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Volumn 19, Issue 1, 2014, Pages 97-105

Differential RNA-seq: The approach behind and the biological insight gained

Author keywords

[No Author keywords available]

Indexed keywords

COMPLEMENTARY RNA; MESSENGER RNA; TRANSCRIPTOME; UNTRANSLATED RNA; RNA;

EID: 84904265834     PISSN: 13695274     EISSN: 18790364     Source Type: Journal    
DOI: 10.1016/j.mib.2014.06.010     Document Type: Review
Times cited : (161)

References (80)
  • 1
    • 72849114230 scopus 로고    scopus 로고
    • Prokaryotic transcriptomics: a new view on regulation, physiology and pathogenicity
    • Sorek R., Cossart P. Prokaryotic transcriptomics: a new view on regulation, physiology and pathogenicity. Nat Rev Genet 2010, 11(1):9-16.
    • (2010) Nat Rev Genet , vol.11 , Issue.1 , pp. 9-16
    • Sorek, R.1    Cossart, P.2
  • 2
    • 79958047291 scopus 로고    scopus 로고
    • Cis-antisense RNA, another level of gene regulation in bacteria
    • Georg J., Hess W.R. cis-antisense RNA, another level of gene regulation in bacteria. Microbiol Mol Biol Rev 2011, 75(2):286-300.
    • (2011) Microbiol Mol Biol Rev , vol.75 , Issue.2 , pp. 286-300
    • Georg, J.1    Hess, W.R.2
  • 3
    • 78149421813 scopus 로고    scopus 로고
    • Bacterial antisense RNAs: how many are there, and what are they doing?
    • Thomason M.K., Storz G. Bacterial antisense RNAs: how many are there, and what are they doing?. Annu Rev Genet 2010, 44:167-188.
    • (2010) Annu Rev Genet , vol.44 , pp. 167-188
    • Thomason, M.K.1    Storz, G.2
  • 4
    • 84866623270 scopus 로고    scopus 로고
    • An effort to make sense of antisense transcription in bacteria
    • Lasa I., Toledo-Arana A., Gingeras T.R. An effort to make sense of antisense transcription in bacteria. RNA Biol 2012, 9(8):1039-1044.
    • (2012) RNA Biol , vol.9 , Issue.8 , pp. 1039-1044
    • Lasa, I.1    Toledo-Arana, A.2    Gingeras, T.R.3
  • 5
    • 77957802374 scopus 로고    scopus 로고
    • Studying bacterial transcriptomes using RNA-seq
    • Croucher N.J., Thomson N.R. Studying bacterial transcriptomes using RNA-seq. Curr Opin Microbiol 2010, 13(5):619-624.
    • (2010) Curr Opin Microbiol , vol.13 , Issue.5 , pp. 619-624
    • Croucher, N.J.1    Thomson, N.R.2
  • 7
    • 70949102952 scopus 로고    scopus 로고
    • Next generation sequencing of microbial transcriptomes: challenges and opportunities
    • van Vliet A.H. Next generation sequencing of microbial transcriptomes: challenges and opportunities. FEMS Microbiol Lett 2010, 302(1):1-7.
    • (2010) FEMS Microbiol Lett , vol.302 , Issue.1 , pp. 1-7
    • van Vliet, A.H.1
  • 8
    • 84886067784 scopus 로고    scopus 로고
    • Differential RNA sequencing (dRNA-seq): deep-sequencing-based analysis of primary transcriptomes
    • Wiley-Blackwell-VCH
    • Borries A., Vogel J., Sharma C.M. Differential RNA sequencing (dRNA-seq): deep-sequencing-based analysis of primary transcriptomes. Tag-based approaches for next-generation sequencing 2012, Wiley-Blackwell-VCH.
    • (2012) Tag-based approaches for next-generation sequencing
    • Borries, A.1    Vogel, J.2    Sharma, C.M.3
  • 9
    • 84865189152 scopus 로고    scopus 로고
    • Strand-specific RNA-seq reveals ordered patterns of sense and antisense transcription in Bacillus anthracis
    • Passalacqua K.D., et al. Strand-specific RNA-seq reveals ordered patterns of sense and antisense transcription in Bacillus anthracis. PLoS ONE 2012, 7(8):e43350.
    • (2012) PLoS ONE , vol.7 , Issue.8
    • Passalacqua, K.D.1
  • 10
    • 84855916545 scopus 로고    scopus 로고
    • Protein-RNA interactions: new genomic technologies and perspectives
    • Konig J., et al. Protein-RNA interactions: new genomic technologies and perspectives. Nat Rev Genet 2012, 13(2):77-83.
