功能性微肽通量发现和功能验证的研究进展
收稿日期: 2022-02-28
修回日期: 2022-04-02
网络出版日期: 2022-04-14
基金资助
国家科技重大专项编号(2019ZX09301-124);中国药科大学天然药物活性组分与药效国家重点实验编号(SKLNMZZ202028);中国博士后科学基金资助项目编号(2020M681787);江苏省自然科学基金资助编号(BK20210418)
Research progress on high throughput discovery and functional verification of functional micropeptides
Received date: 2022-02-28
Revised date: 2022-04-02
Online published: 2022-04-14
Supported by
Supported by the National Science and Technology Major Projects No(2019ZX09301-124);the Project Program of State Key Laboratory of Natural Medicines No(SKLNMZZ202028);China Postdoctoral Science Foundation No(2020M681787);the Natural Science Foundation of Jiangsu Province No(BK20210418)
吕雪, 李帮洁, 徐寒梅 . 功能性微肽通量发现和功能验证的研究进展[J]. 遗传, 2022 , 44(6) : 478 -490 . DOI: 10.16288/j.yczz.22-007
With the rapid development of computational biology and deep sequencing technology, more and more studies have shown that a large number of non-classical open reading frames that have not been annotated and hidden in non-coding RNA can encode functional micropeptide. This article reviewed the current research status and technology strategy of gene sources, biological properties, predicted methods and functional verification of micropeptide, providing theoretical and reference basis for the subsequent discovery of micropeptides, research on regulatory mechanisms and development of novel targets and biomarkers.
Key words： noncoding RNA; sORFs; functional micropeptides
| [1] | Ng PC, Kirkness EF. Whole genome sequencing. Methods Mol Biol, 2010, 628:215-226. |
| [2] | Liu SH, Qiu J, He WT, Geng C, He GF, Liu CC, Cai D, Liu XP, Tian B, Pan HZ. TUG1 long non-coding RNA enlists the USF1 transcription factor to overexpress ROMO1 leading to hepatocellular carcinoma growth and metastasis. Med Comm, 2020, 1(3):386-399. |
| [3] | Basrai MA, Hieter P, Boeke JD. Small open reading frames: beautiful needles in the haystack. Genome Res, 1997, 7(8):768-771. |
| [4] | Chen J, Brunner AD, Cogan JZ, Nuñez JK, Fields AP, Adamson B, Itzhak DN, Li JY, Mann M, Leonetti MD, Weissman JS. Pervasive functional translation of noncanonical human open reading frames. Science, 2020, 367(6482):1140-1146. |
| [5] | Ma YL, Yue Y, Ma YB, Zhang Q, Zhou QT, Song YP, Shen YQ, Li X, Ma XC, Li C, Hanson MA, Han GW, Sickmier EA, Swaminath G, Zhao SW, Stevens RC, Hu LA, Zhong WG, Zhang MQ, Xu F. Structural basis for apelin control of the human apelin receptor. 《 Structure, 2017, 25(6): 858-866.e4. |
| [6] | Pauli A, Norris ML, Valen E, Chew GL, Gagnon JA, Zimmerman S, Mitchell A, Ma J, Dubrulle J, Reyon D, Tsai SQ, Joung JK, Saghatelian A, Schier AF. Toddler: an embryonic signal that promotes cell movement via apelin receptors. Science, 2014, 343(6172):1248636. |
| [7] | Freyer L, Hsu CW, Nowotschin S, Pauli A, Ishida J, Kuba K, Fukamizu A, Schier AF, Hoodless PA, Dickinson ME, Hadjantonakis AK. Loss of apela peptide in mice causes low penetrance embryonic lethality and defects in early mesodermal derivatives. Cell Rep, 2017, 20(9):2116-2130. |
| [8] | Lee C, Zeng J, Drew BG, Sallam T, Martin-Montalvo A, Wan JX, Kim SJ, Mehta H, Hevener AL,de Cabo R,Cohen P. The mitochondrial-derived peptide MOTS-c promotes metabolic homeostasis and reduces obesity and insulin resistance. Cell Metab, 2015, 21(3):443-454. |
