[1] Mussolino C,Cathomen T.RNA guides genome engineering.Nat Biotechnol,2013,31(3):208-209.
[2] Pan Y,Xiao L,Li A S,et al.Biological and biomedical applications of engineered nucleases.Molecular Biotechnology,2013,55(1):54-62.
[3] Sander J D,Joung J K.CRISPR-Cas systems for editing,regulating and targeting genomes.Nat Biotechnol,2014,32(4):347-355.
[4] Ramalingam S,London V,Kandavelou K,et al.Generation and genetic engineering of human induced pluripotent stem cells using designed zinc finger nucleases.Stem Cells Dev,2013,22(4):595-610.
[5] Dong P,Yu F,Fan X,et al.Inhibition of ATIR by shRNA prevents collagen synthesis in hepatic stellate cells.Molecular and Cellular Biochemistry,2010,344(1-2):195-202.
[6] Carroll D,Beumer K J.Genome engineering with TALENs and ZFNs:repair pathways and donor design.Methods,2014,69(2):137-141.
[7] Bedell V M,Wang Y,Campbell J M,et al.In vivo genome editing using a high-efficiency TALEN system.Nature,2012,491(7422):114-118.
[8] Sung Y H,Baek I J,Kim D H,et al.Knockout mice created by TALEN-mediated gene targeting.Nat Biotechnol,2013,31(1):23-24.
[9] Matzke M A,Mosher R A.RNA-directed DNA methylation:an epigenetic pathway of increasing complexity.Nature Reviews Genetics,2014,15(6):394-408.
[10] Wang H,Yang H,Shivalila C S,et al.One-step generation of mice carrying mutations in multiple genes by CRISPR/Cas-mediated genome engineering.Cell,2013,153(4):910-918.
[11] Chylinski K,Makarova K S,Charpentier E,et al.Classification and evolution of type Ⅱ CRISPR-Cas systems.Nucleic Acids Res,2014,42(10):6091-6105.
[12] Cong L,Ran F A,Cox D,et al.Multiplex genome engineering using CRISPR/Cas systems.Science,2013,339(6121):819-823.
[13] Alaiyan B,Ilyayev N,Stojadinovic A,et al.Differential expression of colon cancer associated transcript1(CCAT1) along the colonic adenoma-carcinoma sequence.BMC cancer,2013,13(1):196.
[14] Westra E R,Swarts D C,Staals R H,et al.The CRISPRs,they are a-changin:how prokaryotes generate adaptive immunity.Annu Rev Genet,2012,46:311-339.
[15] Labrie S J,Samson J E,Moineau S.Bacteriophage resistance mechanisms.Nat Rev Microbiol,2010,8(5):317-327.
[16] Barrangou R,Fremaux C,Deveau H,et al.CRISPR provides acquired resistance against viruses in prokaryotes.Science,2007,315(5819):1709-1712.
[17] Marraffini L A,Sontheimer E J.CRISPR interference:RNA-directed adaptive immunity in bacteria and archaea.Nature Reviews Genetics,2010,11(3):181-190.
[18] Lillestøl R,Redder P,Garrett R A,et al.A putative viral defence mechanism in archaeal cells.Archaea,2006,2(1):59-72.
[19] Mojica F J,García-Martínez J,Soria E.Intervening sequences of regularly spaced prokaryotic repeats derive from foreign genetic elements.Journal of Molecular Evolution,2005,60(2):174-182.
[20] Magadán A H,Dupuis M-È,Villion M,et al.Cleavage of phage DNA by the Streptococcus thermophilus CRISPR3-Cas system.PLoS One,2012,7(7):e40913.
[21] Bland C,Ramsey T L,Sabree F,et al.CRISPR recognition tool (CRT):a tool for automatic detection of clustered regularly interspaced palindromic repeats.BMC Bioinformatics,2007,8(1):209.
[22] Jansen R,Embden J,Gaastra W,et al.Identification of genes that are associated with DNA repeats in prokaryotes.Molecular Microbiology,2002,43(6):1565-1575.
[23] Deveau H,Garneau J E,Moineau S.CRISPR/Cas system and its role in phage-bacteria interactions.Annual review of Microbiology,2010,64:475-493.
[24] Makarova K S,Grishin N V,Shabalina S A,et al.A putative RNA-interference-based immune system in prokaryotes:computational analysis of the predicted enzymatic machinery,functional analogies with eukaryotic RNAi,and hypothetical mechanisms of action.Biology Direct,2006,1(1):7.
