[1] | Carninci P, Kasukawa T, Katayama S, Gough J, Frith MC, Maeda N, Oyama R, Ravasi T, Lenhard B, Wells C, Kodzius R, Shimokawa K, Bajic VB, Brenner SE, Batalov S, Forrest ARR, Zavolan M, Davis MJ, Wilming LG, Aidinis V, Allen JE, Ambesi-Impiombato A, Apweiler R, Aturaliya RN, Bailey TL, Bansal M, Baxter L, Beisel KW, Bersano T, Bono H, Chalk AM, Chiu KP, Choudhary V, Christoffels A, Clutterbuck DR, Crowe ML, Dalla E , Dalrymple BP, de Bono B, Della Gatta G, di Bernardo D, Down T, Engstrom P, Fagiolini M, Faulkner G, Fletcher CF, Fukushima T, Furuno M, Futaki S, Gariboldi M, Georgii-Hemming P, Gingeras TR, Gojobori T, Green RE, Gustincich S, Harbers M, Hayashi Y, Hensch TK, Hirokawa N, Hill D, Huminiecki L, Iacono M, Ikeo K, Iwama A, Ishikawa T, Jakt M, Kanapin A, Katoh M, Kawasawa Y, Kelso J, Kitamura H, Kitano H, Kollias G, Krishnan SPT, Kruger A, Kummerfeld SK, Kurochkin IV, Lareau LF, Lazarevic D, Lipovich L, Liu J, Liuni S, McWilliam S, Madan Babu M, Madera M, Marchionni L, Matsuda H, Matsuzawa S, Miki H, Mignone F, Miyake S, Morris K, Mottagui-Tabar S, Mulder N, Nakano N, Nakauchi H, Ng P, Nilsson R, Nishiguchi S, Nishikawa S, Nori F, Ohara O, Okazaki Y, Orlando V, Pang KC, Pavan WJ, Pavesi G, Pesole G, Petrovsky N, Piazza S, Reed J, Reid JF, Ring BZ, Ringwald M, Rost B, Ruan Y, Salzberg SL, Sandelin A, Schneider C, Schonbach C, Sekiguchi K, Semple CAM, Seno S, Sessa L, Sheng Y, Shibata Y, Shimada H, Shimada K, Silva D, Sinclair B, Sperling S, Stupka E, Sugiura K, Sultana R, Takenaka Y, Taki K, Tammoja K, Tan SL, Tang S, Taylor MS, Tegner J, Teichmann SA, Ueda HR, van Nimwegen E, Verardo R, Wei CL, Yagi K, Yamanishi H, Zabarovsky E, Zhu S, Zimmer A, Hide W, Bult C, Grimmond SM, Teasdale RD, Liu ET, Brusic V, Quackenbush J, Wahlestedt C, Mattick JS, Hume DA, Kai C, Sasaki D, Tomaru Y, Fukuda S, Kanamori-Katayama M, Suzuki M, Aoki J, Arakawa T, Iida J, Imamura K, Itoh M, Kato T, Kawaji H, Kawagashira N, Kawashima T, Kojima M, Kondo S, Konno H, Nakano K, Ninomiya N, Nishio T, Okada M, Plessy C, Shibata K, Shiraki T, Suzuki S, Tagami M, Waki K, Watahiki A, Okamura-Oho Y, Suzuki H, Kawai J, Hayashizaki Y, FANTOM Consortium, RIKEN Genome Exploration Research Group and Genome Science Group (Genome Network Project Core Group). The transcriptional landscape of the mammalian genome. Science, 2005,309(5740):1559-1563. | [2] | Nelson BR, Makarewich CA, Anderson DM, Winders BR, Troupes CD, Wu FF, Reese AL , McAnally JR, Chen XW, Kavalali ET, Cannon SC, Houser SR, Bassel-Duby R, Olson EN. A peptide encoded by a transcript annotated as long noncoding RNA enhances SERCA activity in muscle. Science, 2016,351(6270):271-275. | [3] | Anderson DM, Anderson KM, Chang CL, Makarewich CA, Nelson BR , McAnally JR, Kasaragod P, Shelton JM, Liou J, Bassel-Duby R, Olson EN. A micropeptide encoded by a putative long noncoding RNA regulates muscle performance. Cell, 2015,160(4):595-606. | [4] | Anderson DM, Makarewich CA, Anderson