高通量技术挖掘猪microRNA的研究进展

doi:10.11843/j.issn.0366-6964.2013.12.001

摘要/Abstract

摘要：

microRNA（miRNA）是一类功能强大的小RNA分子，大量的研究表明miRNA在生物的各种生命活动中发挥着重要的作用。本文首先对miRNA的发现、生成与作用机制进行了简单的阐述，并对测序技术的发展历史与新一代测序技术的出现进行了回顾；之后重点对高通量miRNA芯片技术与深度测序技术在猪miRNA研究中的应用进行了综述，并对未来miRNA的研究重点进行了展望。

关键词: microRNA, miRNA芯片, 深度测序, 猪

Abstract:

MicroRNA (miRNA) is a class of small RNA with powerful function, a larger number of studies indicate that miRNA play an important role in the life activities of various species. In this summary, we firstly described the discovery, biogenesis and function of miRNA, and reviewed the developmental history of sequencing technology and the emergence of next-generation sequencing technology. Following, we summarized the application of miRNA microarray and deep sequencing technology in the porcine miRNA researches, and proposed the miRNA research emphasis in the future.

Key words: microRNA, miRNA microarray, deep sequencing, pig

中图分类号:

S828
S813.1

吴望军，陈杰，黄瑞华，刘红林. 高通量技术挖掘猪microRNA的研究进展[J]. 畜牧兽医学报, 2013, 44(12): 1857-1866.

WU Wang-jun, CHEN Jie, HUANG Rui-hua, LIU Hong-lin. Advances in Porcine microRNA Research Using High-throughput Technologies[J]. ACTA VETERINARIA ET ZOOTECHNICA SINICA, 2013, 44(12): 1857-1866.

