title: Directional RNA-seq reveals highly complex condition-dependent transcriptomes in E. coli K12 through accurate full-length transcripts assembling.
abstract: BACKGROUND
  Although prokaryotic gene transcription has been studied over decades, many aspects of the process remain poorly understood. Particularly, recent studies have revealed that transcriptomes in many prokaryotes are far more complex than previously thought. Genes in an operon are often alternatively and dynamically transcribed under different conditions, and a large portion of genes and intergenic regions have antisense RNA (asRNA) and non-coding RNA (ncRNA) transcripts, respectively. Ironically, similar studies have not been conducted in the model bacterium E coli K12, thus it is unknown whether or not the bacterium possesses similar complex transcriptomes. Furthermore, although RNA-seq becomes the major method for analyzing the complexity of prokaryotic transcriptome, it is still a challenging task to accurately assemble full length transcripts using short RNA-seq reads.
  
  
  RESULTS
  To fill these gaps, we have profiled the transcriptomes of E. coli K12 under different culture conditions and growth phases using a highly specific directional RNA-seq technique that can capture various types of transcripts in the bacterial cells, combined with a highly accurate and robust algorithm and tool TruHMM (http://bioinfolab.uncc.edu/TruHmm_package/) for assembling full length transcripts. We found that 46.9 ~ 63.4% of expressed operons were utilized in their putative alternative forms, 72.23 ~ 89.54% genes had putative asRNA transcripts and 51.37 ~ 72.74% intergenic regions had putative ncRNA transcripts under different culture conditions and growth phases.
  
  
  CONCLUSIONS
  As has been demonstrated in many other prokaryotes, E. coli K12 also has a highly complex and dynamic transcriptomes under different culture conditions and growth phases. Such complex and dynamic transcriptomes might play important roles in the physiology of the bacterium. TruHMM is a highly accurate and robust algorithm for assembling full-length transcripts in prokaryotes using directional RNA-seq short reads.
authors.affiliation: Department of Bioinformatics and Genomics, College of Computing and Informatics, The University of North Carolina at Charlotte, 9201 University City Blvd, Charlotte, NC 28223, USA.
authors.forename: Shan
authors.initials: S
authors.lastname: Li
authors.forename: Xia
authors.initials: X
authors.lastname: Dong
authors.forename: Zhengchang
authors.initials: Z
authors.lastname: Su
mesh_terms: D000465:Algorithms; D004926:Escherichia coli / Q000235:genetics*; D005798:Genes, Bacterial; D012333:RNA, Messenger / Q000235:genetics*; D017423:Sequence Analysis, RNA; D059467:Transcriptome
chemical_list: D012333:RNA, Messenger
references.citation: Genome Biol. 2011;12(3):R22
references.pmid: 21410973
references.citation: BMC Genomics. 2011 Jun 28;12:332
references.pmid: 21711558
references.citation: Nucleic Acids Res. 2006 Jan 05;34(1):1-9
references.pmid: 16397293
references.citation: Nat Methods. 2010 Sep;7(9):709-15
references.pmid: 20711195
references.citation: Nat Methods. 2010 Nov;7(11):909-12
references.pmid: 20935650
references.citation: Nucleic Acids Res. 2011 Nov;39(21):e141
references.pmid: 21890899
references.citation: Nucleic Acids Res. 2007;35(1):288-98
references.pmid: 17170009
references.citation: Nucleic Acids Res. 2010 Sep;38(17):e170
references.pmid: 20671027
references.citation: PLoS Genet. 2009 Jul;5(7):e1000569
references.pmid: 19609351
references.citation: Brief Bioinform. 2009 Jul;10(4):354-66
references.pmid: 19482960
references.citation: Nature. 2010 Mar 11;464(7286):250-5
references.pmid: 20164839
references.citation: J Bacteriol. 2000 Jan;182(1):225-7
references.pmid: 10613886
references.citation: J Bacteriol. 1991 Apr;173(8):2665-72
references.pmid: 1840580
references.citation: Nat Biotechnol. 2000 Dec;18(12):1262-8
references.pmid: 11101804
references.citation: Genome Inform. 2004;15(2):211-22
references.pmid: 15706507
references.citation: Microbiol Mol Biol Rev. 2011 Jun;75(2):286-300
references.pmid: 21646430
references.citation: Nat Biotechnol. 2007 May;25(5):584-92