| [9] | Sousa ME, Farkas MH. Micropeptide. PLoS Genet, 2018, 14(12):e1007764. |
| [10] | Kondo T, Hashimoto Y, Kato K, Inagaki S, Hayashi S, Kageyama Y. Small peptide regulators of actin-based cell morphogenesis encoded by a polycistronic mRNA. Nat Cell Biol, 2007, 9(6):660-665. |
| [11] | He CT, Jia CX, Zhang Y, Xu P. Enrichment-based proteogenomics identifies microproteins, missing proteins, and novel smORFs in saccharomyces cerevisiae. J Proteome Res, 2018, 17(7):2335-2344. |
| [12] | Ingolia NT, Ghaemmaghami S, Newman JRS, Weissman JS. Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science, 2009, 324(5924):218-223. |
| [13] | Thompson A, Schäfer J, Kuhn K, Kienle S, Schwarz J, Schmidt G, Neumann T, Johnstone R, Mohammed AKA, Hamon C. Tandem mass tags: a novel quantification strategy for comparative analysis of complex protein mixtures by MS/MS. Anal Chem, 2003, 75(8):1895-1904. |
| [14] | Tinoco AD, Saghatelian A. Investigating endogenous peptides and peptidases using peptidomics. Biochemistry, 2011, 50(35):7447-7461. |
| [15] | Cong L, Zhang F. Genome engineering using CRISPR- Cas9 system. Methods Mol Biol, 2015, 1239:197-217. |
| [16] | Sberro H, Fremin BJ, Zlitni S, Edfors F, Greenfield N, Snyder MP, Pavlopoulos GA, Kyrpides NC, Bhatt AS. Large-scale analyses of human microbiomes reveal thousands of small, novel genes. Cell, 2019, 178(5): 1245-1259.e14. |
| [17] | Bazin J, Baerenfaller K, Gosai SJ, Gregory BD, Crespi M, Bailey-Serres J. Global analysis of ribosome- associated noncoding RNAs unveils new modes of translational regulation. Proc Natl Acad Sci USA, 2017, 114(46):E10018-E10027. |
| [18] | Couso JP, Patraquim P. Classification and function of small open reading frames. Nat Rev Mol Cell Biol, 2017, 18(9):575-589. |
| [19] | 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. |
| [20] | Lauressergues D, Couzigou JM, Clemente HS, Martinez Y, Dunand C, Bécard G, Combier JP. Primary transcripts of microRNAs encode regulatory peptides. Nature, 2015, 520(7545):90-93. |
| [21] | Zhang ML, Zhao K, Xu XP, Yang YB, Yan S, Wei P, Liu H, Xu JB, Xiao FZ, Zhou HK, Yang XS, Huang NN, Liu JL, He KJ, Xie KP, Zhang G, Huang SY, Zhang N. A peptide encoded by circular form of LINC-PINT suppresses oncogenic transcriptional elongation in glioblastoma. Nat Commun, 2018, 9(1):4475. |
| [22] | Cobb LJ, Lee CH, Xiao JL, Yen K, Wong RG, Nakamura HK, Mehta HH, Gao QL, Ashur C, Huffman DM, Wan JX, Muzumdar R, Barzilai N, Cohen P. Naturally occurring mitochondrial-derived peptides are age-dependent regulators of apoptosis, insulin sensitivity, and inflammatory markers. Aging (Albany NY), 2016, 8(4):796-809. |
| [23] | Denli AM, Narvaiza I, Kerman BE, Pena M, Benner C, Marchetto MCN, Diedrich JK, Aslanian A, Ma J, Moresco JJ, Moore L, Hunter T, Saghatelian A, Gage FH. Primate-specific ORF0 contributes to retrotransposon- mediated diversity. Cell, 2015, 163(3):583-593. |
| [24] | Renz PF, Valdivia-Francia F, Sendoel A. Some like it translated: small ORFs in the 5'UTR. Exp cell Res, 2020, 396(1):112229. |
