翻译组研究技术进展

doi:10.13560/j.cnki.biotech.bull.1985.2019-0006

摘要/Abstract

摘要： 基于高通量测序的RNA-Seq广泛被用于检测组织和细胞中基因的表达和调控机理研究,然而已有的文献表明mRNA水平并不能反映蛋白质的丰度,而研究正在翻译的mRNA的翻译组则比转录组更能反映蛋白组的实际水平,因此翻译组研究比转录组研究更具有理论和实践意义。对翻译组研究最为经典的多聚核糖体图谱技术到最近发展起来的核糖体图谱技术、核糖体亲和纯化技术以及翻译谱分析技术进行了综述比较,并介绍了翻译组研究前景,以便为翻译组研究提供参考。

关键词: 翻译组, 多聚核糖体图谱, 核糖体亲和纯化技术, 核糖体图谱, 翻译谱分析技术

Abstract: High-throughput sequencing-based RNA-Seq has been widely used to detect the expression and regulation mechanism of genes in tissues and cells. However,published literature have shown that mRNA level cannot reflect the real abundance of the related protein,while translatome that studies the being-translated mRNAs is more correlated to the actual abundance of proteins than the transcriptome. Therefore,studying translatome is more theoretical and practical meaning than studying transcriptome. In this paper,we reviewed the main techniques in studying translatome,from the most classical polysome profiling to the recently developed ribosome profiling,ribosomal affinity-purification,and RNC-RNA-Seq,and further compared the advantages and limitations of each technique. We also briefly discussed the prospect of studying translatome for providing a reference in studying translatome.

Key words: translatome, polysome profiling, ribosome affinity-purification, ribosomalprofiling, RNC-mRNA-Seq

魏康宁, 崔俊霞, 王梦蕾, 王丽, 李用芳. 翻译组研究技术进展[J]. 生物技术通报, 2019, 35(7): 222-229.

WEI Kang-ning, CUI Jun-xia, WANG Meng-lei, WANG Li, LI Yong-fang. Advances in the Techniques of Studying Translatome[J]. Biotechnology Bulletin, 2019, 35(7): 222-229.