    • (2012) Nat Rev Genet , vol.13 , Issue.2 , pp. 77-83
    • Konig, J.1
  • 11
    • 74949137952 scopus 로고    scopus 로고
    • A single-base resolution map of an archaeal transcriptome
    • Wurtzel O., et al. A single-base resolution map of an archaeal transcriptome. Genome Res 2010, 20(1):133-141.
    • (2010) Genome Res , vol.20 , Issue.1 , pp. 133-141
    • Wurtzel, O.1
  • 12
    • 70449380939 scopus 로고    scopus 로고
    • Genome-wide identification of transcription start sites, promoters and transcription factor binding sites in E. coli
    • Mendoza-Vargas A., et al. Genome-wide identification of transcription start sites, promoters and transcription factor binding sites in E. coli. PLoS ONE 2009, 4(10):e7526.
    • (2009) PLoS ONE , vol.4 , Issue.10
    • Mendoza-Vargas, A.1
  • 13
    • 70449370314 scopus 로고    scopus 로고
    • The transcription unit architecture of the Escherichia coli genome
    • Cho B.K., et al. The transcription unit architecture of the Escherichia coli genome. Nat Biotechnol 2009, 27(11):1043-1049.
    • (2009) Nat Biotechnol , vol.27 , Issue.11 , pp. 1043-1049
    • Cho, B.K.1
  • 14
    • 84892843450 scopus 로고    scopus 로고
    • Identification of regulatory RNA in bacterial genomes by genome-scale mapping of transcription start sites
    • Singh N., Wade J.T. Identification of regulatory RNA in bacterial genomes by genome-scale mapping of transcription start sites. Methods Mol Biol 2014, 1103:1-10.
    • (2014) Methods Mol Biol , vol.1103 , pp. 1-10
    • Singh, N.1    Wade, J.T.2
  • 15
    • 84885410721 scopus 로고    scopus 로고
    • A combination of improved differential and global RNA-seq reveals pervasive transcription initiation and events in all stages of the life-cycle of functional RNAs in Propionibacterium acnes, a major contributor to wide-spread human disease
    • Lin Y.F., et al. A combination of improved differential and global RNA-seq reveals pervasive transcription initiation and events in all stages of the life-cycle of functional RNAs in Propionibacterium acnes, a major contributor to wide-spread human disease. BMC Genomics 2013, 14:620.
    • (2013) BMC Genomics , vol.14 , pp. 620
    • Lin, Y.F.1
  • 16
    • 84876543942 scopus 로고    scopus 로고
    • RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more
    • Salgado H., et al. RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more. Nucleic Acids Res 2013, 41(Database issue):D203-D213.
    • (2013) Nucleic Acids Res , vol.41 , Issue.DATABASE ISSUE
    • Salgado, H.1
  • 17
    • 77949425194 scopus 로고    scopus 로고
    • The primary transcriptome of the major human pathogen Helicobacter pylori
    • Sharma C.M., et al. The primary transcriptome of the major human pathogen Helicobacter pylori. Nature 2010, 464(7286):250-255.
    • (2010) Nature , vol.464 , Issue.7286 , pp. 250-255
    • Sharma, C.M.1
  • 18
    • 80051915419 scopus 로고    scopus 로고
    • RNA-seq-based monitoring of infection-linked changes in Vibrio cholerae gene expression
    • Mandlik A., et al. RNA-seq-based monitoring of infection-linked changes in Vibrio cholerae gene expression. Cell Host Microbe 2011, 10(2):165-174.
    • (2011) Cell Host Microbe , vol.10 , Issue.2 , pp. 165-174
    • Mandlik, A.1
  • 19
    • 0017724552 scopus 로고
    • Sizing and mapping of early adenovirus mRNAs by gel electrophoresis of S1 endonuclease-digested hybrids
    • Berk A.J., Sharp P.A. Sizing and mapping of early adenovirus mRNAs by gel electrophoresis of S1 endonuclease-digested hybrids. Cell 1977, 12(3):721-732.
    • (1977) Cell , vol.12 , Issue.3 , pp. 721-732
    • Berk, A.J.1    Sharp, P.A.2
  • 20
    • 0018775570 scopus 로고
    • Characterization of the 5'-terminal structure of simian virus 40 early mRNA's
    • Thompson J.A., Radonovich M.F., Salzman N.P. Characterization of the 5'-terminal structure of simian virus 40 early mRNA's. J Virol 1979, 31(2):437-446.
    • (1979) J Virol , vol.31 , Issue.2 , pp. 437-446
    • Thompson, J.A.1    Radonovich, M.F.2    Salzman, N.P.3
  • 21
    • 0035954304 scopus 로고    scopus 로고
    • Novel small RNA-encoding genes in the intergenic regions of Escherichia coli
    • Argaman L., et al. Novel small RNA-encoding genes in the intergenic regions of Escherichia coli. Curr Biol 2001, 11(12):941-950.
