title: Relationship between nucleosome positioning and progesterone-induced alternative splicing in breast cancer cells.
abstract: Splicing of mRNA precursors can occur cotranscriptionally and it has been proposed that chromatin structure influences splice site recognition and regulation. Here we have systematically explored potential links between nucleosome positioning and alternative splicing regulation upon progesterone stimulation of breast cancer cells. We confirm preferential nucleosome positioning in exons and report four distinct profiles of nucleosome density around alternatively spliced exons, with RNA polymerase II accumulation closely following nucleosome positioning. Hormone stimulation induces switches between profile classes, correlating with a subset of alternative splicing changes. Hormone-induced exon inclusion often correlates with higher nucleosome occupancy at the exon or the preceding intronic region and with higher RNA polymerase II accumulation. In contrast, exons skipped upon hormone stimulation display low nucleosome densities even before hormone treatment, suggesting that chromatin structure primes alternative splicing regulation. Skipped exons frequently harbor binding sites for hnRNP AB, a hormone-induced splicing regulator whose knock down prevents some hormone-induced skipping events. Collectively, our results argue that a variety of chromatin architecture mechanisms can influence alternative splicing decisions.
authors.forename: Camilla
authors.initials: C
authors.lastname: Iannone
authors.forename: Andy
authors.initials: A
authors.lastname: Pohl
authors.forename: Panagiotis
authors.initials: P
authors.lastname: Papasaikas
authors.forename: Daniel
authors.initials: D
authors.lastname: Soronellas
authors.forename: Guillermo P
authors.initials: GP
authors.lastname: Vicent
authors.forename: Miguel
authors.initials: M
authors.lastname: Beato
authors.forename: Juan
authors.initials: J
authors.lastname: ValcáRcel
mesh_terms: D017398:Alternative Splicing / Q000235:genetics*; D001943:Breast Neoplasms / Q000235:genetics* / Q000473:pathology; D045744:Cell Line, Tumor; D002843:Chromatin / Q000235:genetics / Q000378:metabolism; D005091:Exons / Q000235:genetics; D005260:Female; D006801:Humans; D007438:Introns / Q000235:genetics; D009707:Nucleosomes / Q000235:genetics* / Q000378:metabolism; D011374:Progesterone / Q000235:genetics / Q000378:metabolism*; D012319:RNA Polymerase II / Q000235:genetics; D022821:RNA Splice Sites / Q000235:genetics; D012333:RNA, Messenger / Q000235:genetics
chemical_list: D002843:Chromatin; D009707:Nucleosomes; D022821:RNA Splice Sites; D012333:RNA, Messenger; D011374:Progesterone; D012319:RNA Polymerase II