| [25] | Bazzini AA, Johnstone TG, Christiano R, Mackowiak SD, Obermayer B, Fleming ES, Vejnar CE, Lee MT, Rajewsky N, Walther TC, Giraldez AJ. Identification of small ORFs in vertebrates using ribosome footprinting and evolutionary conservation. EMBO J, 2014, 33(9):981-993. |
| [26] | Ma J, Diedrich JK, Jungreis I, Donaldson C, Vaughan J, Kellis M, Yates JR, Saghatelian A. Improved identification and analysis of small open reading frame encoded polypeptides. Anal Chem, 2016, 88(7):3967-3975. |
| [27] | Vanderperre B, Lucier JF, Bissonnette C, Motard J, Tremblay G, Vanderperre S, Wisztorski M, Salzet M, Boisvert FM, Roucou X. Direct detection of alternative open reading frames translation products in human significantly expands the proteome. PLoS One, 2013, 8(8):e70698. |
| [28] | van Heesch S, Witte F, Schneider-Lunitz V, Schulz JF, Adami E, Faber AB, Kirchner M, Maatz H, Blachut S, Sandmann CL, Kanda M, Worth CL, Schafer S, Calviello L, Merriott R, Patone G, Hummel O, Wyler E, Obermayer B, Mücke MB, Lindberg EL, Trnka F, Memczak S, Schilling M, Felkin LE, Barton PJR, Quaife NM, Vanezis K, Diecke S, Mukai M, Mah N, Oh SJ, Kurtz A, Schramm C, Schwinge D, Sebode M, Harakalova M, Asselbergs FW, Vink A, de Weger RA, Viswanathan S, Widjaja AA, Gärtner-Rommel A, Milting H, Remedios CD, Knosalla C, Mertins P, Landthaler M, Vingron M, Linke WA, Seidman JG, Seidman CE, Rajewsky N, Ohler U, Cook SA, Hubner N. The translational landscape of the human heart. Cell, 2019, 178(1): 242-260.e29. |
| [29] | Ma J, Ward CC, Jungreis I., Slavoff SA, Schwaid AG, Neveu J, Budnik BA, Kellis M, Saghatelian A. Discovery of human sORF-encoded polypeptides (SEPs) in cell lines and tissue. J Proteome Res, 2014, 13(3):1757-1765. |
| [30] | Lu SH, Wang T, Zhang G, He QY. Understanding the proteome encoded by “non-coding RNAs”: new insights into human genome. Sci China Life Sci, 2020, 63(7):986-995. |
| [31] | 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. |
| [32] | 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. |
| [33] | Lee C, Yen K, Cohen P. Humanin: a harbinger of mitochondrial-derived peptides? Trends Endocrinol Metab, 2013, 24(5):222-228. |
| [34] | Huang JZ, Chen M, Chen D, Gao XC, Zhu S, Huang HY, Hu M, Zhu HF, Yan GR. A peptide encoded by a putative lncRNA HOXB-AS3 suppresses colon cancer growth. Mol Cell, 2017, 68(1): 171-184.e6. |
| [35] | 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. |
| [36] | Shen PS, Park J, Qin YD, Li XM, Parsawar K, Larson MH, Cox J, Cheng YF, Lambowitz AM, Weissman JS, Brandman O, Frost A. Protein synthesis. Rqc2p and 60S ribosomal subunits mediate mRNA-independent elongation of nascent chains. Science, 2015, 347(6217):75-78. |
| [37] | Walther DM, Rapaport D. Biogenesis of mitochondrial outer membrane proteins. Biochim Biophys Acta, 2009, 1793(1):42-51. |
| [38] | Dembowski M, Kunkele KP, Nargang FE, Neupert W, Rapaport D. Assembly of Tom6 and Tom7 into the TOM core complex of neurospora crassa. J Biol Chem, 2001, 276(21):17679-17685. |
| [39] | Magny EG, Pueyo JI, Pearl FMG, Cespedes MA, Niven JE, Bishop SA, Couso JP. Conserved regulation of cardiac calcium uptake by peptides encoded in small open reading frames. Science, 2013, 341(6150):1116-1120. |
| [40] | 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. |