KM, Shelton JM, Bezprozvannaya S, Bassel-Duby R , Olson EN. Widespread control of calcium signaling by a family of SERCA-inhibiting micropeptides. Sci Signal, 2016, 9(457): ra119. | [5] | Quan MY, Chen JH, Zhang DQ . Exploring the secrets of long noncoding RNAs. Int J Mol Sci, 2015,16(3):5467-5496. | [6] | Li YY, Chen XN, Sun H, Wang HT . Long non-coding RNAs in the regulation of skeletal myogenesis and muscle diseases. Cancer Lett, 2018,417:58-64. | [7] | Salmena L, Poliseno L, Tay Y, Kats L, Pandolfi PP . A ceRNA hypothesis: the Rosetta stone of a hidden RNA language? Cell, 2011,146(3):353-358. | [8] | Gong CG, Li ZZ, Ramanujan K, Clay I, Zhang YY, Lemire-Brachat S, Glass DJ . A long non-coding RNA, LncMyoD, regulates skeletal muscle differentiation by blocking IMP2-mediated mRNA translation. Dev Cell, 2015,34(2):181-191. | [9] | Watts R, Johnsen VL, Shearer J, Hittel DS . Myostatin- induced inhibition of the long noncoding RNA Malat1 is associated with decreased myogenesis. Am J Physiol Cell Physiol, 2013,304(10):C995-C1001. | [10] | Li SJ, Czubryt MP , McAnally J, Bassel-Duby R, Richardson JA, Wiebel FF, Nordheim A, Olson EN. Requirement for serum response factor for skeletal muscle growth and maturation revealed by tissue-specific gene deletion in mice. Proc Natl Acad Sci USA, 2005,102(4):1082-1087. | [11] | Han XR, Yang F, Cao HQ, Liang ZC . Malat1 regulates serum response factor through miR-133 as a competing endogenous RNA in myogenesis. FASEB J, 2015,29(7):3054-3064. | [12] | Cesana M, Cacchiarelli D, Legnini I, Santini T, Sthandier O, Chinappi M, Tramontano A, Bozzoni I . A long noncoding RNA controls muscle differentiation by functioning as a competing endogenous RNA. Cell, 2011,147(2):358-369. | [13] | Legnini I, Morlando M, Mangiavacchi A, Fatica A, Bozzoni I . A feedforward regulatory loop between HuR and the long noncoding RNA linc-MD1 controls early phases of myogenesis. Mol Cell, 2014,53(3):506-514. | [14] | Qin CY, Cai H, Qing HR, Li L, Zhang HP . Recent advances on the role of long non-coding RNA H19 in regulating mammalian muscle growth and development. Hereditas (Beijing), 2017,39(12):1150-1157. | [14] | 秦辰雨, 蔡禾, 卿涵睿, 李利, 张红平 . 长链非编码RNA H19对哺乳动物肌肉生长发育的调控. 遗传, 2017,39(12):1150-1157. | [15] | Kallen AN, Zhou XB, Xu J, Qiao C, Ma J, Yan L, Lu LG, Liu CC, Yi JS, Zhang HF, Min W, Bennett AM, Gregory RI, Ding Y, Huang YQ . The imprinted H19 lncRNA antagonizes let-7 microRNAs. Mol Cell, 2013,52(1):101-112. | [16] | Zhu M, Liu JF, Xiao J, Yang L, Cai MX, Shen HY, Chen XJ, Ma Y, Hu SM, Wang ZL, Hong A, Li YX, Sun Y, Wang XG . Lnc-mg is a long non-coding RNA that promotes myogenesis. Nat Commun, 2017,8:14718. | [17] | Wang LJ, Zhao Y, Bao XC, Zhu XH, Kwok YKY, Sun K, Chen XN, Huang YH, Jauch R, Esteban MA, Sun H, Wang HT . LncRNA Dum interacts with Dnmts to regulate Dppa2 expression during myogenic differentiation and muscle regeneration. Cell Res, 2015,25(3):335-350. | [18] | Cabianca DS, Casa V, Bodega