    • (2001) Curr Biol , vol.11 , Issue.12 , pp. 941-950
    • Argaman, L.1
  • 22
    • 0344237410 scopus 로고    scopus 로고
    • RNomics in Escherichia coli detects new sRNA species and indicates parallel transcriptional output in bacteria
    • Vogel J., et al. RNomics in Escherichia coli detects new sRNA species and indicates parallel transcriptional output in bacteria. Nucleic Acids Res 2003, 31(22):6435-6443.
    • (2003) Nucleic Acids Res , vol.31 , Issue.22 , pp. 6435-6443
    • Vogel, J.1
  • 23
    • 0029845782 scopus 로고    scopus 로고
    • Sensitive detection of bacterial transcription initiation sites and differentiation from RNA processing sites in the pheromone-induced plasmid transfer system of Enterococcus faecalis
    • Bensing B.A., Meyer B.J., Dunny G.M. Sensitive detection of bacterial transcription initiation sites and differentiation from RNA processing sites in the pheromone-induced plasmid transfer system of Enterococcus faecalis. Proc Natl Acad Sci USA 1996, 93(15):7794-7799.
    • (1996) Proc Natl Acad Sci USA , vol.93 , Issue.15 , pp. 7794-7799
    • Bensing, B.A.1    Meyer, B.J.2    Dunny, G.M.3
  • 24
    • 84878482772 scopus 로고    scopus 로고
    • High-resolution transcriptome maps reveal strain-specific regulatory features of multiple Campylobacter jejuni isolates
    • Dugar G., et al. High-resolution transcriptome maps reveal strain-specific regulatory features of multiple Campylobacter jejuni isolates. PLoS Genet 2013, 9(5):e1003495.
    • (2013) PLoS Genet , vol.9 , Issue.5
    • Dugar, G.1
  • 25
    • 77950349491 scopus 로고    scopus 로고
    • Deep sequencing-based discovery of the Chlamydia trachomatis transcriptome
    • Albrecht M., et al. Deep sequencing-based discovery of the Chlamydia trachomatis transcriptome. Nucleic Acids Res 2010, 38(3):868-877.
    • (2010) Nucleic Acids Res , vol.38 , Issue.3 , pp. 868-877
    • Albrecht, M.1
  • 26
    • 80053649020 scopus 로고    scopus 로고
    • The transcriptional landscape of Chlamydia pneumoniae
    • Albrecht M., et al. The transcriptional landscape of Chlamydia pneumoniae. Genome Biol 2011, 12(10):R98.
    • (2011) Genome Biol , vol.12 , Issue.10
    • Albrecht, M.1
  • 27
    • 84857757047 scopus 로고    scopus 로고
    • The primary transcriptome of barley chloroplasts: numerous noncoding RNAs and the dominating role of the plastid-encoded RNA polymerase
    • Zhelyazkova P., et al. The primary transcriptome of barley chloroplasts: numerous noncoding RNAs and the dominating role of the plastid-encoded RNA polymerase. Plant Cell 2012, 24(1):123-136.
    • (2012) Plant Cell , vol.24 , Issue.1 , pp. 123-136
    • Zhelyazkova, P.1
  • 28
    • 84898923218 scopus 로고    scopus 로고
    • TSSAR: TSS annotation regime for dRNA-seq data
    • Amman F., et al. TSSAR: TSS annotation regime for dRNA-seq data. BMC Bioinform 2014, 15(1):89.
    • (2014) BMC Bioinform , vol.15 , Issue.1 , pp. 89
    • Amman, F.1
  • 29
    • 84897435888 scopus 로고    scopus 로고
    • TSSer: an automated method to identify transcription start sites in prokaryotic genomes from differential RNA sequencing data
    • Jorjani H., Zavolan M. TSSer: an automated method to identify transcription start sites in prokaryotic genomes from differential RNA sequencing data. Bioinformatics 2014, 30(7):971-974.
    • (2014) Bioinformatics , vol.30 , Issue.7 , pp. 971-974
    • Jorjani, H.1    Zavolan, M.2
  • 30
    • 84890302568 scopus 로고    scopus 로고
    • An infection-relevant transcriptomic compendium for Salmonella enterica serovar typhimurium
    • Kroger C., et al. An infection-relevant transcriptomic compendium for Salmonella enterica serovar typhimurium. Cell Host Microbe 2013, 14(6):683-695.
    • (2013) Cell Host Microbe , vol.14 , Issue.6 , pp. 683-695
    • Kroger, C.1
  • 31
    • 70849119931 scopus 로고    scopus 로고
    • Transcriptome complexity in a genome-reduced bacterium
    • Guell M., et al. Transcriptome complexity in a genome-reduced bacterium. Science 2009, 326(5957):1268-1271.