| [41] | Chu Q, Martinez TF, Novak SW, Donaldson CJ, Tan D, Vaughan JM, Chang TN, Diedrich JK, Andrade L, Kim A, Zhang T, Manor U, Saghatelian A. Regulation of the ER stress response by a mitochondrial microprotein. Nat Commun, 2019, 10(1):4883. |
| [42] | Stein CS, Jadiya P, Zhang XM, McLendon JM, Abouassaly GM, Witmer NH, Anderson EJ, Elrod JW, Boudreau RL. Mitoregulin: a lncRNA-encoded microprotein that supports mitochondrial supercomplexes and respiratory efficiency. Cell Rep, 2018, 23(13): 3710- 3720.e8. |
| [43] | Wu SQ, Zhang LY, Deng JQ, Guo BB, Li F, Wang YR, Wu R, Zhang SH, Lu JC, Zhou YF. A novel micropeptide encoded by Y-linked LINC00278 links cigarette smoking and AR signaling in male esophageal squamous cell carcinoma. Cancer Res, 2020, 80(13):2790-2803. |
| [44] | Li MW, Li X, Zhang YN, Wu HM, Zhou HZ, Ding X, Zhang XM, Jin XR, Wang Y, Yin XQ, Li CC, Yang PW, Xu HM. Micropeptide MIAC inhibits HNSCC progression by interacting with aquaporin 2. J Am Chem Soc, 2020, 142(14):6708-6716. |
| [45] | Guo BB, Wu SQ, Zhu X, Zhang LY, Deng JQ, Li F, Wang YR, Zhang SH, Wu R, Lu JC, Zhou YF. Micropeptide CIP2A-BP encoded by LINC00665 inhibits triple-negative breast cancer progression. EMBO J, 2020, 39(1):e102190. |
| [46] | Bhatta A, Atianand M, Jiang ZZ, Crabtree J, Blin J, Fitzgerald KA. A mitochondrial micropeptide is required for activation of the Nlrp3 inflammasome. J Immunol, 2020, 204(2):428-437. |
| [47] | Zhang S, Reljić B, Liang C, Kerouanton B, Francisco JC, Peh JH, Mary C, Jagannathan NS, Olexiouk V, Tang C, Fidelito G, Nama S, Cheng RK, Wee CL, Wang LC, Roggli PD, Sampath P, Lane L, Petretto E, Sobota RM, Jesuthasan S, Tucker-Kellogg L, Reversade B, Menschaert G, Sun L, Stroud DA, Ho L. Mitochondrial peptide BRAWNIN is essential for vertebrate respiratory complex III assembly. Nat Commun, 2020, 11(1):1312. |
| [48] | Lee C, Yen K, Cohen P. Humanin: a harbinger of mitochondrial-derived peptides? Trends Endocrinol Metab, 2013, 24(5):222-228. |
| [49] | Nashine S, Cohen P, Nesburn AB, Kuppermann BD, Kenney MC. Characterizing the protective effects of SHLP2, a mitochondrial-derived peptide, in macular degeneration. Sci Rep, 2018, 8(1):15175. |
| [50] | Liu Y, Shi YF. Mitochondria as a target in cancer treatment. MedComm, 2020, 1(2):129-139. |
| [51] | Chen XY, Li MW, Wang Y, Chen Q, Xu HM. Progress on sORF-encoded micropeptides. Hereditas(Beijing), 2021, 43(8):737-746. |
| [51] | 陈相颖, 李梦玮, 王颖, 陈权, 徐寒梅. 小开放阅读框编码微肽的研究进展. 遗传, 2021, 43(8):737-746. |
| [52] | Pueyo JI, Magny EG, Sampson CJ, Amin U, Evans IR, Bishop SA, Couso JP. Hemotin, a regulator of phagocytosis encoded by a small ORF and conserved across metazoans. PLoS Biol, 2016, 14(3):e1002395. |
| [53] | Guo B, Zhai DY, Cabezas E, Welsh K, Nouraini S, Satterthwait AC, Reed JC. Humanin peptide suppresses apoptosis by interfering with Bax activation. Nature, 2003, 423(6938):456-461. |
| [54] | Niu LM, Lou FZ, Sun Y, Sun LB, Cai XJ, Liu ZY, Zhou H, Wang H, Wang ZK, Bai J, Yin QQ, Zhang JX, Chen LJ, Peng DH, Xu ZY, Gao YY, Tang SB, Fan L, Wang HL. A micropeptide encoded by lncRNA MIR155HG suppresses autoimmune inflammation via modulating antigen presentation. Sci Adv, 2020, 6(21): eaaz2059. |