B, Xynos A, Ginelli E, Tanaka Y, Gabellini D . A long ncRNA links copy number variation to a polycomb/trithorax epigenetic switch in FSHD muscular dystrophy. Cell, 2012,149(4):819-831. | [19] | Lee JT, Bartolomei MS . X-inactivation, imprinting, and long noncoding RNAs in health and disease. Cell, 2013,152(6):1308-1323. | [20] | Dey BK, Pfeifer K, Dutta A . The H19 long noncoding RNA gives rise to microRNAs miR-675-3p and miR- 675-5p to promote skeletal muscle differentiation and regeneration. Genes Dev, 2014,28(5):491-501. | [21] | Zhao J, Ohsumi TK, Kung JT, Ogawa Y, Grau DJ, Sarma K, Song JJ, Kingston RE, Borowsky M, Lee JT . Genome-wide identification of polycomb-associated RNAs by RIP-seq. Mol Cell, 2010,40(6):939-953. | [22] | Zhou YL, Cheunsuchon P, Nakayama Y, Lawlor MW, Zhong Y, Rice KA, Zhang L, Zhang X, Gordon FE, Lidov HGW, Bronson RT, Klibanski A . Activation of paternally expressed genes and perinatal death caused by deletion of the Gtl2 gene. Development, 2010,137(16):2643-2652. | [23] | Davis E, Jensen CH, Schroder HD, Farnir F, Shay-Hadfield T, Kliem A, Cockett N, Georges M, Charlier C . Ectopic expression of DLK1 protein in skeletal muscle of padumnal heterozygotes causes the callipyge phenotype. Curr Biol, 2004,14(20):1858-1862. | [24] | Wang JS, Gong CG, Maquat LE . Control of myogenesis by rodent SINE-containing lncRNAs. Genes Dev, 2013,27(7):793-804. | [25] | Tripathi V, Ellis JD, Shen Z, Song DY, Pan Q, Watt AT, Freier SM, Bennett CF, Sharma A, Bubulya PA, Blencowe BJ, Prasanth SG, Prasanth KV . The nuclear-retained noncoding RNA MALAT1 regulates alternative splicing by modulating SR splicing factor phosphorylation. Mol Cell, 2010,39(6):925-938. | [26] | Odelberg SJ, Kollhoff A, Keating MT . Dedifferentiation of mammalian myotubes induced by msx1. Cell, 2000,103(7):1099-1109. | [27] | Blin-Wakkach C, Lezot F, Ghoul-Mazgar S, Hotton D, Monteiro S, Teillaud C, Pibouin L, Orestes-Cardoso S, Papagerakis P, Macdougall M, Robert B, Berdal A . Endogenous Msx1 antisense transcript: in vivo and in vitro evidences, structure, and potential involvement in skeleton development in mammals. Proc Natl Acad Sci USA, 2001,98(13):7336-7341. | [28] | Pardo PS, Boriek AM . The physiological roles of Sirt1 in skeletal muscle. Aging, 2011,3(4):430-437. | [29] | Wang GQ, Wang Y, Xiong Y, Chen XC, Ma ML, Cai R, Gao Y, Sun YM, Yang GS, Pang WJ . Sirt1 AS lncRNA interacts with its mRNA to inhibit muscle formation by attenuating function of miR-34a. Sci Rep, 2016,6:21865. | [30] | Mueller AC, Cichewicz MA, Dey BK, Layer R, Reon BJ, Gagan JR, Dutta A . MUNC, a long noncoding RNA that facilitates the function of MyoD in skeletal myogenesis. Mol Cell Biol, 2015,35(3):498-513. | [31] | Mousavi K, Zare H , Dell'orso S, Grontved L, Gutierrez-Cruz G, Derfoul A, Hager GL, Sartorelli V. eRNAs promote transcription by establishing chromatin accessibility at defined genomic loci. Mol Cell, 2013,51(5):606-617. | [32] | Caretti