    • (2009) Science , vol.326 , Issue.5957 , pp. 1268-1271
    • Guell, M.1
  • 32
    • 84876234571 scopus 로고    scopus 로고
    • Small RNA-mediated activation of sugar phosphatase mRNA regulates glucose homeostasis
    • Papenfort K., et al. Small RNA-mediated activation of sugar phosphatase mRNA regulates glucose homeostasis. Cell 2013, 153(2):426-437.
    • (2013) Cell , vol.153 , Issue.2 , pp. 426-437
    • Papenfort, K.1
  • 33
    • 84893387968 scopus 로고    scopus 로고
    • A variable homopolymeric G-repeat defines small RNA-mediated posttranscriptional regulation of a chemotaxis receptor in Helicobacter pylori
    • Pernitzsch S.R., et al. A variable homopolymeric G-repeat defines small RNA-mediated posttranscriptional regulation of a chemotaxis receptor in Helicobacter pylori. Proc Natl Acad Sci USA 2014, 111(4):E501-E510.
    • (2014) Proc Natl Acad Sci USA , vol.111 , Issue.4
    • Pernitzsch, S.R.1
  • 34
    • 84888432432 scopus 로고    scopus 로고
    • Genome-wide mapping of transcriptional start sites defines an extensive leaderless transcriptome in Mycobacterium tuberculosis
    • Cortes T., et al. Genome-wide mapping of transcriptional start sites defines an extensive leaderless transcriptome in Mycobacterium tuberculosis. Cell Rep 2013, 5(4):1121-1131.
    • (2013) Cell Rep , vol.5 , Issue.4 , pp. 1121-1131
    • Cortes, T.1
  • 35
    • 84877013921 scopus 로고    scopus 로고
    • Ribosome heterogeneity: another level of complexity in bacterial translation regulation
    • Byrgazov K., Vesper O., Moll I. Ribosome heterogeneity: another level of complexity in bacterial translation regulation. Curr Opin Microbiol 2013, 16(2):133-139.
    • (2013) Curr Opin Microbiol , vol.16 , Issue.2 , pp. 133-139
    • Byrgazov, K.1    Vesper, O.2    Moll, I.3
  • 36
    • 76049099044 scopus 로고    scopus 로고
    • Deep sequencing analysis of the Methanosarcina mazei Go1 transcriptome in response to nitrogen availability
    • Jager D., et al. Deep sequencing analysis of the Methanosarcina mazei Go1 transcriptome in response to nitrogen availability. Proc Natl Acad Sci USA 2009, 106(51):21878-21882.
    • (2009) Proc Natl Acad Sci USA , vol.106 , Issue.51 , pp. 21878-21882
    • Jager, D.1
  • 37
    • 84870600743 scopus 로고    scopus 로고
    • An archaeal sRNA targeting cis- and trans-encoded mRNAs via two distinct domains
    • Jager D., et al. An archaeal sRNA targeting cis- and trans-encoded mRNAs via two distinct domains. Nucleic Acids Res 2012, 40(21):10964-10979.
    • (2012) Nucleic Acids Res , vol.40 , Issue.21 , pp. 10964-10979
    • Jager, D.1
  • 38
    • 80053019485 scopus 로고    scopus 로고
    • Regulation by small RNAs in bacteria: expanding frontiers
    • Storz G., Vogel J., Wassarman K.M. Regulation by small RNAs in bacteria: expanding frontiers. Mol Cell 2011, 43(6):880-891.
    • (2011) Mol Cell , vol.43 , Issue.6 , pp. 880-891
    • Storz, G.1    Vogel, J.2    Wassarman, K.M.3
  • 39
    • 84860742976 scopus 로고    scopus 로고
    • The transcriptional landscape and small RNAs of Salmonella enterica serovar typhimurium
    • Kroger C., et al. The transcriptional landscape and small RNAs of Salmonella enterica serovar typhimurium. Proc Natl Acad Sci USA 2012, 109(20):E1277-E1286.
    • (2012) Proc Natl Acad Sci USA , vol.109 , Issue.20
    • Kroger, C.1
  • 40
    • 84904260973 scopus 로고    scopus 로고
    • Riboregulators and the role of Hfq in photosynthetic bacteria
    • Hess W.R., et al. Riboregulators and the role of Hfq in photosynthetic bacteria. RNA Biol 2014, 11(5).
    • (2014) RNA Biol , vol.11 , Issue.5
    • Hess, W.R.1
  • 41
    • 84885530009 scopus 로고    scopus 로고
    • Comprehensive discovery and characterization of small RNAs in Corynebacterium glutamicum ATCC 13032
    • Mentz A., et al. Comprehensive discovery and characterization of small RNAs in Corynebacterium glutamicum ATCC 13032. BMC Genomics 2013, 14:714.