| [55] | Guo BB, Wu SQ, Zhu X, Zhang LY, Deng JQ, Li F, Wang YR, Zhang SH, Wu R, Lu JC, Zhou YF. Micropeptide CIP2A-BP encoded by LINC00665 inhibits triple-negative breast cancer progression. EMBO J, 2020, 39(1):e102190. |
| [56] | Polycarpou-Schwarz M, Groß M, Mestdagh P, Schott J, Grund SE, Hildenbrand C, Rom J, Aulmann S, Sinn HP, Vandesompele J, Diederichs S. The cancer-associated microprotein CASIMO1 controls cell proliferation and interacts with squalene epoxidase modulating lipid droplet formation. Oncogene, 2018, 37(34):4750-4768. |
| [57] | Chng SC, Ho L, Tian J, Reversade B. ELABELA: a hormone essential for heart development signals via the apelin receptor. Dev Cell, 2013, 27(6):672-680. |
| [58] | Ho L, van Dijk M, Chye STJ, Messerschmidt DM, Chng SC, Ong S, Yi LK, Boussata S, Goh GHY, Afink GB, Lim CY, Dunn NR, Solter D, Knowles BB, Reversade B. ELABELA deficiency promotes preeclampsia and cardiovascular malformations in mice. Science, 2017, 357(6352):707-713. |
| [59] | Makarewich CA, Baskin KK, Munir AZ, Bezprozvannaya S, Sharma G, Khemtong C, Shah AM, McAnally JR,Malloy CR,Szweda LI,Bassel-Duby R,Olson EN. MOXI is a mitochondrial micropeptide that enhances fatty acid β-oxidation. Cell Rep, 2018, 23(13):3701-3709. |
| [60] | Bi PP, Mcanally JR, Shelton JM, Sánchez-Ortiz E, Bassel-Duby R, Olson EN. Fusogenic micropeptide Myomixer is essential for satellite cell fusion and muscle regeneration. Proc Natl Acad Sci USA, 2018, 115(15):3864-3869. |
| [61] | Diao MQ, Li C, Xu JD, Zhao XF, Wang JX. RPS27, a sORF-encoded polypeptide, functions antivirally by activating the NF-κB pathway and interacting with viral envelope proteins in shrimp. Front Immunol, 2019, 10:2763. |
| [62] | Ingolia NT, Lareau LF, Weissman JS. Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes. Cell, 2011, 147(4):789-802. |
| [63] | Aspden JL, Eyre-Walker YC, Phillips RJ, Amin U, Mumtaz MAS, Brocard M, Couso JP. Extensive translation of small Open Reading Frames revealed by Poly-Ribo-Seq. eLife, 2014, 3:e03528. |
| [64] | Calviello L, Mukherjee N, Wyler E, Zauber H, Hirsekorn A, Selbach M, Landthaler M, Obermayer B, Ohler U. Detecting actively translated open reading frames in ribosome profiling data. Nat Methods, 2016, 13(2):165-170. |
| [65] | Hao YJ, Zhang LL, Niu YW, Cai TX, Luo JJ, He SM, Zhang B, Zhang DJ, Qin Y, Yang FQ, Chen RS. SmProt: a database of small proteins encoded by annotated coding and non-coding RNA loci. Brief Bioinform, 2018, 19(4):636-643. |
| [66] | Olexiouk V, Van Criekinge W, Menschaert G. An update on sORFs.org: a repository of small ORFs identified by ribosome profiling. Nucleic Acids Res, 2018, 46(D1):D497-D502. |
| [67] | Liu Q, Shvarts T, Sliz P, Gregory RI. RiboToolkit: an integrated platform for analysis and annotation of ribosome profiling data to decode mRNA translation at codon resolution. Nucleic Acids Res, 2020, 48(W1):W218-W229. |
| [68] | Lin MF, Jungreis I, Kellis M. PhyloCSF: a comparative genomics method to distinguish protein coding and non- coding regions. Bioinformatics, 2011, 27(13):i275-i282. |
| [69] | Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou MM, Rosenbloom K, Clawson H, Spieth J, Hillier LW, Richards S, Weinstock GM, Wilson RK, Gibbs RA, Kent WJ, Miller W, Haussler D. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res, 2005, 15(8):1034-1050. |
