title: Arabidopsis SWI/SNF chromatin remodeling complex binds both promoters and terminators to regulate gene expression.
abstract: ATP-dependent chromatin remodeling complexes are important regulators of gene expression in Eukaryotes. In plants, SWI/SNF-type complexes have been shown critical for transcriptional control of key developmental processes, growth and stress responses. To gain insight into mechanisms underlying these roles, we performed whole genome mapping of the SWI/SNF catalytic subunit BRM in Arabidopsis thaliana, combined with transcript profiling experiments. Our data show that BRM occupies thousands of sites in Arabidopsis genome, most of which located within or close to genes. Among identified direct BRM transcriptional targets almost equal numbers were up- and downregulated upon BRM depletion, suggesting that BRM can act as both activator and repressor of gene expression. Interestingly, in addition to genes showing canonical pattern of BRM enrichment near transcription start site, many other genes showed a transcription termination site-centred BRM occupancy profile. We found that BRM-bound 3΄ gene regions have promoter-like features, including presence of TATA boxes and high H3K4me3 levels, and possess high antisense transcriptional activity which is subjected to both activation and repression by SWI/SNF complex. Our data suggest that binding to gene terminators and controlling transcription of non-coding RNAs is another way through which SWI/SNF complex regulates expression of its targets.
authors.affiliation: Laboratory of Systems Biology, Faculty of Biology, University of Warsaw, Warsaw 02-096, Poland.|Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw 02-106, Poland.
authors.forename: Rafal
authors.initials: R
authors.lastname: Archacki
authors.affiliation: Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw 02-106, Poland.
authors.forename: Ruslan
authors.initials: R
authors.lastname: Yatusevich
authors.affiliation: Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw 02-106, Poland.
authors.forename: Daniel
authors.initials: D
authors.lastname: Buszewicz
authors.affiliation: Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw 02-106, Poland.
authors.forename: Katarzyna
authors.initials: K
authors.lastname: Krzyczmonik
authors.affiliation: Laboratory of Systems Biology, Faculty of Biology, University of Warsaw, Warsaw 02-096, Poland.|College of Inter-FacultyIndividual Studies in Mathematics and Natural Sciences, Warsaw 02-089, Poland.
authors.forename: Jacek
authors.initials: J
authors.lastname: Patryn
authors.affiliation: Laboratory of Systems Biology, Faculty of Biology, University of Warsaw, Warsaw 02-096, Poland.|Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw 02-106, Poland.
authors.forename: Roksana
authors.initials: R
authors.lastname: Iwanicka-Nowicka
authors.affiliation: Institute of Informatics, Faculty of Mathematics, Informatics and Mechanics,University of Warsaw, Warsaw 02-097, Poland.|Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw 00-662, Poland.
authors.forename: Przemyslaw
authors.initials: P
authors.lastname: Biecek
authors.affiliation: Institute of Informatics, Faculty of Mathematics, Informatics and Mechanics,University of Warsaw, Warsaw 02-097, Poland.
authors.forename: Bartek
authors.initials: B
authors.lastname: Wilczynski
authors.affiliation: Laboratory of Systems Biology, Faculty of Biology, University of Warsaw, Warsaw 02-096, Poland.|Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw 02-106, Poland.
authors.forename: Marta
authors.initials: M
authors.lastname: Koblowska
authors.affiliation: Laboratory of Systems Biology, Faculty of Biology, University of Warsaw, Warsaw 02-096, Poland.|Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw 02-106, Poland.
authors.forename: Andrzej
authors.initials: A
authors.lastname: Jerzmanowski
authors.affiliation: Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw 02-106, Poland.
authors.forename: Szymon
authors.initials: S
authors.lastname: Swiezewski
mesh_terms: D024509:3' Flanking Region; D000251:Adenosine Triphosphatases / Q000378:metabolism*; D017360:Arabidopsis / Q000235:genetics* / Q000378:metabolism; D029681:Arabidopsis Proteins / Q000378:metabolism*; D001665:Binding Sites; D018506:Gene Expression Regulation, Plant; D011401:Promoter Regions, Genetic; D016372:RNA, Antisense / Q000096:biosynthesis; D012333:RNA, Messenger / Q000096:biosynthesis; D013728:Terminator Regions, Genetic; D014158:Transcription, Genetic
chemical_list: D029681:Arabidopsis Proteins; D016372:RNA, Antisense; D012333:RNA, Messenger; D000251:Adenosine Triphosphatases; C514541:BRM protein, Arabidopsis