Abstract B11: Coupling between the DNA methylation and the alternative splicing

Abstract Pre-messenger RNAs (pre-mRNAs) maturation is initiated cotranscriptionally and chromatin-borne information participates in alternative splicing. We have found recently that elevated levels of trimethylation of histone H3 on Lys9 (H3K9me3) and the chromodomain protein HP1γ are a characteristic of the alternative exons of several genes including CD44 (Saint-André et al. 2011). On this gene, we have shown that the endogenous RNA interference pathway is involved in the H3K9me3 targeting on the variant exons through the recruitment of the nuclear argonaute proteins (AGO1 or AGO2) (Ameyar-Zazoua et al. 2012). Because the DNA methylation is an epigenetic mark accompanying the transcriptional silencing, we now explore whether the DNA modification into the active genes could play a role in the regulation of the alternative splicing. Studying the transcriptome and the genome of murine ES cells, allowed us to show that the enzymes that methylate DNA (DNMT1, 3a and 3b) regulate the splicing of many genes. In Hela cells the DNMT1 depletion causes a decrease in the inclusion of alternative exons of CD44. Similar results were obtained after depletion of MBD1 and MBD2, two proteins that bind to methylated DNA. Together these results suggest that DNA methylation regulates splicing of CD44 by a direct mechanism involving MBD1 and MBD2. The disregulation of the DNA methylation on CpGs is a hallmark of the tumorigenesis. However, the effect of DNA methylation changes within coding regions of the genes is poorly understood. We used the well-known model of breast tumor progression based on the MCF10A cells, to investigate the changes into the DNA methylation of the CD44 coding region. We found that the intragenic DNA methylation is modified between the MCF10A parental cells and the derived DCIS and CA1A transformed cells and this is correlated with the inclusion of the CD44 alternative exons. Altogether these results suggest that modifications of DNA methylation could contribute to the disregulations of alternative splicing decisions contributing to the tumor progression. Ameyar-Zazoua M, Rachez C, Souidi M, Robin P, Fritsch L, Young R, Morozova N, Fenouil R, Descostes N, Andrau JC, Mathieu J, Hamiche A, Ait-Si-Ali S, Muchardt C, Harel-Bellan A, Batsché E (2012) Argonaute proteins couple chromatin silencing to alternative splicing. Nat. Struc. Mol. Biol 19:998-1004. Saint-André V., Batsché E., Rachez C. and Muchardt C. (2011) Histone H3 lysine 9 tri-methylation and HP1γ favor inclusion of alternative exons. Nat. Struc. Mol. Biol 18:337-44. Citation Format: Oriane Mauger, Christian Muchardt, Eric Batsché. Coupling between the DNA methylation and the alternative splicing. [abstract]. In: Proceedings of the AACR Special Conference on Chromatin and Epigenetics in Cancer; Jun 19-22, 2013; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2013;73(13 Suppl):Abstract nr B11.