[25] Jansen R,van Embden J D,Gaastra W,et al.Identification of a novel family of sequence repeats among prokaryotes.Omics:A Journal of Integrative Biology,2002,6(1):23-33.
[26] Pourcel C,Salvignol G,Vergnaud G.CRISPR elements in Yersinia pestis acquire new repeats by preferential uptake of bacteriophage DNA,and provide additional tools for evolutionary studies.Microbiology,2005,151(3):653-663.
[27] Haft D H,Selengut J,Mongodin E F,et al.A guild of 45 CRISPR-associated (Cas) protein families and multiple CRISPR/Cas subtypes exist in prokaryotic genomes.PLoS Computational Biology,2005,1(6):e60.
[28] Makarova K S,Haft D H,Barrangou R,et al.Evolution and classification of the CRISPR-Cas systems.Nature Reviews Microbiology,2011,9(6):467-477.
[29] Han D,Krauss G.Characterization of the endonuclease SSO2001 from Sulfolobus solfataricus P2.FEBS Letters,2009,583(4):771-776.
[30] Wiedenheft B,Zhou K,Jinek M,et al.Structural basis for DNase activity of a conserved protein implicated in CRISPR-mediated genome defense.Structure,2009,17(6):904-912.
[31] Beane J D,Lee G K,Zheng Z,et al.Clinical scale zinc finger nuclease (ZFN)-driven gene-editing of PD-1 in tumor infiltrating lymphocytes (TIL) for the potential treatment of metastatic melanoma.Journal for Immunotherapy of Cancer,2014,2(Suppl 3):P2.
[32] Wood A J,Lo T-W,Zeitler B,et al.Targeted genome editing across species using ZFNs and TALENs.Science,2011,333(6040):307-307.
[33] Umasankar P K,Ma L,Thieman J R,et al.A clathrin coat assembly role for the muniscin protein central linker revealed by TALEN-mediated gene editing.eLife,2014,10(3):1-33.
[34] Barrangou R,Fremaux C,Deveau H,et al.CRISPR provides acquired resistance against viruses in prokaryotes.Science,2007,315(5819):1709-1712.
[35] Li T,Du B.CRISPR-Cas system and coevolution of bacteria and phages.Hereditas,2011,33(3):213-218.
[36] Garneau J E,Dupuis M-È,Villion M,et al.The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA.Nature,2010,468(7320):67-71.
[37] Beloglazova N,Brown G,Zimmerman M D,et al.A novel family of sequence-specific endoribonucleases associated with the clustered regularly interspaced short palindromic repeats.Journal of Biological Chemistry,2008,283(29):20361-20371.
[38] Koonin E V,Wolf Y I.Genomics of bacteria and archaea:the emerging dynamic view of the prokaryotic world.Nucleic Acids Research,2008,36(21):6688-6719.
[39] Sorek R,Kunin V,Hugenholtz P.CRISPR-a widespread system that provides acquired resistance against phages in bacteria and archaea.Nature Reviews Microbiology,2008,6(3):181-186.
[40] Bolotin A,Quinquis B,Sorokin A,et al.Clustered regularly interspaced short palindrome repeats (CRISPRs) have spacers of extrachromosomal origin.Microbiology,2005,151(8):2551-2561.
[41] Horvath P,Romero D A,Coûté-Monvoisin A C,et al.Diversity,activity,and evolution of CRISPR loci in Streptococcus thermophilus.Journal of Bacteriology,2008,190(4):1401-1412.
[42] Lillestøl R K,Shah S A,Brügger K,et al.CRISPR families of the crenarchaeal genus Sulfolobus:bidirectional transcription and dynamic properties.Molecular Microbiology,2009,72(1):259-272.
[43] Mojica F,Diez-Villasenor C,Garcia-Martinez J,et al.Short motif sequences determine the targets of the prokaryotic CRISPR defence system.Microbiology,2009,155(3):733-740.
[44] Gudbergsdottir S,Deng L,Chen Z,et al.Dynamic properties of the Sulfolobus CRISPR/Cas and CRISPR/Cmr systems when challenged with vector-borne viral and plasmid genes and protospacers.Molecular Microbiology,2011,79(1):35-49.
[45] Swarts D C,Mosterd C,Van Passel M W,et al.CRISPR interference directs strand specific spacer acquisition.PloS One,2012,7(4):e35888.