参考文献

［1］BUSHATI N, COHEN S M. microRNA functions ［J］. Annu Rev Cell Dev Biol, 2007, 23: 175-205. ［2］AMBROS V. The functions of animal microRNAs ［J］. Nature, 2004, 431(7006): 350-355. ［3］LYNAM-LENNON N, MAHER S G, REYNOLDS J V. The roles of microRNA in cancer and apoptosis ［J］.Biol Rev Camb Philos Soc, 2009, 84(1): 55-71. ［4］WANG Y, STRICKER H M, GOU D, et al. MicroRNA: past and present ［J］. Front Biosci, 2007, 12: 2316-2329. ［5］VAN ROOIJ E. The art of microRNA research ［J］. Circ Res, 2011, 108(2): 219-234. ［6］LI W, RUAN K. MicroRNA detection by microarray ［J］. Anal Bioanal Chem, 2009, 394(4): 1117-1124. ［7］BARTEL D P. MicroRNAs: target recognition and regulatory functions ［J］. Cell, 2009, 136(2): 215-233. ［8］BARTEL D P. MicroRNAs: genomics, biogenesis, mechanism, and function ［J］. Cell, 2004, 116(2): 281-297. ［9］LEE R C, FEINBAUM R L, AMBROS V. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14 ［J］. Cell, 1993, 75(5): 843-854. ［10］PASQUINELLI A E, REINHART B J, SLACK F, et al. Conservation of the sequence and temporal expression of let-7 heterochronic regulatory RNA ［J］. Nature, 2000, 408(6808): 86-89. ［11］REINHART B J, SLACK F J, BASSON M, et al. The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans ［J］. Nature, 2000, 403(6772): 901-906. ［12］LAGOS-QUINTANA M, RAUHUT R, LENDECKEL W, et al. Identification of novel genes coding for small expressed RNAs ［J］. Science, 2001, 294(5543): 853-858. ［13］LAU N C, LIM L P, WEINSTEIN E G, et al. An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans ［J］. Science, 2001, 294(5543): 858-862. ［14］LEE R, CAMBROS V. An extensive class of small RNAs in Caenorhabditis elegans ［J］. Science, 2001, 294(5543): 862-864. ［15］KOZOMAR A， AGRIFFITHS-JONES S. miRBase: integrating microRNA annotation and deep-sequencing data ［J］. Nucleic Acids Res, 2011, 39(Database issue): D152-157. ［16］CAI X, HAGEDORN C H, CULLEN B R. Human microRNAs are processed from capped, polyadenylated transcripts that can also function as mRNAs ［J］. RNA, 2004, 10(12): 1957-1966. ［17］LEE Y, KIM M, HAN J, et al. MicroRNA genes are transcribed by RNA polymerase II ［J］. EMBO J, 2004, 23(20): 4051-4060. ［18］BORCHERT G M, LANIER W, DAVIDSON B L. RNA polymerase III transcribes human microRNAs ［J］.Nat Struct Mol Biol, 2006, 13(12): 1097-1101. ［19］LEE Y, AHN C, HAN J, et al. The nuclear RNase III Drosha initiates microRNA processing ［J］. Nature, 2003, 425(6956): 415-419. ［20］DENLI A M, TOPS B B, PLASTERK R H, et al. Processing of primary microRNAs by the Microprocessor complex ［J］. Nature, 2004, 432(7014): 231-235. ［21］GREGORY R I, YAN K P, AMUTHAN G, et al. The Microprocessor complex mediates the genesis of microRNAs ［J］. Nature, 2004, 432(7014): 235-240. ［22］LUND E, GUTTINGER S, CALADO A, et al. Nuclear export of microRNA precursors ［J］. Science, 2004, 303(5654): 95-98. ［23］BOHNSACK M T, CZAPLINSKI K, GORLICH D. Exportin 5 is a RanGTP-dependent dsRNA-binding protein that mediates nuclear export of pre-miRNAs ［J］. RNA, 2004, 10(2): 185-191. ［24］YI R, QIN Y, MACARA I G, et al. Exportin-5 mediates the nuclear export of pre-microRNAs and short hairpin RNAs ［J］. Genes Dev, 2003, 17(24): 3011-3016. ［25］GREGORY R I, CHENDRIMADA T P, COOCH N, et al. Human RISC couples microRNA biogenesis and posttranscriptional gene silencing ［J］. Cell, 2005, 123(4): 631-640. ［26］MANIATAKI E, MOURELATOS Z. A human, ATP-independent, RISC assembly