Changes in the cellular environment result in chromatin structure alteration, which in turn regulates gene expression. To learn about the effect of the cellular environment on the transcriptome, we studied the H3K9 demethylase KDM3A. Using RNA-seq, we found that KDM3A regulates the transcription and alternative splicing of genes associated with cell cycle and DNAdamage.Weshowed thatKDM3A undergoes phosphorylation by PKA at serine 265 following DNAdamage, and that the phosphorylation is important for proper cell-cycle regulation. We demonstrated that SAT1 alternative splicing, regulated by KDM3A, plays a role in cell-cycle regulation. Furthermore we found that KDM3A's demethylase activity is not needed for SAT1 alternative splicing regulation. In addition, we identified KDM3A's protein partner ARID1A, the SWI/SNF subunit, and SRSF3 as regulators of SAT1 alternative splicing and showed that KDM3A is essential for SRSF3 binding to SAT1 pre-mRNA. These results suggest that KDM3A serves as a sensor of the environment and an adaptor for splicing factor binding. Our work reveals chromatin sensing of the environment in the regulation of alternative splicing.
Bibliographical noteFunding Information:
We thank Professor Juro Sakai and Professor Takeshi Inagaki for plasmids and p-KDM3A antibody. We thank Abed Nasereddin and Idit Shiff from the Genomic Applications Laboratory, The Core Research Facility, The Faculty of Medicine - Ein Kerem, The Hebrew University of Jerusalem, Israel, for their professional advice and RNA-seq service. We thank Maxim Mogilevsky for advice on oligo design. This work was in part supported by the Israeli Cancer Association, Alon Award by the Israeli Planning and Budgeting Committee (PBC), Israel Cancer Research Fund (ICRF), and the Israel Science Foundation (ISF 1154/17). The RNA-seq reagents were funded by a Core Lab Grant Program launched by Danyel Biotech, the authorized Illumina Channel Partner in Israel.
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- Alternative splicing
- Pre-mRNA splicing
- alternative splicing
- pre-mRNA splicing