[46] Westra E R,van Erp P B,Künne T,et al.CRISPR immunity relies on the consecutive binding and degradation of negatively supercoiled invader DNA by Cascade and Cas3.Molecular Cell,2012,46(5):595-605.
[47] Semenova E,Jore M M,Datsenko K A,et al.Interference by clustered regularly interspaced short palindromic repeat (CRISPR) RNA is governed by a seed sequence.Proceedings of the National Academy of Sciences,2011,108(25):10098-10103.
[48] Zhang J,Rouillon C,Kerou M,et al.Structure and mechanism of the CMR complex for CRISPR-mediated antiviral immunity.Molecular Cell,2012,45(3):303-313.
[49] Marraffini L A,Sontheimer E J.Self versus non-self discrimination during CRISPR RNA-directed immunity.Nature,2010,463(7280):568-571.
[50] Agari Y,Sakamoto K,Tamakoshi M,et al.Transcription profile of Thermus thermophilus CRISPR systems after phage infection.Journal of Molecular Biology,2010,395(2):270-281.
[51] Kunin V,Sorek R,Hugenholtz P.Evolutionary conservation of sequence and secondary structures in CRISPR repeats.Genome Biol,2007,8(4):R61.
[52] Marraffini L A,Sontheimer E J.Self versus non-self discrimination during CRISPR RNA-directed immunity.Nature,2010,463(7280):568-571.
[53] Mojica F J,Díez-Villaseñor C.The on-off switch of CRISPR immunity against phages in Escherichia coli.Molecular Microbiology,2010,77(6):1341-1345.
[54] Pul V,Wurm R,Arslan Z,et al.Identification and characterization of E.coli CRISPR-cas promoters and their silencing by H-NS,Molecular Microbiology,2010,75(6):1495-1512.
[55] Westra E R,Pul V,Heidrich N,et al.H-NS-mediated repression of CRISPR-based immunity in Escherichia coli K12 can be relieved by the transcription activator LeuO.Molecular Microbiology,2010,77(6):1380-1393.
[56] Horvath P,Barrangou R.CRISPR/Cas,the immune system of bacteria and archaea.Science,2010,327(5962):167-170.
[57] Marraffini L A,Sontheimer E J.CRISPR interference limits horizontal gene transfer in staphylococci by targeting DNA.Science,2008,322(5909):1843-1845.
[58] Hale C R,Zhao P,Olson S,et al.RNA-guided RNA cleavage by a CRISPR RNA-Cas protein complex.Cell,2009,139(5):945-956.
[59] Van der Oost J,Brouns S J.RNAi:prokaryotes get in on the act.Cell,2009,139(5):863-865.
[60] Sinkunas T,Gasiunas G,Fremaux C,et al.Cas3 is a single-stranded DNA nuclease and ATP-dependent helicase in the CRISPR/Cas immune system.The EMBO journal,2011,30(7):1335-1342.
[61] Wiedenheft B,van Duijn E,Bultema J B,et al.RNA-guided complex from a bacterial immune system enhances target recognition through seed sequence interactions.Proceedings of the National Academy of Sciences,2011,108(25):10092-10097.
[62] Haurwitz R E,Jinek M,Wiedenheft B,et al.Sequence-and structure-specific RNA processing by a CRISPR endonuclease.Science,2010,329(5997):1355-1358.
[63] Friedland A E,Tzur Y B,Esvelt KM,et al.Heritable genome editing in C.elegans via a CRISPR-Cas9 system.Nature Methods,2013,10(8):741-743.
[64] Deltcheva E,Chylinski K,Sharma C M,et al.CRISPR RNA maturation by trans-encoded small RNA and host factor RNase Ⅲ.Nature,2011,471(7340):602-607.
[65] Anantharaman V,Iyer L M,Aravind L.Discovery notes presence of a classical RRM-fold palm domain in Thg1-type 3'-5'nucleic acid polymerases and the origin of the GGDEF and CRISPR polymerase domains,2010,5(43):1-9.
[66] Cermak T,Doyle E L,Christian M,et al.Efficient design and assembly of custom TALEN and other TAL effector-based constructs for DNA targeting.Nucleic Acids Research,2011,39(12):H1.
[67] Jiang W,Bikard D,Cox D,et al.RNA-guided editing of bacterial genomes using CRISPR-Cas systems.Nature Biotechnology,2013,31(3):233-239.
[68] Mali P,Yang L,Esvelt K M,et al.RNA-guided human genome engineering via Cas9.Science,2013,339(6121):823-826.
