메뉴 건너뛰기




Volumn 18, Issue 1, 2017, Pages

Not all predicted CRISPR-Cas systems are equal: Isolated cas genes and classes of CRISPR like elements

Author keywords

CRISPR Cas system; False CRISPR; STAR like element; Tandem repeat

Indexed keywords

BACTERIA; NUCLEIC ACIDS; STARS;

EID: 85011663107     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/s12859-017-1512-4     Document Type: Article
Times cited : (129)

References (55)
  • 1
    • 0037059610 scopus 로고    scopus 로고
    • Phage genomics: small is beautiful
    • Brussow H, Hendrix RW. Phage genomics: small is beautiful. Cell. 2002;108:13-6.
    • (2002) Cell , vol.108 , pp. 13-16
    • Brussow, H.1    Hendrix, R.W.2
  • 3
    • 34250662138 scopus 로고    scopus 로고
    • The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats
    • Grissa I, Vergnaud G, Pourcel C. The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats. BMC Bioinformatics. 2007;8:172.
    • (2007) BMC Bioinformatics , vol.8 , pp. 172
    • Grissa, I.1    Vergnaud, G.2    Pourcel, C.3
  • 6
    • 0036267740 scopus 로고    scopus 로고
    • Identification of genes that are associated with DNA repeats in prokaryotes
    • Jansen R, Embden JD, Gaastra W, Schouls LM. Identification of genes that are associated with DNA repeats in prokaryotes. Mol Microbiol. 2002;43(6):1565-75.
    • (2002) Mol Microbiol , vol.43 , Issue.6 , pp. 1565-1575
    • Jansen, R.1    Embden, J.D.2    Gaastra, W.3    Schouls, L.M.4
  • 7
    • 84859294085 scopus 로고    scopus 로고
    • Modulation of CRISPR locus transcription by the repeat-binding protein Cbp1 in Sulfolobus
    • Deng L, Kenchappa CS, Peng X, She Q, Garrett RA. Modulation of CRISPR locus transcription by the repeat-binding protein Cbp1 in Sulfolobus. Nucleic Acids Res. 2012;40(6):2470-80.
    • (2012) Nucleic Acids Res , vol.40 , Issue.6 , pp. 2470-2480
    • Deng, L.1    Kenchappa, C.S.2    Peng, X.3    She, Q.4    Garrett, R.A.5
  • 8
    • 84887929636 scopus 로고    scopus 로고
    • RNA-Seq analyses reveal CRISPR RNA processing and regulation patterns
    • Zoephel J, Randau L. RNA-Seq analyses reveal CRISPR RNA processing and regulation patterns. Biochem Soc Trans. 2013;41(6):1459-63.
    • (2013) Biochem Soc Trans , vol.41 , Issue.6 , pp. 1459-1463
    • Zoephel, J.1    Randau, L.2
  • 9
    • 84943160849 scopus 로고    scopus 로고
    • CRISPR-Cas immunity in prokaryotes
    • Marraffini LA. CRISPR-Cas immunity in prokaryotes. Nature. 2015;526(7571):55-61.
    • (2015) Nature , vol.526 , Issue.7571 , pp. 55-61
    • Marraffini, L.A.1
  • 11
    • 80755187812 scopus 로고    scopus 로고
    • CRISPR-Cas systems in bacteria and archaea: versatile small RNAs for adaptive defense and regulation
    • Bhaya D, Davison M, Barrangou R. CRISPR-Cas systems in bacteria and archaea: versatile small RNAs for adaptive defense and regulation. Annu Rev Genet. 2011;45:273-97.
    • (2011) Annu Rev Genet , vol.45 , pp. 273-297
    • Bhaya, D.1    Davison, M.2    Barrangou, R.3
  • 13
    • 84899134190 scopus 로고    scopus 로고
    • CRISPR-Cas systems: prokaryotes upgrade to adaptive immunity
    • Barrangou R, Marraffini LA. CRISPR-Cas systems: prokaryotes upgrade to adaptive immunity. Mol Cell. 2014;54(2):234-44.
    • (2014) Mol Cell , vol.54 , Issue.2 , pp. 234-244
    • Barrangou, R.1    Marraffini, L.A.2
  • 15
    • 84896731736 scopus 로고    scopus 로고
    • CRISPR-based technologies: prokaryotic defense weapons repurposed
    • Terns RM, Terns MP. CRISPR-based technologies: prokaryotic defense weapons repurposed. Trends Genet. 2014;30(3):111-8.
    • (2014) Trends Genet , vol.30 , Issue.3 , pp. 111-118
    • Terns, R.M.1    Terns, M.P.2