参考文献

[1] Nagaraj N, Wisniewski JR, Geiger T, et al.Deep proteome and transcriptome mapping of a human cancer cell line[J]. Molecular Systems Biology, 2011, 7(11):548-554.
[2] Chen G, Gharib TG, Huang CC, et al.Discordant protein and mRNA expression in lung adenocarcinomas[J]. Molecular & Cellular Proteomics, 2002, 1(4):304-313.
[3] Wang T, Cui Y, Jin J, et al.Translating mRNAs strongly correlate to proteins in a multivariate manner and their translation ratios are phenotype specific[J]. Nucleic Acids Research, 2013, 41(9):4743-4754.
[4] Maier T, Güell M, Serrano L.Correlation of mRNA and protein in complex biological samples[J]. Febs Letters, 2009, 583(24):3966-3973.
[5] Ranjbar L, Foley JP, Breadmore MC.Multidimensional liquid-phase separations combining both chromatography and electrophoresis - A review[J]. Analytica Chimica Acta, 2017, 950:7-31.
[6] Cox J, Mann M.MaxQuant enables high peptide identification rates, individualized p. p. b. -range mass accuracies and proteome-wide protein quantification[J]. Nature Biotechnology, 2008, 26(12):1367-1372.
[7] Cox J, Neuhauser N, Michalski A, et al.Andromeda:a peptide search engine integrated into the MaxQuant environment[J]. J Proteome Res, 2011, 10(4):1794-1805.
[8] Jackson RJ, Hellen CU, Pestova TV.The mechanism of eukaryotic translation initiation and principles of its regulation[J]. Nature Reviews Molecular Cell Biology, 2010, 11(2):113-127.
[9] Ali MU, Ur Rahman MS, Jia Z, et al.Eukaryotic translation initiation factors and cancer[J]. Tumor Biology, 2017, 39(6):101042831770980.
[10] Shirokikh NE, Archer SK, Beilharz TH, et al.Translation complex profile sequencing to study the in vivo dynamics of mRNA-ribosome interactions during translation initiation, elongation and termination[J]. Nature Protocols, 2017, 12(4):697-731.
[11] Mengardi C, Limousin T, Ricci EP, et al.microRNAs stimulate translation initiation mediated by HCV-like IRESes[J]. Nucleic Acids Research, 2017, 45(8):4810-4824.
[12] Li YF, Mahalingam R, Sunkar R.Isolation of polysomal RNA for analyzing stress-responsive genes regulated at the translational level in plants[J]. Methods Mol Biol, 2017, 1631(10):151-161.
[13] Mašek T, Valášek L, Pospíšek M.Polysome analysis and RNA purification from sucrose gradients[J]. Methods Mol Biol, 2011, 703(10):293-309.
[14] Spangenberg L, Shigunov P, Abud AP, et al.Polysome profiling shows extensive posttranscriptional regulation during human adipocyte stem cell differentiation into adipocytes[J]. Stem Cell Research, 2013, 11(2):902-912.
[15] Chassé H, Boulben S, Costache V, et al.Analysis of translation using polysome profiling[J]. Nucleic Acids Research, 2017, 45(3):e15.
[16] Kuhn KM, Derisi JL, Brown PO, et al.Global and specific translational regulation in the genomic response of Saccharomyces cerevisiae to a rapid transfer from a fermentable to a nonfermentable carbon source[J]. Molecular & Cellular Biology, 2001, 21(3):916-927.
[17] Arava Y, Wang Y, Storey JD, et al.Genome-wide analysis of mRNA translation profiles in Saccharomyces cerevisiae[J]. Proc Natl Acad Sci USA, 2003, 100(7):3889-3894.
[18] Flora P, Hélène M, Pascal L, et al.Bacterial translational regulations:high diversity between all mRNAs and major role in gene expression[J]. Genomics, 2012, 13(1):528-534.
[19] Thomas JD, Johannes GJ.Identification of mRNAs that continue to associate with polysomes during hypoxia[J]. RNA, 2007, 13(7):1116-1131.
[20] Johannes G, Carter MS, Eisen MB, et al.Identification of eukaryotic mRNAs that are translated at reduced cap binding complex eIF4F concentrations using a cDNA microarray[J]. Proc Natl Acad Sci USA, 1999, 96(23):13118-13123.
[21] Powley IR, Kondrashov A, Young LA, et al.Translational reprogramming following UVB irradiation is mediated by DNA-PKcs and allows selective recruitment to the polysomes of mRNAs encoding DNA repair enzymes[J]. Genes & Development, 2009, 23(10):1207-1220.
[22] Bernabò P, Tebaldi T, Groen E, et al.In Vivo translatome profiling in spinal muscular atrophy reveals a role for SMN protein in ribosome biology[J]. Cell Reports, 2017, 21(4):953-965.
[23] Puckette M, Lyer NJ, Tang YJ, et al.Differential mRNA translation in medicago truncatula accessions with contrasting responses to ozone-induced oxidative stress[J]. Molecular Plant, 2012, 5(1):187-204.
[24] Brancoprice C, Kawaguchi R, Ferreira RB, et al.Genome-wide analysis of transcript abundance and translation in Arabidopsis seedlings subjected to oxygen deprivation[J]. Annals of Botany, 2005, 96(4):647-660.