G, Schiltz RL, Dilworth FJ, Di Padova M, Zhao P, Ogryzko V, Fuller-Pace FV, Hoffman EP, Tapscott SJ, Sartorelli V . The RNA helicases p68/p72 and the noncoding RNA SRA are coregulators of MyoD and skeletal muscle differentiation. Dev Cell, 2006,11(4):547-560. | [33] | Hubé F, Velasco G, Rollin J, Furling D, Francastel C . Steroid receptor RNA activator protein binds to and counteracts SRA RNA-mediated activation of MyoD and muscle differentiation. Nucleic Acids Res, 2011,39(2):513-525. | [34] | Lu LN, Sun K, Chen XN, Zhao Y, Wang LJ, Zhou L, Sun H, Wang HT . Genome-wide survey by ChIP-seq reveals YY1 regulation of lincRNAs in skeletal myogenesis. EMBO J, 2013,32(19):2575-2588. | [35] | Yu XH, Zhang Y, Li TT, Ma Z, Jia HX, Chen Q, Zhao YX, Zhai LL, Zhong R, Li CY, Zou XT, Meng J, Chen AK, Puri PL, Chen MH, Zhu DH . Long non-coding RNA Linc-RAM enhances myogenic differentiation by interacting with MyoD. Nat Commun, 2017,8:14016. | [36] | Matsumoto A, Pasut A, Matsumoto M, Yamashita R, Fung J, Monteleone E, Saghatelian A, Nakayama KI, Clohessy JG , Pandolfi PP. mTORC1 and muscle regeneration are regulated by the LINC00961-encoded SPAR polypeptide. Nature, 2017,541(7636):228-232. | [37] | Neguembor MV, Jothi M, Gabellini D . Long noncoding RNAs, emerging players in muscle differentiation and disease. Skelet Muscle, 2014,4(1):8. | [38] | Dey BK, Mueller AC, Dutta A . Long non-coding RNAs as emerging regulators of differentiation, development, and disease. Transcription, 2014,5(4):e944014. | [39] | Lopez-Pajares V . Long non-coding RNA regulation of gene expression during differentiation. Pflügers Arch-Eur J Physiol, 2016,468(6):971-981. | [40] | Kashi K, Henderson L, Bonetti A, Carninci P . Discovery and functional analysis of lncRNAs: methodologies to investigate an uncharacterized transcriptome. Biochim Biophys Acta (BBA)-Gene Regul Mech, 2016,1859(1):3-15. | [41] | Lee JH, Daugharthy ER, Scheiman J, Kalhor R, Ferrante TC, Terry R, Turczyk BM, Yang JL, Lee HS, Aach J, Zhang K, Church GM . Fluorescent in situ sequencing (FISSEQ) of RNA for gene expression profiling in intact cells and tissues. Nat Protoc, 2015,10(3):442-458. | [42] | Zhang T, Tan PW, Wang LQ, Jin NN, Li YN, Zhang L, Yang H, Hu ZY, Zhang LN, Hu CY, Li CH, Qian K, Zhang CJ, Huang Y, Li KN, Lin H, Wang D . RNALocate: a resource for RNA subcellular localizations. Nucleic Acids Res, 2017,45(D1):D135-D138. | [43] | Yang JH, Li JH, Jiang S, Zhou H, Qu LH . ChIPBase: a database for decoding the transcriptional regulation of long non-coding RNA and microRNA genes from ChIP- Seq data. Nucleic Acids Res, 2013,41(D):D177-D187. | [44] | Paraskevopoulou MD, Georgakilas G, Kostoulas N, Reczko M, Maragkakis M, Dalamagas TM, Hatzigeorgiou AG . DIANA-LncBase: experimentally verified and computationally predicted microRNA targets on long non- coding RNAs. Nucleic Acids Res, 2013,41(D):D239-D245. | [45] | Jiang QH, Ma R, Wang JX, Wu XL, Jin SL, Peng JJ, Tan RJ, Zhang TJ, Li