  • 17
    • 84866859751 scopus 로고    scopus 로고
    • Cas9-crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria
    • Gasiunasa G, Barrangoub R, Horvathc P, Siksnys V. Cas9-crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria. Proc Natl Acad Sci. 2012;109:39.
    • (2012) Proc Natl Acad Sci , vol.109 , pp. 39
    • Gasiunasa, G.1    Barrangoub, R.2    Horvathc, P.3    Siksnys, V.4
  • 20
    • 34248400310 scopus 로고    scopus 로고
    • A guild of 45 CRISPR-associated (Cas) protein families and multiple CRISPR/Cas subtypes exist in prokaryotic genomes
    • Haft DH, Selengut J, Mongodin EF, Nelson KE. A guild of 45 CRISPR-associated (Cas) protein families and multiple CRISPR/Cas subtypes exist in prokaryotic genomes. PLoS Comput Biol. 2005;1(6):e60.
    • (2005) PLoS Comput Biol , vol.1 , Issue.6
    • Haft, D.H.1    Selengut, J.2    Mongodin, E.F.3    Nelson, K.E.4
  • 21
    • 33847371621 scopus 로고    scopus 로고
    • Identification of new noncoding RNAs in Listeria monocytogenes and prediction of mRNA targets
    • Mandin P, Repoila F, Vergassola M, Geissmann T, Cossart P. Identification of new noncoding RNAs in Listeria monocytogenes and prediction of mRNA targets. Nucleic Acids Res. 2007;35(3):962-74.
    • (2007) Nucleic Acids Res , vol.35 , Issue.3 , pp. 962-974
    • Mandin, P.1    Repoila, F.2    Vergassola, M.3    Geissmann, T.4    Cossart, P.5
  • 22
    • 84868372186 scopus 로고    scopus 로고
    • An evolutionary link between natural transformation and CRISPR adaptive immunity
    • Jorth P, Whiteley M. An evolutionary link between natural transformation and CRISPR adaptive immunity. MBio. 2012;3:5.
    • (2012) MBio , vol.3 , pp. 5
    • Jorth, P.1    Whiteley, M.2
  • 23
    • 84946962335 scopus 로고    scopus 로고
    • Comparative analysis of the orphan CRISPR2 locus in 242 Enterococcus faecalis Strains
    • Hullahalli K, Rodrigues M, Schmidt BD, Li X, Bhardwaj P, Palmer KL. Comparative analysis of the orphan CRISPR2 locus in 242 Enterococcus faecalis Strains. PLoS One. 2015;10(9):e0138890.
    • (2015) PLoS One , vol.10 , Issue.9
    • Hullahalli, K.1    Rodrigues, M.2    Schmidt, B.D.3    Li, X.4    Bhardwaj, P.5    Palmer, K.L.6
  • 24
    • 77955085897 scopus 로고    scopus 로고
    • Self-targeting by CRISPR: gene regulation or autoimmunity
    • Stern A, Keren L, Wurtzel O, Amitai G, Sorek R. Self-targeting by CRISPR: gene regulation or autoimmunity Trends Genet. 2010;26(8):335-40.
    • (2010) Trends Genet , vol.26 , Issue.8 , pp. 335-340
    • Stern, A.1    Keren, L.2    Wurtzel, O.3    Amitai, G.4    Sorek, R.5
  • 26
    • 34547579396 scopus 로고    scopus 로고
    • CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats
    • Web Server issue
    • Grissa I, Vergnaud G, Pourcel C. CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats. Nucleic Acids Res. 2007;35(Web Server issue):W52-7.
    • (2007) Nucleic Acids Res , vol.35 , pp. 52-57
    • Grissa, I.1    Vergnaud, G.2    Pourcel, C.3
  • 27
    • 0034097451 scopus 로고    scopus 로고
    • Identification of a new repetitive element in Staphylococcus aureus
    • Cramton SE, Schnell NF, Gotz F, Bruckner R. Identification of a new repetitive element in Staphylococcus aureus. Infect Immun. 2000;68(4):2344-8.
    • (2000) Infect Immun , vol.68 , Issue.4 , pp. 2344-2348
    • Cramton, S.E.1    Schnell, N.F.2    Gotz, F.3    Bruckner, R.4
  • 28
    • 84866647398 scopus 로고    scopus 로고
    • Variation in the genomic locations and sequence conservation of STAR elements among staphylococcal species provides insight into DNA repeat evolution