machine fueled by pre-miRNA ［J］. Genes Dev, 2005, 19(24): 2979-2990. ［27］SCHWARZ D S, HUTVAGNER G, DU T, et al. Asymmetry in the assembly of the RNAi enzyme complex［J］. Cell, 2003, 115(2): 199-208. ［28］DU T T, ZAMORE P D. microPrimer: the biogenesis and function of microRNA ［J］. Development, 2005, 132(21): 4645-4652. ［29］CHELOUFI S, DOS SANTOS C O, CHONG M M, et al. A dicer-independent miRNA biogenesis pathway that requires Ago catalysis ［J］. Nature, 2010, 465(7298): 584-589. ［30］LEWIS B P, BURGE C B, BARTEL D P. Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets ［J］. Cell, 2005, 120(1): 15-20. ［31］HUTVAGNER G, ZAMORE P D. A microRNA in a multiple-turnover RNAi enzyme complex ［J］. Science, 2002, 297(5589): 2056-2060. ［32］MARTINEZ J, TUSCHL T. RISC is a 5′ phosphomonoester-producing RNA endonuclease ［J］. Genes Dev, 2004, 18(9): 975-980. ［33］WU L, FAN J, BELASCO J G. MicroRNAs direct rapid deadenylation of mRNA ［J］. Proc Natl Acad Sci U S A, 2006, 103(11): 4034-4039. ［34］CARRINGTON J, CAMBROS V. Role of microRNAs in plant and animal development ［J］. Science, 2003, 301(5631): 336-338. ［35］MEISTER G, LANDTHALER M, PATKANIOWSKA A, et al. Human Argonaute2 mediates RNA cleavage targeted by miRNAs and siRNAs ［J］. Mol Cell, 2004, 15(2): 185-197. ［36］OKAMURA K, ISHIZUKA A, SIOMI H, et al. Distinct roles for Argonaute proteins in small RNA-directed RNA cleavage pathways ［J］. Genes Dev, 2004, 18(14): 1655-1666. ［37］LIU J, CARMELL M A, RIVAS F V, et al. Argonaute2 is the catalytic engine of mammalian RNAi ［J］. Science, 2004, 305(5689): 1437-1441. ［38］HUMPHREYS D T, WESTMAN B J, MARTIN D I, et al. MicroRNAs control translation initiation by inhibiting eukaryotic initiation factor 4E/cap and poly(A) tail function ［J］. Proc Natl Acad Sci U S A, 2005, 102(47): 16961-16966. ［39］MARONEY P A, YU Y, FISHER J, et al. Evidence that microRNAs are associated with translating messenger RNAs in human cells ［J］. Nat Struct Mol Biol, 2006, 13(12): 1102-1107. ［40］NOTTROTT S, SIMARD M J, RICHTER J D. Human let-7a miRNA blocks protein production on actively translating polyribosomes ［J］. Nat Struct Mol Biol, 2006, 13(12): 1108-1114. ［41］PETERSEN C P, BORDELEAU M E, PELLETIER J, et al. Short RNAs repress translation after initiation in mammalian cells ［J］. Mol Cell, 2006, 21(4): 533-542. ［42］PILLAI R S, BHATTACHARYYA S N, ARTUS C G, et al. Inhibition of translational initiation by Let-7 MicroRNA in human cells ［J］. Science, 2005, 309(5740): 1573-1576. ［43］YEKTA S, SHIH I H, BARTEL D P. MicroRNA-directed cleavage of HOXB8 mRNA ［J］. Science, 2004, 304(5670): 594-596. ［44］SCHANEN B C A X L. Transcriptional regulation of mammalian miRNA genes ［J］. Genomics, 2011, 97(1): 1-6. ［45］LIM L P, GLASNER M E, YEKTA S, et al. Vertebrate microRNA genes ［J］. Science, 2003, 299(5612): 1540. ［46］LIM L P, LAU N C, WEINSTEIN E G, et al. The microRNAs of Caenorhabditis elegans ［J］. Genes Dev, 2003, 17(8): 991-1008. ［47］LAI E C, TOMANCAK P, WILLIAMS R W, et al. Computational identification of Drosophila microRNA genes ［J］. Genome Biol, 2003, 4(7): R42. ［48］GRAD Y, AACH J, HAYES G D, et al. Computational and experimental identification of C. elegans microRNAs ［J］. Mol Cell, 2003, 11(5): 1253-1263. ［49］WANG X, ZHANG J, LI F, et al. MicroRNA identification based on sequence and structure alignment ［J］. Bioinformatics, 2005, 21(18): 3610-3614. ［50］NAM J W, KIM J, KIM S K, et