[69] Hwang W Y,Fu Y,Reyon D,et al.Efficient genome editing in zebrafish using a CRISPR-Cas system.Nature Biotechnology,2013,31(3):227-229.
[70] Brouns S J,Jore M M,Lundgren M,et al.Small CRISPR RNAs guide antiviral defense in prokaryotes.Science,2008,321(5891):960-964.
[71] Jinek M,East A,Cheng A,et al.RNA-programmed genome editing in human cells.Elife,2013,2(e00471):1-9.
[72] Cho S W,Kim S,Kim J M,et al.Targeted genome engineering in human cells with the Cas9 RNA-guided endonuclease.Nature Biotechnology,2013,31(3):230-232.
[73] Ding Q,Regan S N,Xia Y,et al.Enhanced efficiency of human pluripotent stem cell genome editing through replacing TALENs with CRISPRs.Cell Stem Cell,2013,12(4):393.
[74] Qi L S,Larson M H,Gilbert L A,et al.Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression.Cell,2013,152(5):1173-1183.
[75] Schwank G,Koo B-K,Sasselli V,et al.Functional repair of CFTR by CRISPR/Cas9 in intestinal stem cell organoids of cystic fibrosis patients.Cell Stem Cell,2013,13(6):653-658.
[76] Wu Y,Liang D,Wang Y,et al.Correction of a genetic disease in mouse via use of CRISPR-Cas9.Cell Stem Cell,2013,13(6):659-662.
[77] Raghavan A,Peters D,Kuperwasser N,et al.Functional characterization of a Cis-eQTL locus for plasma cholesterol using CRISPR/Cas genome editing in human pluripotent stem cells.Arteriosclerosis,Thrombosis,and Vascular Biology,2014,34(Suppl 1):A242-A242.
[78] Chen B,Gilbert L A,Cimini B A,et al.Dynamic imaging of genomic loci in living human cells by an optimized CRISPR/Cas system.Cell,2014,156(1):373.
[79] Deans J R,Titova N V,Wickramaratne A,et al.SAT-272:Verifying affinity altering SNPs with Crispr/Cas system in HepG2 Cells.2015.
[80] Wang H,Yang H,Shivalila C S,et al.One-step generation of mice carrying mutations in multiple genes by CRISPR/Cas-mediated genome engineering.Cell,2013,153(4):910-918.
[81] Li W,Teng F,Li T,et al.Simultaneous generation and germline transmission of multiple gene mutations in rat using CRISPR-Cas systems.Nature Biotechnology,2013,31(8):684-686.
[82] Carlson D F,Tan W,Lillico S G,et al.Efficient TALEN-mediated gene knockout in livestock.Proceedings of the National Academy of Sciences,2012,109(43):17382-17387.
[83] Yu S,Luo J,Song Z,et al.Highly efficient modification of beta-lactoglobulin (BLG) gene via zinc-finger nucleases in cattle.Cell Research,2011,21(11):1638-1640.
[84] Kennedy E M,Bassit LC,Mueller H,et al.Suppression of hepatitis B virus DNA accumulation in chronically infected cells using a bacterial CRISPR/Cas RNA-guided DNA endonuclease.Virology,2015,2(476):196-205.
[85] Kennedy E M,Kornepati A V,Goldstein M,et al.Inactivation of the human papillomavirus E6 or E7 gene in cervical carcinoma cells by using a bacterial CRISPR/Cas RNA-guided endonuclease.J Virol,2014,88(20):11965-11972.
[86] Yang H,Wang H,Jaenisch R.Generating genetically modified mice using CRISPR/Cas-mediated genome engineering.Nat Protoc,2014,9(8):1956-1968.
[87] Li X,Yang Y,Bu L,et al.Rosa26-targeted swine models for stable gene over-expression and Cre-mediated lineage tracing.Cell Res,2014,24(4):501-504.
[88] Hwang W Y,Fu Y,Reyon D,et al.Efficient genome editing in zebrafish using a CRISPR-Cas system.Nat Biotechnol,2013,31(3):227-229.
[89] Wang H C,Yang Y,Xu S Y,et al.The CRISPR/Cas system inhibited the pro-oncogenic effects of alternatively spliced fibronectin extra domain A via editing the genome in salivary adenoid cystic carcinoma cells.Oral Dis,2015,21(5):608-618.
