title: The transcriptionally active regions in the genome of Bacillus subtilis.
abstract: The majority of all genes have so far been identified and annotated systematically through in silico gene finding. Here we report the finding of 3662 strand-specific transcriptionally active regions (TARs) in the genome of Bacillus subtilis by the use of tiling arrays. We have measured the genome-wide expression during mid-exponential growth on rich (LB) and minimal (M9) medium. The identified TARs account for 77.3% of the genes as they are currently annotated and additionally we find 84 putative non-coding RNAs (ncRNAs) and 127 antisense transcripts. One ncRNA, ncr22, is predicted to act as a translational control on cstA and an antisense transcript was observed opposite the housekeeping sigma factor sigA. Through this work we have discovered a long conserved 3' untranslated region (UTR) in a group of membrane-associated genes that is predicted to fold into a large and highly stable secondary structure. One of the genes having this tail is efeN, which encodes a target of the twin-arginine translocase (Tat) protein translocation system.
authors.affiliation: Center for Biological Sequence Analysis, Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark.
authors.forename: Simon
authors.initials: S
authors.lastname: Rasmussen
authors.forename: Henrik Bjørn
authors.initials: HB
authors.lastname: Nielsen
authors.forename: Hanne
authors.initials: H
authors.lastname: Jarmer
mesh_terms: D001412:Bacillus subtilis / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism*; D001483:Base Sequence; D003470:Culture Media / Q000737:chemistry; D020869:Gene Expression Profiling / Q000379:methods*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D016372:RNA, Antisense / Q000096:biosynthesis; D022661:RNA, Untranslated / Q000096:biosynthesis; D014158:Transcription, Genetic
chemical_list: D003470:Culture Media; D016372:RNA, Antisense; D022661:RNA, Untranslated
references.citation: Mol Microbiol. 2003 Sep;49(6):1685-97
references.pmid: 12950930
references.citation: Bioinformatics. 2007 Nov 1;23(21):2947-8
references.pmid: 17846036
references.citation: FEMS Microbiol Rev. 1994 Dec;15(4):355-67
references.pmid: 7848659
references.citation: Bioinformatics. 2006 Aug 15;22(16):1963-70
references.pmid: 16787969
references.citation: J Bacteriol. 2004 Aug;186(15):4875-84
references.pmid: 15262924
references.citation: Nucleic Acids Res. 2005 Feb 17;33(3):1040-50
references.pmid: 15718303
references.citation: Nucleic Acids Res. 2007;35(19):e128
references.pmid: 17897965
references.citation: Nucleic Acids Res. 2006 May 22;34(9):2791-802
references.pmid: 16717284
references.citation: Proc Natl Acad Sci U S A. 2008 Aug 19;105(33):11927-32
references.pmid: 18697947
references.citation: J Bacteriol. 2006 Sep;188(17):6387-95
references.pmid: 16923906
references.citation: J Bacteriol. 2006 Jan;188(2):532-41
references.pmid: 16385044
references.citation: Mol Cell. 2006 Dec 8;24(5):747-757
references.pmid: 17157257
references.citation: J Bacteriol. 2009 Feb;191(3):1101-5
references.pmid: 19047346
references.citation: Proc Natl Acad Sci U S A. 2007 Oct 2;104(40):15641-6
references.pmid: 17901208
references.citation: J Bacteriol. 1961 May;81(5):741-6
references.pmid: 16561900
references.citation: Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W70-4
references.pmid: 18424795
references.citation: Nature. 2009 Feb 19;457(7232):1033-7
references.pmid: 19169243
references.citation: J Mol Biol. 1995 Jun 23;249(5):843-56
references.pmid: 7540694
references.citation: Microbiology (Reading). 1999 May;145 ( Pt 5):1055-1067
references.pmid: 10376821
references.citation: Mol Microbiol. 2005 Oct;58(1):189-206
references.pmid: 16164558
references.citation: Curr Opin Microbiol. 2007 Jun;10(3):262-70
references.pmid: 17574901
references.citation: J Bacteriol. 2006 May;188(10):3664-73
references.pmid: 16672620
references.citation: Science. 2004 Dec 24;306(5705):2242-6
references.pmid: 15539566
references.citation: J Bacteriol. 2003 Aug;185(15):4450-60
references.pmid: 12867454
references.citation: J Bacteriol. 1977 Jan;129(1):556-8
references.pmid: 401505