    • (2013) BMC Genomics , vol.14 , pp. 714
    • Mentz, A.1
  • 42
    • 84884737727 scopus 로고    scopus 로고
    • RNA-seq of Bacillus licheniformis: active regulatory RNA features expressed within a productive fermentation
    • Wiegand S., et al. RNA-seq of Bacillus licheniformis: active regulatory RNA features expressed within a productive fermentation. BMC Genomics 2013, 14:667.
    • (2013) BMC Genomics , vol.14 , pp. 667
    • Wiegand, S.1
  • 43
    • 84867577054 scopus 로고    scopus 로고
    • An atlas of Hfq-bound transcripts reveals 3' UTRs as a genomic reservoir of regulatory small RNAs
    • Chao Y., et al. An atlas of Hfq-bound transcripts reveals 3' UTRs as a genomic reservoir of regulatory small RNAs. EMBO J 2012, 31(20):4005-4019.
    • (2012) EMBO J , vol.31 , Issue.20 , pp. 4005-4019
    • Chao, Y.1
  • 44
    • 33845450357 scopus 로고    scopus 로고
    • Synthesis-mediated release of a small RNA inhibitor of RNA polymerase
    • Wassarman K.M., Saecker R.M. Synthesis-mediated release of a small RNA inhibitor of RNA polymerase. Science 2006, 314(5805):1601-1603.
    • (2006) Science , vol.314 , Issue.5805 , pp. 1601-1603
    • Wassarman, K.M.1    Saecker, R.M.2
  • 45
    • 79952174199 scopus 로고    scopus 로고
    • An experimentally anchored map of transcriptional start sites in the model cyanobacterium Synechocystis sp. PCC6803
    • Mitschke J., et al. An experimentally anchored map of transcriptional start sites in the model cyanobacterium Synechocystis sp. PCC6803. Proc Natl Acad Sci USA 2011, 108(5):2124-2129.
    • (2011) Proc Natl Acad Sci USA , vol.108 , Issue.5 , pp. 2124-2129
    • Mitschke, J.1
  • 46
    • 84859423675 scopus 로고    scopus 로고
    • In vivo and in vitro analysis of 6S RNA-templated short transcripts in Bacillus subtilis
    • Beckmann B.M., et al. In vivo and in vitro analysis of 6S RNA-templated short transcripts in Bacillus subtilis. RNA Biol 2011, 8(5):839-849.
    • (2011) RNA Biol , vol.8 , Issue.5 , pp. 839-849
    • Beckmann, B.M.1
  • 47
    • 79954623270 scopus 로고    scopus 로고
    • An expanding universe of small proteins
    • Hobbs E.C., et al. An expanding universe of small proteins. Curr Opin Microbiol 2011, 14(2):167-173.
    • (2011) Curr Opin Microbiol , vol.14 , Issue.2 , pp. 167-173
    • Hobbs, E.C.1
  • 48
    • 78049392640 scopus 로고    scopus 로고
    • Identification of regulatory RNAs in Bacillus subtilis
    • Irnov I., et al. Identification of regulatory RNAs in Bacillus subtilis. Nucleic Acids Res 2010, 38(19):6637-6651.
    • (2010) Nucleic Acids Res , vol.38 , Issue.19 , pp. 6637-6651
    • Irnov, I.1
  • 49
    • 84880820841 scopus 로고    scopus 로고
    • Genome-wide annotation and quantitation of translation by ribosome profiling
    • Chapter 4: Unit 4 18
    • Ingolia N.T., et al. Genome-wide annotation and quantitation of translation by ribosome profiling. Curr Protoc Mol Biol 2013, Chapter 4: p. Unit 4 18.
    • (2013) Curr Protoc Mol Biol
    • Ingolia, N.T.1
  • 50
    • 84857097177 scopus 로고    scopus 로고
    • RNA-guided genetic silencing systems in bacteria and archaea
    • Wiedenheft B., Sternberg S.H., Doudna J.A. RNA-guided genetic silencing systems in bacteria and archaea. Nature 2012, 482(7385):331-338.
    • (2012) Nature , vol.482 , Issue.7385 , pp. 331-338
    • Wiedenheft, B.1    Sternberg, S.H.2    Doudna, J.A.3
  • 51
    • 79953250082 scopus 로고    scopus 로고
    • CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III
    • Deltcheva E., et al. CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III. Nature 2011, 471(7340):602-607.
    • (2011) Nature , vol.471 , Issue.7340 , pp. 602-607
    • Deltcheva, E.1
  • 52
    • 84865070369 scopus 로고    scopus 로고
    • A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity
    • Jinek M., Chylinski K., Fonfara I., Hauer M., Doudna J.A., Charpentier E. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 2012, 337(6096):816-821. 10.1126/science.1225829.
