ABSTRACT
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 DNA damage. We showed that KDM3A undergoes phosphorylation by PKA at serine 265 following DNA damage, 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.
Subject(s)
Acetyltransferases/metabolism , Alternative Splicing , Breast Neoplasms/pathology , DNA-Binding Proteins/metabolism , Gene Expression Regulation, Neoplastic , Jumonji Domain-Containing Histone Demethylases/metabolism , Serine-Arginine Splicing Factors/metabolism , Transcription Factors/metabolism , Acetyltransferases/genetics , Breast Neoplasms/genetics , Breast Neoplasms/metabolism , DNA Damage , DNA-Binding Proteins/genetics , Humans , Jumonji Domain-Containing Histone Demethylases/genetics , MCF-7 Cells , Phosphorylation , Protein Binding , RNA Precursors/genetics , RNA Precursors/metabolism , Serine-Arginine Splicing Factors/genetics , Transcription Factors/geneticsABSTRACT
Pre-mRNA splicing is a fundamental process in mammalian gene expression, and alternative splicing plays an extensive role in generating protein diversity. Because the majority of genes undergo pre-mRNA splicing, most cellular processes depend on proper spliceosome function. We focus on the cell cycle and describe its dependence on pre-mRNA splicing and accurate alternative splicing. We outline the key cell-cycle factors and their known alternative splicing isoforms. We discuss different levels of pre-mRNA splicing regulation such as post-translational modifications and changes in the expression of splicing factors. We describe the effect of chromatin dynamics on pre-mRNA splicing during the cell cycle. In addition, we focus on spliceosome component SF3B1, which is mutated in many types of cancer, and describe the link between SF3B1 and its inhibitors and the cell cycle.