[25] Li Y, Zheng Y, Sunkar R, et al.Comparative transcriptome and translatome analysis in rice revealed differential mRNA translation in Pokkali compared to IR29 under salt stress[J]. BMC Genomics, 2018, 19(10):935.
[26] Thermann R, Hentze MW.Drosophila miR2 induces pseudo-polysomes and inhibits translation initiation[J]. Nature, 2012, 447(7146):875-882.
[27] 赵晶, 张弓. 翻译组学:方法及应用[J]. 生命的化学, 2017, 37(1):70-79.
[28] Zhong J, Xiao C, Gu W, et al.Transfer RNAs mediate the rapid adaptation of Escherichia coli to oxidative stress[J]. PLOS Genetics, 2015, 11(6):10-19.
[29] Morello LG, Hesling C, Coltri PP, et al.The NIP7 protein is required for accurate pre-rRNA processing in human cells[J]. Nucleic Acids Research, 2011, 39(2):648-665.
[30] Zhang G, Hubalewska M, Ignatova Z.Transient ribosomal attenuation coordinates protein synthesis and co-translational folding[J]. Nat Struct Mol Biol, 2009, 16(3):274-280.
[31] Zhong J, Cui Y, Guo J, et al.Resolving chromosome-centric human proteome with translating mRNA analysis:a strategic demonstration[J]. J Proteome Res, 2014, 13(1):50-59.
[32] Lazarowitz SG, Robertson HD.Initiator regions from the small size class of reovirus messenger RNA protected by rabbit reticulocyte ribosomes[J]. J Biol Chem, 1977, 252(21):7842-7849.
[33] Kozak M.Nucleotide sequences of 5'-terminal ribosome-protected initiation regions from two reovirus messages[J]. Nature, 1977, 269(5627):391-394.
[34] Steitz JA.Polypeptide chain initiation:nucleotide sequences of the three ribosomal binding sites in bacteriophage R17 RNA[J]. Nature, 1969, 224(5223):957-964.
[35] Ingolia NT, Ghaemmaghami S.Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling[J]. Science, 2009, 324(5924):218-223.
[36] Ingolia NT, Brar GA, Rouskin S, et al.The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments[J]. Nature Protocols, 2012, 7(8):1534-1550.
[37] Souza ND.Deep sequencing of ribosome footprints[J]. Nature Methods, 2009, 6(4):244-244.
[38] Janich P, Arpat AB, Castelo-Szekely V, et al.Ribosome profiling reveals the rhythmic liver translatome and circadian clock regulation by upstream open reading frames[J]. Genome Research, 2015, 25(12):1848-1859.
[39] Terenin IM, Akulich KA, Andreev DE, et al.Sliding of a 43S ribosomal complex from the recognized AUG codon triggered by a delay in eIF2-bound GTP hydrolysis[J]. Nucleic Acids Research, 2016, 44(4):1882-1893.
[40] Inada T, Winstall E, Jr TS, et al.One-step affinity purification of the yeast ribosome and its associated proteins and mRNAs[J]. RNA, 2002, 8(7):948-958.
[41] Zywicki M, Bakowska-Zywicka K, Polacek N.Revealing stable processing products from ribosome-associated small RNAs by deep-sequencing data analysis[J]. Nucleic Acids Research, 2012, 40(9):4013-4024.
[42] Zanetti ME, Chang IF, Gong F, et al.Immunopurification of polyribosomal complexes of Arabidopsis for global analysis of gene expression[J]. Plant Physiology, 2005, 138(2):624-635.
[43] Mustroph A, Zanetti M E, Jang C J, et al.Profiling translatomes of discrete cell populations resolves altered cellular priorities during hypoxia in Arabidopsis[J]. Plant Signaling & Behavior, 2009, 106(44):18843-18848.
[44] Vragovic K, Sela A, Friedlander-Shani L, et al.Translatome analyses capture of opposing tissue-specific brassinosteroid signals orchestrating root meristem differentiation[J]. Proceedings of the National Academy of Sciences, 2015, 112(3):923-928.
[45] Heiman M, Schaefer A, Gong S, et al.A translational profiling approach for the molecular characterization of CNS cell types[J]. Cell, 2008, 135(4):738-748.
[46] Sanz E, Yang L, Su T, et al.Cell-type-specific isolation of ribosome-associated mRNA from complex tissues[J]. Proc Natl Acad Sci USA, 2009, 106(33):13939-13944.
[47] Heiman M, Kulicke R, Fenster RJ, et al.Cell type-specific mRNA purification by translating ribosome affinity purification(TRAP)[J]. Nature Protocols, 2014, 9(6):1282-1291.
[48] Wang Y, Jiao Y.Translating ribosome affinity purification(TRAP)for cell-specific translation profiling in developing flowers[J]. Methods in Molecular Biology, 2014, 1110(10):323-328.
[49] Clamer M, Tebaldi T, Lauria F, et al.Active ribosome profiling with ribolace[J]. Cell Rep, 2018, 25(4):1097-1108.
[50] Seimetz J, Arif W, Bangru S, et al.Cell-type specific polysome profiling from mammalian tissues[J]. Methods, 2018, 155:131-139.