    • (2012) Science , vol.337 , Issue.6096 , pp. 816-821
    • Jinek, M.1    Chylinski, K.2    Fonfara, I.3    Hauer, M.4    Doudna, J.A.5    Charpentier, E.6
  • 53
    • 84884856342 scopus 로고    scopus 로고
    • Cas9 as a versatile tool for engineering biology
    • Mali P., Esvelt K.M., Church G.M. Cas9 as a versatile tool for engineering biology. Nat Methods 2013, 10(10):957-963.
    • (2013) Nat Methods , vol.10 , Issue.10 , pp. 957-963
    • Mali, P.1    Esvelt, K.M.2    Church, G.M.3
  • 54
    • 84878193178 scopus 로고    scopus 로고
    • Processing-independent CRISPR RNAs limit natural transformation in Neisseria meningitidis
    • Zhang Y., et al. Processing-independent CRISPR RNAs limit natural transformation in Neisseria meningitidis. Mol Cell 2013, 50(4):488-503.
    • (2013) Mol Cell , vol.50 , Issue.4 , pp. 488-503
    • Zhang, Y.1
  • 55
    • 84860715141 scopus 로고    scopus 로고
    • Comparative transcriptomics of pathogenic and non-pathogenic Listeria species
    • Wurtzel O., et al. Comparative transcriptomics of pathogenic and non-pathogenic Listeria species. Mol Syst Biol 2012, 8:583.
    • (2012) Mol Syst Biol , vol.8 , pp. 583
    • Wurtzel, O.1
  • 56
    • 84865205659 scopus 로고    scopus 로고
    • Diversity of antisense and other non-coding RNAs in archaea revealed by comparative small RNA sequencing in four Pyrobaculum species
    • Bernick D.L., et al. Diversity of antisense and other non-coding RNAs in archaea revealed by comparative small RNA sequencing in four Pyrobaculum species. Front Microbiol 2012, 3:231.
    • (2012) Front Microbiol , vol.3 , pp. 231
    • Bernick, D.L.1
  • 57
    • 84866160409 scopus 로고    scopus 로고
    • Comparative analysis of regulatory elements between Escherichia coli and Klebsiella pneumoniae by genome-wide transcription start site profiling
    • Kim D., et al. Comparative analysis of regulatory elements between Escherichia coli and Klebsiella pneumoniae by genome-wide transcription start site profiling. PLoS Genet 2012, 8(8):e1002867.
    • (2012) PLoS Genet , vol.8 , Issue.8
    • Kim, D.1
  • 58
    • 84921664995 scopus 로고    scopus 로고
    • Comparative transcriptomics of two environmentally relevant cyanobacteria reveals unexpected transcriptome diversity
    • Voigt K., et al. Comparative transcriptomics of two environmentally relevant cyanobacteria reveals unexpected transcriptome diversity. ISME J 2014, 10.1038/ismej.2014.57.
    • (2014) ISME J
    • Voigt, K.1
  • 59
    • 84055214198 scopus 로고    scopus 로고
    • Dynamics of transcriptional start site selection during nitrogen stress-induced cell differentiation in Anabaena sp. PCC7120
    • Mitschke J., et al. Dynamics of transcriptional start site selection during nitrogen stress-induced cell differentiation in Anabaena sp. PCC7120. Proc Natl Acad Sci USA 2011, 108(50):20130-20135.
    • (2011) Proc Natl Acad Sci USA , vol.108 , Issue.50 , pp. 20130-20135
    • Mitschke, J.1
  • 60
    • 84879023629 scopus 로고    scopus 로고
    • Two CRISPR-Cas systems in Methanosarcina mazei strain Go1 display common processing features despite belonging to different types I and III
    • Nickel L., et al. Two CRISPR-Cas systems in Methanosarcina mazei strain Go1 display common processing features despite belonging to different types I and III. RNA Biol 2013, 10(5):779-791.
    • (2013) RNA Biol , vol.10 , Issue.5 , pp. 779-791
    • Nickel, L.1
  • 61
    • 84904266068 scopus 로고    scopus 로고
    • An RNA-seq method for defining endoribonuclease cleavage specificity identifies dual rRNA substrates for toxin MazF-mt3
    • Schifano J.M., et al. An RNA-seq method for defining endoribonuclease cleavage specificity identifies dual rRNA substrates for toxin MazF-mt3. Nat Commun 2014, 5:3538.