    • Purves J, Blades M, Arafat Y, Malik SA, Bayliss CD, Morrissey JA. Variation in the genomic locations and sequence conservation of STAR elements among staphylococcal species provides insight into DNA repeat evolution. BMC Genomics. 2012;13:515.
    • (2012) BMC Genomics , vol.13 , pp. 515
    • Purves, J.1    Blades, M.2    Arafat, Y.3    Malik, S.A.4    Bayliss, C.D.5    Morrissey, J.A.6
  • 29
    • 84903701767 scopus 로고    scopus 로고
    • Accurate computational prediction of the transcribed strand of CRISPR non-coding RNAs
    • Biswas A, Fineran PC, Brown CM. Accurate computational prediction of the transcribed strand of CRISPR non-coding RNAs. Bioinformatics. 2014;30:1805-13.
    • (2014) Bioinformatics , vol.30 , pp. 1805-1813
    • Biswas, A.1    Fineran, P.C.2    Brown, C.M.3
  • 31
    • 84884965371 scopus 로고    scopus 로고
    • CRISPRmap: an automated classification of repeat conservation in prokaryotic adaptive immune systems
    • Lange SJ, Alkhnbashi OS, Rose D, Will S, Backofen R. CRISPRmap: an automated classification of repeat conservation in prokaryotic adaptive immune systems. Nucleic Acids Res. 2013;41:8034-44.
    • (2013) Nucleic Acids Res , vol.41 , pp. 8034-8044
    • Lange, S.J.1    Alkhnbashi, O.S.2    Rose, D.3    Will, S.4    Backofen, R.5
  • 32
    • 84885082551 scopus 로고    scopus 로고
    • RNA-Seq reveals differential gene expression in Staphylococcus aureus with single-nucleotide resolution
    • Osmundson J, Dewell S, Darst SA. RNA-Seq reveals differential gene expression in Staphylococcus aureus with single-nucleotide resolution. PLoS One. 2013;8(10):e76572.
    • (2013) PLoS One , vol.8 , Issue.10
    • Osmundson, J.1    Dewell, S.2    Darst, S.A.3
  • 33
    • 84864042533 scopus 로고    scopus 로고
    • Diverse CRISPRs evolving in human microbiomes
    • Rho M, Wu Y, Tang H, Doak T, Ye Y. Diverse CRISPRs evolving in human microbiomes. PLoS Genet. 2012;8(6):e1002441.
    • (2012) PLoS Genet , vol.8 , Issue.6
    • Rho, M.1    Wu, Y.2    Tang, H.3    Doak, T.4    Ye, Y.5
  • 34
    • 34447644810 scopus 로고    scopus 로고
    • CRISPR Recognition Tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats
    • Bland C, Ramsey TL, Sabree F, Lowe M, Brown K, Kyrpides NC, Hugenholtz P. CRISPR Recognition Tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats. BMC Bioinformatics. 2007;8:209.
    • (2007) BMC Bioinformatics , vol.8 , pp. 209
    • Bland, C.1    Ramsey, T.L.2    Sabree, F.3    Lowe, M.4    Brown, K.5    Kyrpides, N.C.6    Hugenholtz, P.7
  • 35
    • 33745634395 scopus 로고    scopus 로고
    • Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences
    • Li W, Godzik A. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics. 2006;22(13):1658-9.
    • (2006) Bioinformatics , vol.22 , Issue.13 , pp. 1658-1659
    • Li, W.1    Godzik, A.2
  • 36
    • 79959931985 scopus 로고    scopus 로고
    • HMMER web server: interactive sequence similarity searching
    • Web Server issue
    • Finn RD, Clements J, Eddy SR. HMMER web server: interactive sequence similarity searching. Nucleic Acids Res. 2011;39(Web Server issue):W29-37.
    • (2011) Nucleic Acids Res , vol.39 , pp. 29-37
    • Finn, R.D.1    Clements, J.2    Eddy, S.R.3
  • 37
    • 84895793652 scopus 로고    scopus 로고
    • Expanding the catalog of cas genes with metagenomes
    • Zhang Q, Doak TG, Ye Y. Expanding the catalog of cas genes with metagenomes. Nucleic Acids Res. 2014;42(4):2448-9.
    • (2014) Nucleic Acids Res , vol.42 , Issue.4 , pp. 2448-2449
    • Zhang, Q.1    Doak, T.G.2    Ye, Y.3
  • 38
    • 78651326786 scopus 로고    scopus 로고
    • FragGeneScan: predicting genes in short and error-prone reads
