CRISPR/Cas9技术在动物非编码RNA功能研究中的应用

doi:10.11843/j.issn.0366-6964.2020.04.001

Abstract

Abstract: CRISPR/Cas9 system is an immune mechanism that widely exists in bacteria and archaea. In recent years, it has been used as an efficient gene editing tool to investigate the function of coding or non-coding RNA. Non-coding RNA is a type of RNA that is not translated into proteins, and it plays an important role in biological processes such as animal growth, development and disease immunity through a variety of regulatory pathways. CRISPR/Cas9 technology can be used for targeting nucleotide sequence to get stable knockout mice or cell lines. When it is used in the research of non-coding RNA, it may interfere the expression of neighbor genes or host genes. Even though it has some shortages, this technology provides different ways for exploring the functional mechanism of non-coding RNA. In this review, we briefly summarize the history and functional principle of CRISPR/Cas system, and focus on its application in the functional research of miRNA, lncRNA and circRNA in animals in order to provide references for related research.

Key words: CRISPR/Cas9 technology, non-coding RNA, miRNA, lncRNA, circRNA, animal

CLC Number:

XU Xiaoli, CAO Jiaxue. Application of CRISPR/Cas9 Technology in the Study of Animal Non-coding RNA Function[J]. Acta Veterinaria et Zootechnica Sinica, 2020, 51(4): 649-659.