    • (2014) Nat Commun , vol.5 , pp. 3538
    • Schifano, J.M.1
  • 62
    • 84901743101 scopus 로고    scopus 로고
    • Transcriptome-wide analyses of 5'-ends in RNase J mutants of a gram-positive pathogen reveal a role in RNA maturation, regulation and degradation
    • Linder P., Lemeille S., Redder P. Transcriptome-wide analyses of 5'-ends in RNase J mutants of a gram-positive pathogen reveal a role in RNA maturation, regulation and degradation. PLoS Genet 2014, 10(2):e1004207.
    • (2014) PLoS Genet , vol.10 , Issue.2
    • Linder, P.1    Lemeille, S.2    Redder, P.3
  • 63
    • 34250875706 scopus 로고    scopus 로고
    • Initiation of RNA decay in Escherichia coli by 5' pyrophosphate removal
    • Celesnik H., Deana A., Belasco J.G. Initiation of RNA decay in Escherichia coli by 5' pyrophosphate removal. Mol Cell 2007, 27(1):79-90.
    • (2007) Mol Cell , vol.27 , Issue.1 , pp. 79-90
    • Celesnik, H.1    Deana, A.2    Belasco, J.G.3
  • 64
    • 84882455458 scopus 로고    scopus 로고
    • Single-cell sequencing-based technologies will revolutionize whole-organism science
    • Shapiro E., Biezuner T., Linnarsson S. Single-cell sequencing-based technologies will revolutionize whole-organism science. Nat Rev Genet 2013, 14(9):618-630.
    • (2013) Nat Rev Genet , vol.14 , Issue.9 , pp. 618-630
    • Shapiro, E.1    Biezuner, T.2    Linnarsson, S.3
  • 65
    • 84855836835 scopus 로고    scopus 로고
    • Deep sequencing uncovers numerous small RNAs on all four replicons of the plant pathogen Agrobacterium tumefaciens
    • Wilms I., et al. Deep sequencing uncovers numerous small RNAs on all four replicons of the plant pathogen Agrobacterium tumefaciens. RNA Biol 2012, 9(4):446-457.
    • (2012) RNA Biol , vol.9 , Issue.4 , pp. 446-457
    • Wilms, I.1
  • 66
    • 84856777234 scopus 로고    scopus 로고
    • Small RNAs of the Bradyrhizobium/Rhodopseudomonas lineage and their analysis
    • Madhugiri R., et al. Small RNAs of the Bradyrhizobium/Rhodopseudomonas lineage and their analysis. RNA Biol 2012, 9(1):47-58.
    • (2012) RNA Biol , vol.9 , Issue.1 , pp. 47-58
    • Madhugiri, R.1
  • 67
    • 84883672449 scopus 로고    scopus 로고
    • Parallel evolution of genome structure and transcriptional landscape in the Epsilonproteobacteria
    • Porcelli I., et al. Parallel evolution of genome structure and transcriptional landscape in the Epsilonproteobacteria. BMC Genomics 2013, 14:616.
    • (2013) BMC Genomics , vol.14 , pp. 616
    • Porcelli, I.1
  • 68
    • 84890290103 scopus 로고    scopus 로고
    • Comprehensive analysis of the Corynebacterium glutamicum transcriptome using an improved RNAseq technique
    • Pfeifer-Sancar K., et al. Comprehensive analysis of the Corynebacterium glutamicum transcriptome using an improved RNAseq technique. BMC Genomics 2013, 14:888.
    • (2013) BMC Genomics , vol.14 , pp. 888
    • Pfeifer-Sancar, K.1
  • 69
    • 84860771585 scopus 로고    scopus 로고
    • Deep sequencing defines the transcriptional map of L. pneumophila and identifies growth phase-dependent regulated ncRNAs implicated in virulence
    • Sahr T., et al. Deep sequencing defines the transcriptional map of L. pneumophila and identifies growth phase-dependent regulated ncRNAs implicated in virulence. RNA Biol 2012, 9(4):503-519.
    • (2012) RNA Biol , vol.9 , Issue.4 , pp. 503-519
    • Sahr, T.1
  • 70
    • 84875521277 scopus 로고    scopus 로고
    • Insights into the physiology and ecology of the brackish-water-adapted Cyanobacterium Nodularia spumigena CCY9414 based on a genome-transcriptome analysis
    • Voss B., et al. Insights into the physiology and ecology of the brackish-water-adapted Cyanobacterium Nodularia spumigena CCY9414 based on a genome-transcriptome analysis. PLoS ONE 2013, 8(3):e60224.
    • (2013) PLoS ONE , vol.8 , Issue.3
    • Voss, B.1
  • 71
    • 84555203309 scopus 로고    scopus 로고
    • Genome-wide identification of transcriptional start sites in the plant pathogen Pseudomonas syringae pv. tomato str. DC3000
    • Filiatrault M.J., et al. Genome-wide identification of transcriptional start sites in the plant pathogen Pseudomonas syringae pv. tomato str. DC3000. PLoS ONE 2011, 6(12):e29335.
