title: SWI/SNF regulates the alternative processing of a specific subset of pre-mRNAs in Drosophila melanogaster.
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.
authors: Department of Molecular Biology and Functional Genomics, Stockholm University, SE-10691 Stockholm, Sweden.
authors: Johan
authors: J
authors: Waldholm
authors: Zhi
authors: Z
authors: Wang
authors: David
authors: D
authors: Brodin
authors: Anu
authors: A
authors: Tyagi
authors: Simei
authors: S
authors: Yu
authors: Ulrich
authors: U
authors: Theopold
authors: Ann Kristin Östlund
authors: AK
authors: Farrants
authors: Neus
authors: N
authors: Visa
mesh_terms: D017398:Alternative Splicing; D000818:Animals; D018797:Cell Cycle Proteins / Q000235:genetics / Q000378:metabolism; D029721:Drosophila Proteins / Q000235:genetics / Q000378:metabolism*; D004331:Drosophila melanogaster / Q000235:genetics / Q000378:metabolism*; D005786:Gene Expression Regulation; D012322:RNA Precursors / Q000235:genetics / Q000378:metabolism; D017412:Ribonucleoprotein, U1 Small Nuclear / Q000235:genetics / Q000378:metabolism*; D015534:Trans-Activators / Q000235:genetics / Q000378:metabolism
chemical_list: D018797:Cell Cycle Proteins; D029721:Drosophila Proteins; D012322:RNA Precursors; D017412:Ribonucleoprotein, U1 Small Nuclear; C492947:SWI protein, D melanogaster; D015534:Trans-Activators; C086469:brm protein, Drosophila; C089969:snf protein, Drosophila