References 65

[1]	GARNEAU J E,DUPUIS M ō,VILLION M, et al.The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA[J].Nature,2010,468(7320):67-71.
[2]	LIU J Q,ZHOU Y Z,QI X L,et al.CRISPR/Cas9 in zebrafish:an efficient combination for human genetic diseases modeling[J]. Hum Genet,2017,136(1):1-12.
[3]	CAPELLINI T D,CHEN H,CAO J X,et al.Ancient selection for derived alleles at a GDF5 enhancer influencing human growth and osteoarthritis risk[J].Nat Genet,2017,49(8):1202-1210.
[4]	WU M M,WEI C H,LIAN Z X,et al.Rosa26-targeted sheep gene knock-in via CRISPR-Cas9 system[J].Sci Rep,2016,6:24360.
[5]	CONG L,RAN F A,COX D,et al.Multiplex genome engineering using CRISPR/Cas systems[J].Science,2013,339(6121):819-823.
[6]	ISHINO Y, SHINAGAWA H, MAKINO K, et al. Nucleotide sequence of the iap gene, responsible for alkaline phosphatase isozyme conversion in Escherichia coli, and identification of the gene product[J]. J Bacteriol, 1987, 169(12):5429-5433.
[7]	JANSEN R, EMBDEN J D, GAASTRA W, et al. Identification of genes that are associated with DNA repeats in prokaryotes[J]. Mol Microbiol, 2002, 43(6):1565-1575.
[8]	JINEK M, CHYLINSKI K, FONFARA I, et al. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity[J]. Science, 2012, 337(6096):816-821.
[9]	ABUDAYYEH O O, GOOTENBERG J S, ESSLETZBICHLER P, et al. RNA targeting with CRISPR-Cas13[J]. Nature, 2017, 550(7675):280-284.
[10]	HARRINGTON L B, BURSTEIN D, CHEN J S, et al. Programmed DNA destruction by miniature CRISPR-Cas14 enzymes[J]. Science, 2018, 362(6416):839-842.
[11]	DOLAN A E, HOU Z, XIAO Y, et al. Introducing a spectrum of long-range genomic deletions in human embryonic stem cells using type I CRISPR-Cas[J]. Mol Cell, 2019, 74(5):936-950.
[12]	KOONIN E V,MAKAROVA K S,ZHANG F.Diversity,classification and evolution of CRISPR-Cas systems[J].Curr Opin Microbiol, 2017,37:67-78.
[13]	YOU L L,MA J,WANG J Y,et al.Structure studies of the CRISPR-Csm complex reveal mechanism of co-transcriptional interference[J].Cell,2019,176(1-2):239-253.e16.
[14]	DOLAN A E,HOU Z G,XIAO Y B,et al.Introducing a spectrum of long-range genomic deletions in human embryonic stem cells using type I CRISPR-Cas[J].Mol Cell,2019,74(5):936-950.e5.
[15]	JIANG F G,DOUDNA J A.CRISPR-Cas9 structures and mechanisms[J].Annu Rev Biophys,2017,46:505-529.
[16]	HU J H,MILLER S M,GEURTS M H,et al.Evolved Cas9 variants with broad PAM compatibility and high DNA specificity[J].Nature,2018,556(7699):57-63.
[17]	GRAF R,LI X,CHU V T,et al.sgRNA sequence motifs blocking efficient CRISPR/Cas9-mediated gene editing[J].Cell Rep,2019, 26(5):1098-1103.e3.
[18]	FU Y F,SANDER J D,REYON D,et al.Improving CRISPR-Cas nuclease specificity using truncated guide RNAs[J].Nat Biotechnol,2014,32(3):279-284.
[19]	ZHANG J P,LI X L,NEISES A,et al.Different effects of sgRNA length on CRISPR-mediated gene knockout efficiency[J].Sci Rep, 2016,6:28566.
[20]	KOCAK D D,JOSEPHS E A,BHANDARKAR V,et al.Increasing the specificity of CRISPR systems with engineered RNA secondary structures[J].Nat Biotechnol,2019,37(6):657-666.
[21]	LIU L,YIN M L,WANG M,et al.Phage AcrIIA2 DNA mimicry:structural basis of the CRISPR and Anti-CRISPR arms race[J]. Mol Cell,2019,73(3):611-620.e3.
[22]	MAJI B,GANGOPADHYAY S A,LEE M,et al.A high-throughput platform to identify small-molecule inhibitors of CRISPR-Cas9[J]. Cell,2019,177(4):1067-1079.e19.
[23]	BOETTCHER M,MCMANUS M T.Choosing the right tool for the job:RNAi,TALEN,or CRISPR[J].Mol Cell,2015, 58(4):575-585.
[24]	GOYAL A,MYACHEVA K,GROß M,et al.Challenges of CRISPR/Cas9 applications for long non-coding RNA genes[J].Nucleic Acids Res,2017,45(3):e12.
[25]	ZHANG L,SALGADO-SOMOZA A,VAUSORT M,et al.A heart-enriched antisense long non-coding RNA regulates the balance between cardiac and skeletal muscle triadin[J].Biochim Biophys Acta Mol Cell Res,2018,1865(2):247-258.