Y , Wang YD.LncRNA2Function: a comprehensive resource for functional investigation of human lncRNAs based on RNA-seq data. BMC Genomics, 2015,16 Suppl 3: S2. | [46] | Gong J, Liu W, Zhang JY, Miao XP , Guo AY. lncRNASNP: a database of SNPs in lncRNAs and their potential functions in human and mouse. Nucleic Acids Res, 2015,43(D):D181-D186. | [47] | Hao YJ, Wu W, Li H, Yuan J, Luo JJ, Zhao Y, Chen RS . NPInter v3.0: an upgraded database of noncoding RNA- associated interactions. Database (Oxford), 2016, 2016: baw057. | [48] | Terai G, Iwakiri J, Kameda T, Hamada M , Asai K. Comprehensive prediction of lncRNA-RNA interactions in human transcriptome. BMC Genomics, 2016,17 Suppl 1: 12. | [49] | Li JH, Liu S, Zhou H, Qu LH , Yang JH. starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein- RNA interaction networks from large-scale CLIP-Seq data. Nucleic Acids Res, 2014,42(D):D92-D97. | [50] | Marín-Béjar O, Huarte M . RNA pulldown protocol for in vitro detection and identification of RNA-associated proteins. Methods Mol Biol, 2015,1206:87-95. | [51] | Dahm GM, Gubin MM, Magee JD, Techasintana P, Calaluce R, Atasoy U . Method for the isolation and identification of mRNAs, microRNAs and protein components of ribonucleoprotein complexes from cell extracts using RIP-Chip. J Vis Exp, 2012, ( 67):3851. | [52] | Simon MD, Wang CI, Kharchenko PV, West JA, Chapman BA, Alekseyenko AA, Borowsky ML, Kuroda MI, Kingston RE . The genomic binding sites of a noncoding RNA. Proc Natl Acad Sci USA, 2011,108(51):20497-20502. | [53] | Chu C, Qu K, Zhong FL, Artandi SE, Chang HY . Genomic maps of long noncoding RNA occupancy reveal principles of RNA-chromatin interactions. Mol Cell, 2011,44(4):667-678. | [54] | Vance KW. Mapping long noncoding RNA chromatin occupancy using capture hybridization analysis of RNA targets (CHART). In: Ørom U, ed. Enhancer RNAs. New York, NY: Humana Press, 2017: 39-50. | [55] | Danan C, Manickavel S, Hafner M. PAR-CLIP: A method for transcriptome-wide identification of RNA binding protein interaction sites. In: Dassi E, ed. Post-Transcriptional Gene Regulation. New York, NY: Humana Press, 2016: 153-173. | [56] | Yoon JH, De S, Srikantan S, Abdelmohsen K, Grammatikakis I, Kim J, Kim KM, Noh JH, White EJF, Martindale JL, Yang XL, Kang MJ, Wood III WH, Noren Hooten N, Evans MK, Becker KG, Tripathi V, Prasanth KV, Wilson GM, Tuschl T, Ingolia NT, Hafner M, Gorospe M . PAR-CLIP analysis uncovers AUF1 impact on target RNA fate and genome integrity. Nat Commun, 2014,5:5248. | [57] | Cui M, Xiao ZL, Wang Y, Zheng MY, Song TQ, Cai XL, Sun BD, Ye LH, Zhang XD . Long noncoding RNA HULC modulates abnormal lipid metabolism in hepatoma cells through an miR-9-mediated RXRA signaling pathway. Cancer Res, 2015,75(5):846-857. | [58] | Zheng QT, Lin J, Huang JJ, Zhang HY, Zhang R, Zhang XY, Cao CW, Hambly C, Qin GS, Yao J, Song RG, Jia QT, Wang X, Li Y , S Zhang N, Piao ZY, Ye RC, Speakman JR, Wang HM, Zhou Q, Wang YF, Jin