[90] Niu Y,Shen B,Cui Y,et al.Generation of gene-modified cynomolgus monkey via Cas9/RNA-mediated gene targeting in one-cell embryos.Cell,2014,156(4):836-843.
[91] Ramírez O,Quintanilla R,Varona L,et al.DECR1 and ME1 genotypes are associated with lipid composition traits in Duroc pigs.Journal of Animal Breeding and Genetics,2014,131(1):46-52.
[92] Hua T,Wu D,Ding W,et al.Studies of Human 2,4-Dienoyl CoA Reductase Shed New Light on Peroxisomal β-Oxidation of Unsaturated Fatty Acids.Journal of Biological Chemistry,2012,287(34):28956-28965.
[93] Zanou N,Gailly P.Skeletal muscle hypertrophy and regeneration:interplay between the myogenic regulatory factors (MRFs) and insulin-like growth factors (IGFs) pathways.Cellular and Molecular Life Sciences,2013,70(21):4117-4130.
[94] Zhu C,Gi G,Tao Z,et al.Development of skeletal muscle and expression of myogenic regulatory factors during embryonic development in Jinding ducks (Anas platyrhynchos domestica).Poultry Science,2014,93(5):1211-1216.
[95] Choi Y,Suh Y,Ahn J,et al.Muscle hypertrophy in heavy weight Japanese quail line:Delayed muscle maturation and continued muscle growth with prolonged upregulation of myogenic regulatory factors.Poultry Science,2014,93(9):2271-2277.
[96] McPherron A C,Lee S J.Double muscling in cattle due to mutations in the myostatin gene.Proceedings of the National Academy of Sciences,1997,94(23):12457-12461.
[97] Hamilton D N,Ellis M,Miller K D,et al.The effect of the Halothane and Rendement Napole genes on carcass and meat quality characteristics of pigs.Journal of Animal Science-Menasha Then Albany Then Champaign Illinois,2000,78(11):2862-2867.
[98] Gispert M,Faucitano L,Oliver M,et al.A survey of pre-slaughter conditions,halothane gene frequency,and carcass and meat quality in five Spanish pig commercial abattoirs.Meat Science,2000,55(1):97-106.
[99] Zou Q,Wang X,Liu Y,et al.Generation of gene-target dogs using CRISPR/Cas9 system.Journal of Molecular Cell Biology,2015,7(6):580-583.
[100] Davies K T,Tsagkogeorga G,Bennett N C,et al.Molecular evolution of growth hormone and insulin-like growth factor 1 receptors in long-lived,small-bodied mammals.Gene,2014,549(2):228-236.
[101] Standen P,Sferruzzi-Perri A N,Taylor R,et al.Maternal insulin-like growth factor 1 and 2 differentially affect the renin-angiotensin system during pregnancy in the guinea pig.Growth Hormone&IGF Research,2015,25(3):141-147.
[102] Klimenko A,Usatov A,Getmantseva L,et al.Effects of melanocortin-4 receptor gene on growth and meat traits in pigs raised in russia.American Journal of Agricultural and Biological Sciences,2014,9(2):232.
[103] Zuo B,Liu G,Peng Y,et al.Melanocortin-4 receptor (MC4R) polymorphisms are associated with growth and meat quality traits in sheep.Molecular Biology Reports,2014,41(10):6967-6974.
[104] Chu Q,Cai L,Fu Y,et al.Dkk2/Frzb in the dermal papillae regulates feather regeneration.Developmental Biology,2014,387(2):167-178.
[105] Wang Z,Li Q,Zhang B,et al.Single nucleotide polymorphism scanning and expression of the FRZB gene in pig populations.Gene,2014,543(2):198-203.
[106] Van Laere A S,Nguyen M,Braunschweig M,et al.A regulatory mutation in IGF2 causes a major QTL effect on muscle growth in the pig.Nature,2003,425(6960):832-836.
[107] Houston F,Goldmann W,Foster J,et al.Comparative susceptibility of New Zealand sheep with a range of PRNP genotypes to challenge with bovine spongiform encephalopathy and scrapie.In:PRION;2014:Landes Bioscience 1806 Rio Grandest,Austin,TX 78702 USA,2014:102-102.
[108] Czarnik U,Strychalski J,Barcewicz M,et al.The effect of insertion/deletion polymorphisms within the promoter and intron 1 sequences of the PRNP gene on the breeding value of Holstein-Friesian bulls.Animal Science Papers and Reports,2015,33(1):13-22. |