[26]	ROSENBLUH J,XU H,HARRINGTON W,et al.Complementary information derived from CRISPR Cas9 mediated gene deletion and suppression[J].Nat Commun,2017,8:15403.
[27]	INOUE K,HIROSE M,INOUE H,et al.The rodent-specific microRNA cluster within the Sfmbt2 gene is imprinted and essential for placental development[J].Cell Rep,2017,19(5):949-956.
[28]	ONODERA Y,TERAMURA T,TAKEHARA T,et al.Inflammation-associated miR-155 activates differentiation of muscular satellite cells[J].PLoS One,2018,13(10):e0204860.
[29]	GAY S,BUGEON J,BOUCHAREB A,et al.MiR-202 controls female fecundity by regulating medaka oogenesis[J].PLoS Genet, 2018, 14(9):e1007593.
[30]	LI L L,ZHU Y L,CHEN T,et al.MiR-125b-2 knockout in testis is associated with targeting to the PAP gene,mitochondrial copy number,and impaired sperm quality[J].Int J Mol Sci,2019,20(1):148.
[31]	CUI Q,XING J H,YU M,et al.Mmu-miR-185 depletion promotes osteogenic differentiation and suppresses bone loss in osteoporosis through the Bgn-mediated BMP/Smad pathway[J].Cell Death Dis,2019,10(3):172.
[32]	ZHAO Y C,DAI Z,LIANG Y,et al.Sequence-specific inhibition of microRNA via CRISPR/CRISPRi system[J].Sci Rep,2014, 4:3943.
[33]	LI M H,LIU X Y,DAI S F,et al.High efficiency targeting of non-coding sequences using CRISPR/Cas9 system in tilapia[J].G3(Bethesda),2019,9(1):287-295.
[34]	JIANG Q,MENG X,MENG L W,et al.Small indels induced by CRISPR/Cas9 in the 5'region of microRNA lead to its depletion and Drosha processing retardance[J].RNA Biol,2014,11(10):1243-1249.
[35]	YAN Y,QIN D,HU B,et al.Deletion of miR-126a promotes hepatic aging and inflammation in a mouse model of cholestasis[J]. Mol Ther Nucleic Acids,2019,16:494-504.
[36]	李龙龙,朱燕玲,曾斌,等.基于转录组学筛选miR-125b-2敲除小鼠睾丸发育相关基因及信号通路的研究[J].畜牧兽医学报, 2019,50(10):2022-2031.LI L L,ZHU Y L,ZENG B,et al.Screening of genes and signaling pathway related to testicular development in miR-125b-2 knockout mouse based on transcriptomics[J].Acta Veterinaria et Zootechnica Sinica,2019,50(10):2022-2031.(in Chinese)
[37]	GHINI F,RUBOLINO C,CLIMENT M,et al.Endogenous transcripts control miRNA levels and activity in mammalian cells by target-directed miRNA degradation[J].Nat Commun,2018,9:3119.
[38]	WANG X W,HU L F,HAO J,et al.A microRNA-inducible CRISPR-Cas9 platform serves as a microRNA sensor and cell-type-specific genome regulation tool[J].Nat Cell Biol,2019,21(4):522-530.
[39]	HOFFMANN M D,ASCHENBRENNER S,GROSSE S,et al.Cell-specific CRISPR-Cas9 activation by microRNA-dependent expression of anti-CRISPR proteins[J].Nucleic Acids Res,2019,47(13):e75.
[40]	ZHOU S,LI S,ZHANG W W,et al.MiR-139 promotes differentiation of bovine skeletal muscle-derived satellite cells by regulating DHFR gene expression[J].J Cell Physiol,2019,234(1):632-641.
[41]	ZHANG W W,TONG H L,SUN X F,et al.Identification of miR-2400 gene as a novel regulator in skeletal muscle satellite cells proliferation by targeting MYOG gene[J].Biochem Biophys Res Commun,2015,463(4):624-631.
[42]	LIN Y,WU J H,GU W H,et al.Exosome-liposome hybrid nanoparticles deliver CRISPR/Cas9 system in MSCs[J].Adv Sci (Weinh), 2018,5(4):1700611.
[43]	LI Z L,ZHOU X Y,WEI M Y,et al.In vitro and in vivo RNA inhibition by CD9-HuR functionalized exosomes encapsulated with miRNA or CRISPR/dCas9[J].Nano Lett,2019,19(1):19-28.
[44]	YIN Y F,YAN P X,LU J L,et al.Opposing roles for the lncRNA Haunt and its genomic locus in regulating HOXA gene activation during embryonic stem cell differentiation[J].Cell Stem Cell,2015,16(5):504-516.
[45]	LUO S,LU J Y,LIU L C,et al.Divergent lncRNAs regulate gene expression and lineage differentiation in pluripotent cells[J].Cell Stem Cell,2016,18(5):637-652.