WZ, Zhao JG. Reconstitution of UCP1 using CRISPR/Cas9 in the white adipose tissue of pigs decreases fat deposition and improves thermogenic capacity. Proc Natl Acad Sci USA, 2017,114(45):E9474-E9482. | [59] | Ren H, Li Y, Tang Z, Yang S, Mu Y, Cui W, Ao H, Du L, Wang L, Li K . Genomic structure, chromosomal localization and expression profile of a porcine long non-coding RNA isolated from long SAGE libraries. Anim Genet, 2009,40(4):499-508. | [60] | Sun XM, Li MX, Sun YJ, Cai HF, Lan XY, Huang YZ, Bai YY, Qi XL, Chen H . The developmental transcriptome sequencing of bovine skeletal muscle reveals a long noncoding RNA, lncMD, promotes muscle differentiation by sponging miR-125b. Biochim Biophys Acta (BBA)-Mol Cell Res, 2016,1863(11):2835-2845. | [61] | Cai BL, Li ZH, Ma MT, Wang ZJ, Han PG, Abdalla BA, Nie QH, Zhang XQ . LncRNA-Six1 encodes a micropeptide to activate Six1 in Cis and is involved in cell proliferation and muscle growth. Front Physiol, 2017,8:230. | [62] | Yue YW, Jin CF, Chen MM, Zhang LL, Liu XF, Ma WZ, Guo H . A lncRNA promotes myoblast proliferation by up-regulating GH1. In Vitro Cell Dev Biol Anim, 2017,53(8):699-705. | [63] | Zhao WM, Mu YL, Ma L, Wang C, Tang ZL, Yang SL, Zhou R, Hu XJ, Li MH, Li K . Systematic identification and characterization of long intergenic non-coding RNAs in fetal porcine skeletal muscle development. Sci Rep, 2015,5:8957. | [64] | Xing BS, Bai XX, Guo HX, Chen JF, Hua LS, Zhang JQ, Ma Q, Ren QL, Wang HS, Wang J . Long non-coding RNA analysis of muscular responses to testosterone deficiency in Huainan male pigs. Anim Sci J, 2017,88(9):1451-1456. | [65] | Li TT, Wang SY, Wu RM, Zhou XY, Zhu DH, Zhang Y . Identification of long non-protein coding RNAs in chicken skeletal muscle using next generation sequencing. Genomics, 2012,99(5):292-298. | [66] | Ouyang HJ, Wang ZJ, Chen XL, Yu J, Li ZH, Nie QH . Proteomic analysis of chicken skeletal muscle during embryonic development. Front Physiol, 2017,8:281. | [67] | Li ZH, Ouyang HJ, Zheng M, Cai BL, Han PG, Abdalla BA, Nie QH, Zhang XQ . Integrated analysis of long non-coding RNAs (lncRNAs) and mRNA expression profiles reveals the potential role of lncRNAs in skeletal muscle development of the chicken. Front Physiol, 2016,7:687. | [68] | Zhan SY, Dong Y, Zhao W, Guo JZ, Zhong T, Wang LJ, Li L, Zhang HP . Genome-wide identification and characterization of long non-coding RNAs in developmental skeletal muscle of fetal goat. BMC Genomics, 2016,17:666. | [69] | Ren CF, Deng MT, Fan YX, Yang H, Zhang GM, Feng X, Li FZ, Wang D, Wang F, Zhang YL . Genome-wide analysis reveals extensive changes in lncRNAs during skeletal muscle development in Hu sheep. Genes (Basel), 2017,8(8):E191. | [70] | Billerey C, Boussaha M, Esquerre D, Rebours E, Djari A, Meersseman C, Klopp C, Gautheret D, Rocha D . Identification of large intergenic non-coding RNAs in bovine muscle using next-generation transcriptomic sequencing. BMC Genomics, 2014,15:499. |
|