references.pmid: 17401361
references.citation: PLoS One. 2009 Oct 19;4(10):e7526
references.pmid: 19838305
references.citation: Mol Syst Biol. 2009;5:285
references.pmid: 19536208
references.citation: Nucleic Acids Res. 2007;35(22):7577-90
references.pmid: 17940092
references.citation: BMC Bioinformatics. 2011 Dec 17;12:480
references.pmid: 22177264
references.citation: Appl Environ Microbiol. 2007 Feb;73(3):846-54
references.pmid: 17122389
references.citation: BMC Bioinformatics. 2010 Apr 29;11 Suppl 3:S10
references.pmid: 20438648
references.citation: Genome Biol. 2009;10(3):R25
references.pmid: 19261174
references.citation: J Bacteriol. 2010 Jan;192(1):370-4
references.pmid: 19854894
references.citation: Nat Biotechnol. 2010 May;28(5):511-5
references.pmid: 20436464
references.citation: BMC Bioinformatics. 2010 Feb 18;11:94
references.pmid: 20167110
references.citation: J Bacteriol. 2012 Jan;194(1):100-14
references.pmid: 22037400
references.citation: Nat Rev Genet. 2010 Jan;11(1):9-16
references.pmid: 19935729
references.citation: Nucleic Acids Res. 2002 Jan 1;30(1):56-8
references.pmid: 11752253
references.citation: Nat Biotechnol. 2011 May 15;29(7):644-52
references.pmid: 21572440
references.citation: Science. 1997 Sep 5;277(5331):1453-62
references.pmid: 9278503
references.citation: Trends Genet. 2005 Jan;21(1):16-20
references.pmid: 15680508
references.citation: Cold Spring Harb Perspect Biol. 2011 Dec 01;3(12):
references.pmid: 20980440
references.citation: Bioessays. 2010 Jun;32(6):461-7
references.pmid: 20486131
references.citation: Science. 2009 Nov 27;326(5957):1268-71
references.pmid: 19965477
references.citation: Bioinformatics. 2009 Oct 15;25(20):2730-1
references.pmid: 19654113
references.citation: Nat Rev Microbiol. 2004 Jan;2(1):57-65
references.pmid: 15035009
references.citation: Nucleic Acids Res. 2012 May;40(10):e72
references.pmid: 22323520
references.citation: Methods Mol Biol. 2011;733:37-49
references.pmid: 21431761
references.citation: mBio. 2010 May 18;1(1):
references.pmid: 20689751
references.citation: J Bacteriol. 2004 Sep;186(18):6118-23
references.pmid: 15342581
references.citation: Proc Natl Acad Sci U S A. 2011 Jul 12;108(28):11393-8
references.pmid: 21705661
references.citation: BMC Genomics. 2011 Sep 30;12:479
references.pmid: 21962126
references.citation: Bioinformatics. 2008 Dec 15;24(24):2807-13
references.pmid: 18974076
references.citation: Brief Bioinform. 2008 Sep;9(5):367-75
references.pmid: 18420711
references.citation: Genome Res. 2000 Apr;10(4):529-38
references.pmid: 10779493
references.citation: Gene. 1993 Jul 15;129(1):27-32
references.pmid: 8335257
references.citation: Genome Biol. 2010;11(5):R50
references.pmid: 20459815
references.citation: Proc Int Conf Intell Syst Mol Biol. 1994;2:28-36
references.pmid: 7584402
references.citation: Nucleic Acids Res. 2010 Jul;38(12):e130
references.pmid: 20385580
references.citation: Curr Opin Microbiol. 2010 Feb;13(1):18-23
references.pmid: 20022798
references.citation: J Math Biol. 2008 Jan;56(1-2):183-200
references.pmid: 17354017
references.citation: J Mol Biol. 1998 Jan 16;275(2):211-20
references.pmid: 9466904
references.citation: BMC Genomics. 2010 Sep 29;11:527
references.pmid: 20920248
references.citation: Nat Biotechnol. 2009 Jul;27(7):652-8
references.pmid: 19581875
references.citation: Genome Res. 2010 Jul;20(7):989-99
references.pmid: 20519413
references.citation: Nature. 2009 Jun 18;459(7249):950-6
references.pmid: 19448609
references.citation: Bioinformatics. 2011 Feb 15;27(4):502-8
references.pmid: 21169371
references.citation: Biochemistry (Mosc). 2002 Feb;67(2):184-95
references.pmid: 11952414
references.citation: Nat Biotechnol. 2009 Nov;27(11):1043-9
references.pmid: 19881496
references.citation: J Biol Chem. 1990 Mar 15;265(8):4461-71
references.pmid: 2155230
references.citation: Genome Res. 2008 Sep;18(9):1509-17
references.pmid: 18550803
references.citation: Annu Rev Genet. 2010;44:167-88
references.pmid: 20707673
references.citation: Science. 2008 Jun 6;320(5881):1344-9
references.pmid: 18451266
references.citation: Nat Rev Genet. 2009 Jan;10(1):57-63
references.pmid: 19015660