    • (2011) PLoS ONE , vol.6 , Issue.12
    • Filiatrault, M.J.1
  • 72
    • 72049118448 scopus 로고    scopus 로고
    • Photooxidative stress-induced and abundant small RNAs in Rhodobacter sphaeroides
    • Berghoff B.A., et al. Photooxidative stress-induced and abundant small RNAs in Rhodobacter sphaeroides. Mol Microbiol 2009, 74(6):1497-1512.
    • (2009) Mol Microbiol , vol.74 , Issue.6 , pp. 1497-1512
    • Berghoff, B.A.1
  • 73
    • 84855798152 scopus 로고    scopus 로고
    • The architecture and ppGpp-dependent expression of the primary transcriptome of Salmonella typhimurium during invasion gene expression
    • Ramachandran V.K., et al. The architecture and ppGpp-dependent expression of the primary transcriptome of Salmonella typhimurium during invasion gene expression. BMC Genomics 2012, 13:25.
    • (2012) BMC Genomics , vol.13 , pp. 25
    • Ramachandran, V.K.1
  • 74
    • 84899732755 scopus 로고    scopus 로고
    • The primary transcriptome of Salmonella enterica Serovar typhimurium and its dependence on ppGpp during late stationary phase
    • Ramachandran V.K., Shearer N., Thompson A. The primary transcriptome of Salmonella enterica Serovar typhimurium and its dependence on ppGpp during late stationary phase. PLoS ONE 2014, 9(3):e92690.
    • (2014) PLoS ONE , vol.9 , Issue.3
    • Ramachandran, V.K.1    Shearer, N.2    Thompson, A.3
  • 75
    • 84874624264 scopus 로고    scopus 로고
    • Global mapping of transcription start sites and promoter motifs in the symbiotic alpha-proteobacterium Sinorhizobium meliloti 1021
    • Schluter J.P., et al. Global mapping of transcription start sites and promoter motifs in the symbiotic alpha-proteobacterium Sinorhizobium meliloti 1021. BMC Genomics 2013, 14:156.
    • (2013) BMC Genomics , vol.14 , pp. 156
    • Schluter, J.P.1
  • 76
    • 77950914774 scopus 로고    scopus 로고
    • A genome-wide survey of sRNAs in the symbiotic nitrogen-fixing alpha-proteobacterium Sinorhizobium meliloti
    • Schluter J.P., et al. A genome-wide survey of sRNAs in the symbiotic nitrogen-fixing alpha-proteobacterium Sinorhizobium meliloti. BMC Genomics 2010, 11:245.
    • (2010) BMC Genomics , vol.11 , pp. 245
    • Schluter, J.P.1
  • 77
    • 78049393967 scopus 로고    scopus 로고
    • Experimental discovery of small RNAs in Staphylococcus aureus reveals a riboregulator of central metabolism
    • Bohn C., et al. Experimental discovery of small RNAs in Staphylococcus aureus reveals a riboregulator of central metabolism. Nucleic Acids Res 2010, 38(19):6620-6636.
    • (2010) Nucleic Acids Res , vol.38 , Issue.19 , pp. 6620-6636
    • Bohn, C.1
  • 78
    • 84868622935 scopus 로고    scopus 로고
    • Functional characterization of the RNA chaperone Hfq in the opportunistic human pathogen Stenotrophomonas maltophilia
    • Roscetto E., et al. Functional characterization of the RNA chaperone Hfq in the opportunistic human pathogen Stenotrophomonas maltophilia. J Bacteriol 2012, 194(21):5864-5874.
    • (2012) J Bacteriol , vol.194 , Issue.21 , pp. 5864-5874
    • Roscetto, E.1
  • 79
    • 79956086810 scopus 로고    scopus 로고
    • Deep sequencing-based identification of small non-coding RNAs in Streptomyces coelicolor
    • Vockenhuber M.P., et al. Deep sequencing-based identification of small non-coding RNAs in Streptomyces coelicolor. RNA Biol 2011, 8(3):468-477.
    • (2011) RNA Biol , vol.8 , Issue.3 , pp. 468-477
    • Vockenhuber, M.P.1
  • 80
    • 84858400338 scopus 로고    scopus 로고
    • Genome-wide transcriptome analysis of the plant pathogen Xanthomonas identifies sRNAs with putative virulence functions
    • Schmidtke C., et al. Genome-wide transcriptome analysis of the plant pathogen Xanthomonas identifies sRNAs with putative virulence functions. Nucleic Acids Res 2012, 40(5):2020-2031.
    • (2012) Nucleic Acids Res , vol.40 , Issue.5 , pp. 2020-2031
    • Schmidtke, C.1


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