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Open Access Highly Accessed Research article

SWI/SNF regulates the alternative processing of a specific subset of pre-mRNAs in Drosophila melanogaster

Johan Waldholm1, Zhi Wang1, David Brodin2, Anu Tyagi14, Simei Yu1, Ulrich Theopold1, Ann Kristin Östlund Farrants3 and Neus Visa1*

Author Affiliations

1 Department of Molecular Biology and Functional Genomics, Stockholm University, SE-10691 Stockholm, Sweden

2 Bioinformatics and Expression Analysis Core Facility, Department of Biosciences and Nutrition, Karolinska Institutet, SE-14157 Huddinge, Sweden

3 Wenner-Gren Institute, Stockholm University, SE-10691 Stockholm, Sweden

4 Department of Biochemistry, University of Würzburg, Am Hubland, D-97074 Würzburg, Germany

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BMC Molecular Biology 2011, 12:46  doi:10.1186/1471-2199-12-46

Published: 2 November 2011

Abstract

Background

The SWI/SNF chromatin remodeling factors have the ability to remodel nucleosomes and play essential roles in key developmental processes. SWI/SNF complexes contain one subunit with ATPase activity, which in Drosophila melanogaster is called Brahma (Brm). The regulatory activities of SWI/SNF have been attributed to its influence on chromatin structure and transcription regulation, but recent observations have revealed that the levels of Brm affect the relative abundances of transcripts that are formed by alternative splicing and/or polyadenylation of the same pre-mRNA.

Results

We have investigated whether the function of Brm in pre-mRNA processing in Drosophila melanogaster is mediated by Brm alone or by the SWI/SNF complex. We have analyzed the effects of depleting individual SWI/SNF subunits on pre-mRNA processing throughout the genome, and we have identified a subset of transcripts that are affected by depletion of the SWI/SNF core subunits Brm, Snr1 or Mor. The fact that depletion of different subunits targets a subset of common transcripts suggests that the SWI/SNF complex is responsible for the effects observed on pre-mRNA processing when knocking down Brm. We have also depleted Brm in larvae and we have shown that the levels of SWI/SNF affect the pre-mRNA processing outcome in vivo.

Conclusions

We have shown that SWI/SNF can modulate alternative pre-mRNA processing, not only in cultured cells but also in vivo. The effect is restricted to and specific for a subset of transcripts. Our results provide novel insights into the mechanisms by which SWI/SNF regulates transcript diversity and proteomic diversity in higher eukaryotes.