al. ProMiR II: a web server for the probabilistic prediction of clustered, nonclustered, conserved and nonconserved microRNAs ［J］. Nucleic Acids Res, 2006, 34(Web Server issue): W455-458. ［51］NAM J W, SHIN K R, HAN J, et al. Human microRNA prediction through a probabilistic co-learning model of sequence and structure ［J］. Nucleic Acids Res, 2005, 33(11): 3570-3581. ［52］WERNERSSON R, SCHIERUP M H, JORGENSEN F G, et al. Pigs in sequence space: A 0.66X coverage pig genome survey based on shotgun sequencing ［J］. BMC Genomics, 2005, 6： 70. ［53］KIM H J, CUI X S, KIM E J, et al. New porcine microRNA genes found by homology search ［J］. Genome, 2006, 49(10): 1283-1286. ［54］KIM J, CHO I S, HONG J S, et al. Identification and characterization of new microRNAs from pig ［J］. Mamm Genome, 2008, 19(7-8): 570-580. ［55］SANGER F, NICKLEN S, COULSON A R. DNA sequencing with chain-terminating inhibitors ［J］. Proc Natl Acad Sci U S A, 1977, 74(12): 5463-5467. ［56］International human genome sequencing consortium. Finishing the euchromatic sequence of the human genome ［J］. Nature, 2004, 431(7011): 931-945. ［57］MARGULIES M, EGHOLM M, ALTMAN W E, et al. Genome sequencing in microfabricated high-density picolitre reactors ［J］. Nature, 2005, 437(7057): 376-380. ［58］MARDIS E R. Next-generation DNA sequencing methods ［J］. Annu Rev Genomics Hum Genet, 2008, 9: 387-402. ［59］WANG Z, GERSTEIN M, SNYDER M. RNA-Seq: a revolutionary tool for transcriptomics ［J］. Nat Rev Genet, 2009, 10(1): 57-63. ［60］PAREEK C S, SMOCZYNSKI R, TRETYN A. Sequencing technologies and genome sequencing ［J］. J Appl Genet, 2011, 52(4): 413-435. ［61］METZKER M L. Sequencing technologies- the next generation ［J］. Nat Rev Genet, 2010, 11(1): 31-46. ［62］BIRZELE F, SCHAUB J, RUST W, et al. Into the unknown: expression profiling without genome sequence information in CHO by next generation sequencing ［J］. Nucleic Acids Res, 2010, 38(12): 3999-4010. ［63］SCHADT E E, TURNER S, KASARSKIS A. A window into third-generation sequencing ［J］. Hum Mol Genet, 2010, 19(R2): R227-240. ［64］LU C, TEJ S S, LUO S, et al. Elucidation of the small RNA component of the transcriptome ［J］. Science, 2005, 309(5740): 1567-1569. ［65］RUBY J G, JAN C, PLAYER C, et al. Large-scale sequencing reveals 21U-RNAs and additional microRNAs and endogenous siRNAs in C. elegans ［J］. Cell, 2006, 127(6): 1193-1207. ［66］REDDY A M, ZHENG Y, JAGADEESWARAN G, et al. Cloning, characterization and expression analysis of porcine microRNAs ［J］. BMC Genomics, 2009, 10: 65. ［67］NIELSEN M, HANSEN J H, HEDEGAARD J, et al. MicroRNA identity and abundance in porcine skeletal muscles determined by deep sequencing ［J］. Anim Genet, 2010, 41(2): 159-168. ［68］SHARBATI S, FRIEDLANDER M R, SHARBATI J, et al. Deciphering the porcine intestinal microRNA transcriptome ［J］. BMC Genomics, 2010, 11: 275. ［69］LI M, XIA Y, GU Y, et al. MicroRNAome of porcine pre- and postnatal development ［J］. PLoS ONE, 2010, 5(7): e11541. ［70］LI M, LIU Y, WANG T, et al. Repertoire of porcine microRNAs in adult ovary and testis by deep sequencing ［J］. Int J Biol Sci, 2011, 7(7): 1045-1055. ［71］XIE S S, LI X Y, LIU T, et al. Discovery of porcine microRNAs in multiple tissues by a Solexa deep sequencing approach ［J］. PLoS ONE, 2011, 6(1): e16235. ［72］CHEN C, AI H, REN J, et al. A global view of porcine transcriptome in three tissues from a full-sib pair with extreme phenotypes in