    • Rho M, Tang H, Ye Y. FragGeneScan: predicting genes in short and error-prone reads. Nucleic Acids Res. 2010;38(20):e191.
    • (2010) Nucleic Acids Res , vol.38 , Issue.20
    • Rho, M.1    Tang, H.2    Ye, Y.3
  • 40
    • 33745634395 scopus 로고    scopus 로고
    • Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences
    • Li W, Godzik A. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics. 2006;22:2.
    • (2006) Bioinformatics , vol.22 , pp. 2
    • Li, W.1    Godzik, A.2
  • 42
    • 13244255415 scopus 로고    scopus 로고
    • MUSCLE: a multiple sequence alignment method with reduced time and space complexity
    • Edgar RC. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics. 2004;5:113.
    • (2004) BMC Bioinformatics , vol.5 , pp. 113
    • Edgar, R.C.1
  • 43
    • 67649327176 scopus 로고    scopus 로고
    • FastTree: computing large minimum evolution trees with profiles instead of a distance matrix
    • Price MN, Dehal PS, Arkin AP. FastTree: computing large minimum evolution trees with profiles instead of a distance matrix. Mol Biol Evol. 2009;26(7):1641-50.
    • (2009) Mol Biol Evol , vol.26 , Issue.7 , pp. 1641-1650
    • Price, M.N.1    Dehal, P.S.2    Arkin, A.P.3
  • 44
    • 84879005867 scopus 로고    scopus 로고
    • Evidence for the widespread distribution of CRISPR-Cas system in the Phylum Cyanobacteria
    • Cai F, Axen SD, Kerfeld CA. Evidence for the widespread distribution of CRISPR-Cas system in the Phylum Cyanobacteria. RNA Biol. 2013;10(5):687-93.
    • (2013) RNA Biol , vol.10 , Issue.5 , pp. 687-693
    • Cai, F.1    Axen, S.D.2    Kerfeld, C.A.3
  • 48
    • 0033555906 scopus 로고    scopus 로고
    • Tandem repeats finder: a program to analyze DNA sequences
    • Benson G. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 1999;27:573-80.
    • (1999) Nucleic Acids Res , vol.27 , pp. 573-580
    • Benson, G.1
  • 49
    • 84891633577 scopus 로고    scopus 로고
    • The role of variable DNA tandem repeats in bacterial adaptation
    • Zhou K, Aertsen A, Michiels CW. The role of variable DNA tandem repeats in bacterial adaptation. FEMS Microbiol Rev. 2014;38(1):119-41.
    • (2014) FEMS Microbiol Rev , vol.38 , Issue.1 , pp. 119-141
    • Zhou, K.1    Aertsen, A.2    Michiels, C.W.3
  • 50
    • 33847208871 scopus 로고    scopus 로고
    • Timescales of genetic and epigenetic inheritance
    • Rando OJ, Verstrepen KJ. Timescales of genetic and epigenetic inheritance. Cell. 2007;128(4):655-68.
    • (2007) Cell , vol.128 , Issue.4 , pp. 655-668
    • Rando, O.J.1    Verstrepen, K.J.2
  • 53
    • 33846975418 scopus 로고    scopus 로고
    • PILER-CR: fast and accurate identification of CRISPR repeats
    • Edgar RC. PILER-CR: fast and accurate identification of CRISPR repeats. BMC Bioinformatics. 2007;8:18.
    • (2007) BMC Bioinformatics , vol.8 , pp. 18
    • Edgar, R.C.1
  • 54
    • 84868092923 scopus 로고    scopus 로고
    • Genome Reduction and co-evolution between the primary and secondary bacterial symbionts of psyllids
    • Sloan DB, Moran NA. Genome Reduction and co-evolution between the primary and secondary bacterial symbionts of psyllids. Mol Biol Evol. 2012;29(12):3781-92.
    • (2012) Mol Biol Evol , vol.29 , Issue.12 , pp. 3781-3792
    • Sloan, D.B.1    Moran, N.A.2
  • 55
    • 65449136284 scopus 로고    scopus 로고
    • TopHat: discovering splice junctions with RNA-Seq
    • Trapnell C, Pachter L, Salzberg S. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics. 2009;25:1105-11.
    • (2009) Bioinformatics , vol.25 , pp. 1105-1111
    • Trapnell, C.1    Pachter, L.2    Salzberg, S.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.