| [70] | Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol, 1990, 215(3):403-410. |
| [71] | Eddy SR. Multiple alignment using hidden Markov models. Proc Int Conf Intell Syst Mol Biol, 1995, 3:114-120. |
| [72] | Zhu MM, Gribskov M. MiPepid: MicroPeptide identification tool using machine learning. BMC Bioinformatics, 2019, 20(1):559. |
| [73] | Hanada K, Akiyama K, Sakurai T, Toyoda T, Shinozaki K, Shiu SH. sORF finder: a program package to identify small open reading frames with high coding potential. Bioinformatics, 2010, 26(3):399-400. |
| [74] | Slavoff SA, Mitchell AJ, Schwaid AG, Cabili MN, Ma J, Levin JZ, Karger AD, Budnik BA, Rinn JL, Saghatelian A. Peptidomic discovery of short open reading frame-encoded peptides in human cells. Nat Chem Biol, 2013, 9(1):59-64. |
| [75] | Leney AC, Heck AJR. Native mass spectrometry: what is in the name? J Am Soc Mass Spectrom, 2017, 28(1):5-13. |
| [76] | Zhu YF, Orre LM, Johansson HJ, Huss M, Boekel J, Vesterlund M, Fernandez-Woodbridge A, Branca RMM, Lehtiö J. Discovery of coding regions in the human genome by integrated proteogenomics analysis workflow. Nat Commun, 2018, 9(1):903. |
| [77] | Yin XQ, Jing YY, Xu HM. Mining for missed sORF-encoded peptides. Expert Rev Proteomics, 2019, 16(3):257-266. |
| [78] | Martinez TF, Chu Q, Donaldson C, Tan D, Shokhirev MN, Saghatelian A. Accurate annotation of human protein-coding small open reading frames. Nat Chem Biol, 2020, 16(4):458-468. |
| [79] | Lu SH, Zhang J, Lian XL, Sun L, Meng K, Chen Y, Sun ZH, Yin XF, Li YX, Zhao J, Wang T, Zhang G, He QY. A hidden human proteome encoded by 'non-coding' genes. Nucleic Acids Res, 2019, 47(15):8111-8125. |
| [80] | Fälth M, Sköld K, Norrman M, Svensson M, Fenyö D, Andren PE. SwePep, a database designed for endogenous peptides and mass spectrometry. Mol Cell Proteomics, 2006, 5(6):998-1005. |
| [81] | Dayon L, Hainard A, Licker V, Turck N, Kuhn K, Hochstrasser DF, Burkhard PR, Sanchez JC. Relative quantification of proteins in human cerebrospinal fluids by MS/MS using 6-plex isobaric tags. Anal Chem, 2008, 80(8):2921-2931. |
| [82] | Skarshewski A, Stanton-Cook M, Huber T, Al Mansoori S, Smith R, Beatson SA, Rothnagel JA. uPEPperoni: an online tool for upstream open reading frame location and analysis of transcript conservation. BMC Bioinformatics, 2014, 15:36. |
| [83] | Lin MF, Jungreis I, Kellis M. PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions. Bioinformatics, 2011, 27(13):i275-i282. |
| [84] | Guttman M, Russell P, Ingolia NT, Weissman JS, Lander ES. Ribosome profiling provides evidence that large noncoding RNAs do not encode proteins. Cell, 2013, 154(1):240-251. |
| [85] | Ingolia NT, Brar GA, Stern-Ginossar N, Harris MS, Talhouarne GJS, Jackson SE, Wills MR, Weissman JS. Ribosome profiling reveals pervasive translation outside of annotated protein-coding genes. Cell Rep, 2014, 8(5):1365-1379. |
| [86] | Fields AP, Rodriguez EH, Jovanovic M, Stern-Ginossar N, Haas BJ, Mertins P, Raychowdhury R, Hacohen N, Carr SA, Ingolia NT, Regev A, Weissman JS. A regression-based analysis of ribosome-profiling data reveals a conserved complexity to mammalian translation. Mol Cell, 2015, 60(5):816-827. |