references.citation: Microbiology (Reading). 2001 Sep;147(Pt 9):2417-2424
references.pmid: 11535782
references.citation: Microbiology (Reading). 2005 Feb;151(Pt 2):399-420
references.pmid: 15699190
references.citation: Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W611-5
references.pmid: 15980547
references.citation: Genome Biol. 2007;8(2):R22
references.pmid: 17313685
references.citation: Nucleic Acids Res. 2002 Mar 15;30(6):1418-26
references.pmid: 11884641
references.citation: BMC Genomics. 2005 Mar 08;6:31
references.pmid: 15755320
references.citation: J Bacteriol. 1950 Jan;59(1):93-104
references.pmid: 15408888
references.citation: Microbiol Rev. 1995 Mar;59(1):1-30
references.pmid: 7708009
references.citation: Annu Rev Genet. 2005;39:47-68
references.pmid: 16285852
references.citation: J Bacteriol. 2005 Oct;187(19):6641-50
references.pmid: 16166525
references.citation: J Bacteriol. 2005 Apr;187(8):2758-67
references.pmid: 15805522
references.citation: Science. 2008 Jun 6;320(5881):1344-9
references.pmid: 18451266
references.citation: Microbiology (Reading). 2002 Aug;148(Pt 8):2591-2598
references.pmid: 12177353
references.citation: Microbiology (Reading). 2009 Jun;155(Pt 6):1758-1775
references.pmid: 19383706
references.citation: Nat Genet. 2006 Jan;38(1):124-9
references.pmid: 16369532
references.citation: Nature. 1997 Nov 20;390(6657):249-56
references.pmid: 9384377
references.citation: J Bacteriol. 2001 Dec;183(24):7318-28
references.pmid: 11717291
references.citation: J Biol Chem. 2000 May 12;275(19):14031-7
references.pmid: 10799476
references.citation: Am J Bot. 1947 Jun;34(6):345-8
references.pmid: 20252518
references.citation: Proc Natl Acad Sci U S A. 1958 Oct 15;44(10):1072-8
references.pmid: 16590310
references.citation: Proc Natl Acad Sci U S A. 2003 May 13;100(10):6115-20
references.pmid: 12721369
references.citation: Microbiology (Reading). 1995 Feb;141 ( Pt 2):323-7
references.pmid: 7704261
references.citation: J Bacteriol. 2004 Apr;186(8):2240-52
references.pmid: 15060025
references.citation: J Bacteriol. 2006 Jul;188(14):5273-85
references.pmid: 16816200
references.citation: J Bacteriol. 2008 Nov;190(21):6983-95
references.pmid: 18723616
references.citation: Bioinformatics. 2005 Dec 15;21(24):4322-9
references.pmid: 16249266
references.citation: Genome Res. 2002 Apr;12(4):656-64
references.pmid: 11932250
references.citation: Nucleic Acids Res. 2002 Sep 1;30(17):3732-8
references.pmid: 12202758
references.citation: Mol Microbiol. 2007 Jun;64(6):1605-20
references.pmid: 17555441
references.citation: FEMS Immunol Med Microbiol. 2008 Jul;53(2):195-203
references.pmid: 18430003
references.citation: Proc Natl Acad Sci U S A. 2006 Apr 4;103(14):5320-5
references.pmid: 16569694
references.citation: Nucleic Acids Res. 2008 Jan;36(Database issue):D480-4
references.pmid: 18077471
references.citation: J Biol Chem. 2007 Jul 27;282(30):21738-45
references.pmid: 17535816
references.citation: Gene. 2009 Jan 1;428(1-2):2-8
references.pmid: 18948176
references.citation: Microbiology (Reading). 1996 Aug;142 ( Pt 8):2031-40
references.pmid: 8760915
references.citation: Mol Microbiol. 1998 Nov;30(4):737-49
references.pmid: 10094622
references.citation: Trends Biochem Sci. 2003 Feb;28(2):91-8
references.pmid: 12575997
references.citation: J Bacteriol. 1999 Jan;181(1):353-6
references.pmid: 9864351
references.citation: Mol Microbiol. 2004 Dec;54(5):1319-25
references.pmid: 15554971
references.citation: PLoS Comput Biol. 2005 Aug;1(3):e25
references.pmid: 16110342
references.citation: Science. 1988 Jun 3;240(4857):1285-93
references.pmid: 3287615
references.citation: Mol Microbiol. 2005 Jun;56(6):1549-59
references.pmid: 15916605
references.citation: Bioinformatics. 2004 Dec 12;20(18):3682-6
references.pmid: 15256401
references.citation: J Mol Biol. 1990 Oct 5;215(3):403-10
references.pmid: 2231712
references.citation: Nucleic Acids Res. 2008 Jan;36(Database issue):D93-6
references.pmid: 17962296
references.citation: J Bacteriol. 1990 May;172(5):2667-74
references.pmid: 2110147
references.citation: FEMS Microbiol Lett. 2002 Jan 22;207(1):29-33
references.pmid: 11886746