Pre-mRNA splicing is a determinant of nucleosome organization

Abstract

Chromatin organization affects alternative splicing and previous studies have shown that exons have increased nucleosome occupancy compared with their flanking introns. To determine whether alternative splicing affects chromatin organization we developed a system in which the alternative splicing pattern switched from inclusion to skipping as a function of time. Changes in nucleosome occupancy were correlated with the change in the splicing pattern. Surprisingly, strengthening of the 59 splice site or strengthening the base pairing of U1 snRNA with an internal exon abrogated the skipping of the internal exons and also affected chromatin organization. Over-expression of splicing regulatory proteins also affected the splicing pattern and changed nucleosome occupancy. A specific splicing inhibitor was used to show that splicing impacts nucleosome organization endogenously. The effect of splicing on the chromatin required a functional U1 snRNA base pairing with the 59 splice site, but U1 pairing was not essential for U1 snRNA enhancement of transcription. Overall, these results suggest that splicing can affect chromatin organization. Citation: Keren-Shaul H, Lev-Maor G, Ast G (2013) Pre-mRNA Splicing Is a Determinant of Nucleosome Organization. PLoS ONE 8(1): e53506. doi:10.1371/ journal.pone.0053506 Editor: Emanuele Buratti, International Centre for Genetic Engineering and Biotechnology, Italy Received September 19, 2012; Accepted November 29, 2012; Published January 10, 2013 Copyright: 2013 Ast et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: This work was supported by a grant from the Israel Science Foundation (ISF 61/09; ISF bikura 838/10); Joint Germany-Israeli Research Program (ca-139); Deutsche-Israel Project (DIP MI-1317); and Israel Cancer Research Foundation. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. * E-mail: gilast@post.tau.ac.il . These authors contributed equally to this work.