| [87] | Calviello L, Mukherjee N, Wyler E, Zauber H, Hirsekorn A, Selbach M, Landthaler M, Obermayer B, Ohler U. Detecting actively translated open reading frames in ribosome profiling data. Nat Methods, 2016, 13(2):165-170. |
| [88] | Chew GL, Pauli A, Rinn JL, Regev A, Schier AF, Valen E. Ribosome profiling reveals resemblance between long non-coding RNAs and 5' leaders of coding RNAs. Development, 2013, 140(13):2828-2834. |
| [89] | Raj A, Wang SH, Shim H, Harpak A, Li YI, Engelmann B, Stephens M, Gilad Y, Pritchard JK. Thousands of novel translated open reading frames in humans inferred by ribosome footprint profiling. eLife, 2016, 5:e13328. |
| [90] | Chun SY, Rodriguez CM, Todd PK, Mills RE. SPECtre: a spectral coherence--based classifier of actively translated transcripts from ribosome profiling sequence data. BMC Bioinformatics, 2016, 17(1):482. |
| [91] | Ji Z, Song RS, Regev A, Struhl K. Many lncRNAs, 5'UTRs, and pseudogenes are translated and some are likely to express functional proteins. eLife, 2015, 4:e08890. |
| [92] | Malone B, Atanassov I, Aeschimann F, Li XP, Großhans H, Dieterich C. Bayesian prediction of RNA translation from ribosome profiling. Nucleic Acids Res, 2017, 45(6):2960-2972. |
| [93] | Xiao ZT, Huang RY, Xing XD, Chen YL, Deng HT, Yang XR. De novo annotation and characterization of the translatome with ribosome profiling data. Nucleic Acids Res, 2018, 46(10):e61. |
| [94] | Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou MM, Rosenbloom K, Clawson H, Spieth J, Hillier LW, Richards S, Weinstock GM, Wilson RK, Gibbs RA, Kent WJ, Miller W, Haussler D. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res, 2005, 15(8):1034-1050. |
| [95] | Frith MC, Forrest AR, Nourbakhsh E, Pang KC, Kai C, Kawai J, Carninci P, Hayashizaki Y, Bailey TL, Grimmond SM. The abundance of short proteins in the mammalian proteome. PLoS Genet, 2006, 2(4):e52. |
| [96] | Kong L, Zhang Y, Ye ZQ, Liu XQ, Zhao SQ, Wei LP, Gao G. CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine. Nucleic Acids Res, 2007, 35:W345-W349. |
| [97] | Ruiz-Orera J, Albà MM. Translation of small open reading frames: roles in regulation and evolutionary innovation. Trends Genet, 2019, 35(3):186-198. |
| [98] | Makarewich CA, Olson EN. Mining for micropeptides. Trends Cell Biol, 2017, 27(9):685-696. |
| [99] | Chu Q, Rathore A, Diedrich JK, Donaldson CJ, Yates JR, Saghatelian A. Identification of microprotein-protein interactions via APEX tagging. Biochemistry, 2017, 56(26):3299-3306. |
| [100] | Wang YR, Wu SQ, Zhu X, Zhang LY, Deng JQ, Li F, Guo BB, Zhang SH, Wu R, Zhang Z, Wang KX, Lu JC, Zhou YF. LncRNA-encoded polypeptide ASRPS inhibits triple-negative breast cancer angiogenesis. J Exp Med, 2020, 217(3): jem.20190950. |
| [101] | Makarewich CA, Munir AZ, Schiattarella GG, Bezprozvannaya S, Raguimova ON, Cho EE, Vidal AH, Robia SL, Bassel-Duby R, Olson EN. The DWORF micropeptide enhances contractility and prevents heart failure in a mouse model of dilated cardiomyopathy. eLife, 2018, 7:e38319. |
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