growth and fat deposition by paired-end RNA sequencing ［J］. BMC Genomics, 2011, 12: 448. ［73］LI G X, LI Y J, LI X J, et al. MicroRNA identity and abundance in developing swine adipose tissue as determined by solexa sequencing ［J］. J Cell Biochem, 2011, 112(5): 1318-1328. ［74］LIAN C, SUN B, NIU S, et al. A comparative profile of the microRNA transcriptome in immature and mature porcine testes using Solexa deep sequencing ［J］. FEBS J, 2012, 279(6): 964-975. ［75］LI H, XI Q, XIONG Y, et al. A comprehensive expression profile of microRNAs in porcine pituitary ［J］. PLoS ONE, 2011, 6(9): e24883. ［76］DAI C, ZHANG Y M, ZHANG Q, et al. A microRNA catalog of swine umbilical vein endothelial cells identified by deep sequencing ［J］. Agric Sci Chn, 2011, 10(9): 1467-1474. ［77］CHEN C, DENG B, QIAO M, et al. Solexa sequencing identification of conserved and novel microRNAs in backfat of Large White and Chinese Meishan pigs ［J］. PLoS ONE, 2012, 7(2): e31426. ［78］WU Y Q, CHEN D J, HE H B, et al. Pseudorabies virus infected porcine epithelial cell line generates a diverse set of host microRNAs and a special cluster of viral microRNAs ［J］. PLoS ONE, 2012, 7(1): e30988. ［79］HOU X, TANG Z, LIU H, et al. Discovery of microRNAs associated with myogenesis by deep sequencing of serial developmental skeletal muscles in pigs ［J］. PLoS ONE, 7(12): e52123. ［80］CHEN J H, WEI W J, XIAO X, et al. Expression analysis of rniRNAs in porcine fetal skeletal muscle on days 65 and 90 of gestation ［J］. Asian-Austra J Anim Sci, 2008, 21(7): 954-960. ［81］HUANG T H, ZHU M J, LI X Y, et al. Discovery of porcine microRNAs and profiling from skeletal muscle tissues during development ［J］. PLoS ONE, 2008, 3(9): e3225. ［82］SU L, ZHAO S, ZHU M, et al. Differential expression of microRNAs in porcine placentas on days 30 and 90 of gestation ［J］. Reprod Fertil Dev, 2010, 22(8): 1175-1182. ［83］LUO L, YE L, LIU G, et al. Microarray-based approach identifies differentially expressed microRNAs in porcine sexually immature and mature testes ［J］. PLoS ONE, 2010, 5(8): e11744. ［84］ZHOU B, LIU H L, SHI F X, et al. MicroRNA expression profiles of porcine skeletal muscle ［J］. Anim Genet, 2010, 41(5): 499-508. ［85］CURRY E, ELLIS S E, PRATT S L. Detection of porcine sperm microRNAs using a heterologous microRNA microarray and reverse transcriptase polymerase chain reaction ［J］. Mol Reprod Dev, 2009, 76(3): 218-219. ［86］PODOLSKA A, KACZKOWSKI B, KAMP BUSK P, et al. MicroRNA expression profiling of the porcine developing brain ［J］. PLoS ONE, 2011, 6(1): e14494. ［87］KIM H J, CUI X S, KIM E J, et al. New porcine microRNA genes found by homology search ［J］. Genome, 2006, 49(10): 1283-1286. ［88］SHARBATI-TEHRANI S, KUTZ-LOHROFF B, SCHOLVEN J, et al. Concatameric cloning of porcine microRNA molecules after assembly PCR ［J］. Biochem Biophys Res Commun, 2008, 375(3): 484-489. ［89］MCDANELD T G, SMITH T P, DOUMIT M E, et al. MicroRNA transcriptome profiles during swine skeletal muscle development ［J］. BMC Genomics, 2009, 10: 77. ［90］XIE S S, HUANG T H, SHEN Y, et al. Identification and characterization of microRNAs from porcine skeletal muscle ［J］. Anim Genet, 2009, 41(2): 179-190. ［91］CHO I S, KIM J, SEO H Y, et al. Cloning and characterization of microRNAs from porcine skeletal muscle and adipose tissue ［J］. Mol Biol Rep, 2010, 37(7): 3567-3574.

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