[46]	HOSONO Y,NIKNAFS Y S,PRENSNER J R,et al.Oncogenic role of THOR,a conserved cancer/testis long non-coding RNA[J].Cell,2017,171(7):1559-1572.e20.
[47]	WICHMAN L,SOMASUNDARAM S,BREINDEL C,et al.Dynamic expression of long noncoding RNAs reveals their potential roles in spermatogenesis and fertility[J].Biol Reprod,2017,97(2):313-323.
[48]	YANG D D,QIAO J,WANG G Y,et al.N6-Methyladenosine modification of lincRNA 1281 is critically required for mESC differentiation potential[J].Nucleic Acids Res,2018,46(8):3906-3920.
[49]	CHOWDHURY T A,KOCEJA C,EISA-BEYGI S,et al.Temporal and spatial post-transcriptional regulation of zebrafish tie1 mRNA by long noncoding RNA during brain vascular assembly[J].Arterioscler Throm B vasc Biol,2018,38(7):1562-1575.
[50]	WANG H,WANG X X,LI X R,et al.A novel long non-coding RNA regulates the immune response in MAC-T cells and contributes to bovine mastitis[J].FEBS J,2019,286(9):1780-1795.
[51]	STAFFORD D A,DICHMANN D S,CHANG J K,et al.Deletion of the sclerotome-enriched lncRNA PEAT augments ribosomal protein expression[J].Proc NatI Acad Sci U S A,2017,114(1):101-106.
[52]	BALLARINO M,CIPRIANO A,TITA R,et al.Deficiency in the nuclear long noncoding RNA Charme causes myogenic defects and heart remodeling in mice[J].EMBO J,2018,37(18):e99697.
[53]	田净净,刘洋洋,杨哲,等.利用CRISPR/Cas9系统高效敲除斑马鱼lncRNA基因启动子区[J].农业生物技术学报, 2016,24(5):649-656.TIAN J J,LIU Y Y,YANG Z,et al.Efficient knockout of lncRNA promoter region by CRISPR/Cas9 System in zebrafish (Danio rerio)[J].Journal of Agricultural Biotechnology,2016,24(5):649-656.(in Chinese)
[54]	APARICIO-PRAT E,ARNAN C,SALA I,et al.DECKO:single-oligo,dual-CRISPR deletion of genomic elements including long non-coding RNAs[J].BMC Genomics,2015,16:846.
[55]	YAMAZAKI T,FUJIKAWA C,KUBOTA A,et al.CRISPRa-mediated NEAT1 lncRNA upregulation induces formation of intact paraspeckles[J].Biochem Biophys Res Commun,2018,504(1):218-224.
[56]	SHECHNER D M,HACISULEYMAN E,YOUNGER S T,et al.Multiplexable,locus-specific targeting of long RNAs with CRISPR-Display[J].Nat Methods,2015,12(7):664-670.
[57]	STOJIC L,LUN A T L,MANGEI J,et al.Specificity of RNAi,LNA and CRISPRi as loss-of-function methods in transcriptional analysis[J].Nucleic Acids Res,2018,46(12):5950-5966.
[58]	PIWECKA M,GLAŽAR P,HERNANDEZ-MIRANDA L R,et al.Loss of a mammalian circular RNA locus causes miRNA deregulation and affects brain function[J].Science,2017,357(6357):eaam8526.
[59]	KLEAVELAND B,SHI C Y,STEFANO J,et al.A network of noncoding regulatory RNAs acts in the mammalian brain[J].Cell, 2018,174(2):350-362.e17.
[60]	ZHENG Q P,BAO C Y,GUO W J,et al.Circular RNA profiling reveals an abundant circHIPK3 that regulates cell growth by sponging multiple miRNAs[J].Nat Commun,2016,7:11215.
[61]	XIA P Y,WANG S,YE B Q,et al.A circular RNA protects dormant hematopoietic stem cells from DNA sensor cGAS-mediated exhaustion[J].Immunity,2018,48(4):688-701.e7.
[62]	GUPTA S K,GARG A,BAR C,et al.Quaking inhibits doxorubicin-mediated cardiotoxicity through regulation of cardiac circular RNA expression[J].Circ Res,2018,122(2):246-254.
[63]	FEI T,CHEN Y W,XIAO T F,et al.Genome-wide CRISPR screen identifies HNRNPL as a prostate cancer dependency regulating RNA splicing[J].Proc NatI Acad Sci U S A,2017,114(26):E5207-E5215.
[64]	LEGNINI I,DI TIMOTEO G,ROSSI F,et al.Circ-ZNF609 is a circular RNA that can be translated and functions in myogenesis[J]. Mol Cell,2017,66(1):22-37.e9.
[65]	ZHANG M L,ZHAO K,XU X P,et al.A peptide encoded by circular form of LINC-PINT suppresses oncogenic transcriptional elongation in glioblastoma[J].Nat Commun,2018,9(1):4475.

Application of CRISPR/Cas9 Technology in the Study of Animal Non-coding RNA Function

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