadenylation remains unclear. Here, we investigated the impact of a developmental mutant sof78 in FLL2 gene of Arabidopsis leading to many effects on primary root, flowering time and developmental alterations, and tolerance to oxidative stress. To explore the relationship between FLL2 and CPSF73, we employed a boron-containing benzoxaborole compound AN3661, a known inhibitor of the poly(A) factor CPSF73. Our results indicate when treated with AN3661, the phenotypic responses of the sof78 mutant were similar to that control line C2, suggesting both CPSF73 and FLL2 co-modulated the growth and adaptation. Using poly(A) tag sequencing (PAT-seq) to compile poly(A) sites at the transcriptome level, we discovered 2.2% ~12.8% of significant differentially expressed alternative polyadenylation (APA) events were changed in sof78, upon AN3661 or oxidative treatment. Under such conditions, transcripts in sof78 exhibited a preference of less U and more G in their poly(A) signals, along with decreased the usage of canonical poly(A) sites in 3′UTRs but increased the usage of non-canonical poly(A) sites in other genic regions. Gene ontology analyses demonstrate that these APA genes are enriched in abiotic stress, osmotic stress, auxin signaling, and ethylene signaling pathways, which were identified and linked to respective phenotypes. These results provide functional linkages between FLL2 and CPSF73 mediated by APA in critical genes for plant development and environmental responses.
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Regulation of alternative polyadenylation in the yeast Saccharomyces cerevisiae by histone H3K4 and H3K36 methyltransferases
Abstract Adjusting DNA structure via epigenetic modifications, and altering polyadenylation (pA) sites at which precursor mRNA is cleaved and polyadenylated, allows cells to quickly respond to environmental stress. Since polyadenylation occurs co-transcriptionally, and specific patterns of nucleosome positioning and chromatin modifications correlate with pA site usage, epigenetic factors potentially affect alternative polyadenylation (APA). We report that the histone H3K4 methyltransferase Set1, and the histone H3K36 methyltransferase Set2, control choice of pA site in Saccharomyces cerevisiae, a powerful model for studying evolutionarily conserved eukaryotic processes. Deletion of SET1 or SET2 causes an increase in serine-2 phosphorylation within the C-terminal domain of RNA polymerase II (RNAP II) and in the recruitment of the cleavage/polyadenylation complex, both of which could cause the observed switch in pA site usage. Chemical inhibition of TOR signaling, which causes nutritional stress, results in Set1- and Set2-dependent APA. In addition, Set1 and Set2 decrease efficiency of using single pA sites, and control nucleosome occupancy around pA sites. Overall, our study suggests that the methyltransferases Set1 and Set2 regulate APA induced by nutritional stress, affect the RNAP II C-terminal domain phosphorylation at Ser2, and control recruitment of the 3′ end processing machinery to the vicinity of pA sites.
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- Award ID(s):
- 1714603
- PAR ID:
- 10185071
- Date Published:
- Journal Name:
- Nucleic Acids Research
- Volume:
- 48
- Issue:
- 10
- ISSN:
- 0305-1048
- Page Range / eLocation ID:
- 5407 to 5425
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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- Free Publicly Accessible Full Text
-
Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.1093/nar/gkaa292