references.citation: Nat Methods. 2009 Nov;6(11 Suppl):S6-S12
references.pmid: 19844229
references.citation: Nucleic Acids Res. 2011 Jan;39(Database issue):D583-90
references.pmid: 21097882
references.citation: Nucleic Acids Res. 2003 Apr 1;31(7):1813-20
references.pmid: 12654996
references.citation: Bioinformatics. 2009 May 1;25(9):1105-11
references.pmid: 19289445
references.citation: Nucleic Acids Res. 2005 Feb 08;33(3):880-92
references.pmid: 15701760
references.citation: Bioinformatics. 2005 Apr 1;21(7):880-8
references.pmid: 15539453
references.citation: BMC Genomics. 2010 Nov 24;11:663
references.pmid: 21106091
references.citation: Nat Biotechnol. 2010 May;28(5):503-10
references.pmid: 20436462
references.citation: Nat Methods. 2010 Feb;7(2):130-2
references.pmid: 20081834
references.citation: Nucleic Acids Res. 2010 Jul;38(12):e131
references.pmid: 20395217
references.citation: Mol Cell. 2011 Sep 16;43(6):880-91
references.pmid: 21925377
references.citation: Genome Biol. 2011 Oct 11;12(10):R98
references.pmid: 21989159
references.citation: Nucleic Acids Res. 2012 Apr;40(7):e54
references.pmid: 22241775
references.citation: Proc Natl Acad Sci U S A. 2011 Feb 1;108(5):2124-9
references.pmid: 21245330
references.citation: Nucleic Acids Res. 2005 Sep 12;33(16):5156-71
references.pmid: 16157864
references.citation: Proc Natl Acad Sci U S A. 2009 Mar 10;106(10):3976-81
references.pmid: 19234113
references.citation: Genome Biol. 2011 Nov 08;12(11):R112
references.pmid: 22067484
references.citation: J Bacteriol. 2009 May;191(10):3203-11
references.pmid: 19304856
references.citation: Bioinformatics. 2012 Apr 15;28(8):1086-92
references.pmid: 22368243
references.citation: Nat Methods. 2008 Jul;5(7):621-8
references.pmid: 18516045
references.citation: J Bacteriol. 1992 Oct;174(19):6256-63
references.pmid: 1400176
references.citation: Genome Res. 2002 Apr;12(4):656-64
references.pmid: 11932250
references.citation: RNA. 2011 Sep;17(9):1697-712
references.pmid: 21775473
references.citation: Genome Res. 2010 Jan;20(1):133-41
references.pmid: 19884261
references.citation: J Mol Biol. 1997 Apr 25;268(1):78-94
references.pmid: 9149143
references.citation: Bioinformatics. 2012 Apr 1;28(7):921-8
references.pmid: 22285831
references.citation: Proc Natl Acad Sci U S A. 2011 Dec 13;108(50):20172-7
references.pmid: 22123973
references.citation: Cell Host Microbe. 2011 Aug 18;10(2):165-74
references.pmid: 21843873
references.citation: Nat Rev Genet. 2011 Sep 07;12(10):671-82
references.pmid: 21897427
references.citation: Biol Cell. 2009 Feb;101(2):117-31
references.pmid: 19076068
references.citation: Mol Syst Biol. 2012 May 22;8:585
references.pmid: 22617959
references.citation: Nucleic Acids Res. 2011 Jan;39(Database issue):D98-105
references.pmid: 21051347
references.citation: Curr Opin Microbiol. 2011 Oct;14(5):579-86
references.pmid: 21839669
references.citation: Genome Biol. 2011;12(2):R18
references.pmid: 21338519
references.citation: Science. 2012 Mar 2;335(6072):1103-6
references.pmid: 22383849
references.citation: Nucleic Acids Res. 2011 Jul;39(13):e90
references.pmid: 21576222
references.citation: OMICS. 2007 Spring;11(1):58-73
references.pmid: 17411396
references.citation: Nucleic Acids Res. 2011 Aug;39(15):e103
references.pmid: 21646344
references.citation: Nucleic Acids Res. 2007;35(1):11-20
references.pmid: 17148478
references.citation: Nucleic Acids Res. 2009 Jan;37(Database issue):D459-63
references.pmid: 18988623
references.citation: BMC Bioinformatics. 2003 Jun 3;4:21
references.pmid: 12783628
references.citation: Anal Biochem. 2011 Dec 15;419(2):317-22
references.pmid: 21889483
references.citation: Cell. 1994 Dec 2;79(5):743-6
references.pmid: 8001112
references.citation: Nucleic Acids Res. 2008 Jan;36(Database issue):D93-6
references.pmid: 17962296
references.citation: Nucleic Acids Res. 2010 Jan;38(3):868-77
references.pmid: 19923228
references.citation: Methods Mol Biol. 2007;395:475-88
references.pmid: 17993693
references.citation: Genome Res. 2010 Oct;20(10):1432-40
references.pmid: 20693479
references.citation: Mol Microbiol. 2009 Sep;73(6):1043-57
references.pmid: 19682248
references.citation: Genome Biol. 2011;12(5):R47
references.pmid: 21612627