TAIL-seq: Genome-wide determination of poly(A) tail length and 3' end modifications

Molecular Cell

Volumn 53, Issue 6, 2014, Pages 1044-1052

  Chang, Hyeshik ^a,b   Lim, Jaechul ^a,b   Ha, Minju ^a,b   Kim, V Narry ^a,b  

^a Institute for Basic Science   (South Korea)

^b Seoul National University   (South Korea)

Author keywords

[No Author keywords available]

Indexed keywords

MESSENGER RNA; POLYADENYLIC ACID; TRANSCRIPTOME;

ANIMAL CELL; ARTICLE; CELL STRAIN 3T3; GENE SEQUENCE; HUMAN; HUMAN CELL; NONHUMAN; NUCLEOTIDE SEQUENCE; POLYADENYLATION; PROTEIN MODIFICATION; PROTEIN STABILITY; PROTEIN SYNTHESIS; RNA CLEAVAGE; TAIL SEQ; TRANSLATION REGULATION; 3T3 CELL LINE; GENE CONTROL; GENOME; RNA SEQUENCE; RNA STABILITY;

3' UNTRANSLATED REGIONS; ANIMALS; BASE SEQUENCE; GENE EXPRESSION REGULATION; GENOME; GUANINE; HALF-LIFE; HELA CELLS; HUMANS; MICE; MICRORNAS; MOLECULAR SEQUENCE DATA; NIH 3T3 CELLS; POLYADENYLATION; RNA STABILITY; SEQUENCE ANALYSIS, RNA; SIGNAL TRANSDUCTION; URIDINE;

EID: 84896405087     PISSN: 10972765     EISSN: 10974164     Source Type: Journal    
DOI: 10.1016/j.molcel.2014.02.007     Document Type: Article

References (59)

1. Aviner R., Geiger T., Elroy-Stein O. Novel proteomic approach (PUNCH-P) reveals cell cycle-specific fluctuations in mRNA translation. Genes Dev. 2013, 27:1834-1844.
2. Bai Y., Srivastava S.K., Chang J.H., Manley J.L., Tong L. Structural basis for dimerization and activity of human PAPD1, a noncanonical poly(A) polymerase. Mol. Cell 2011, 41:311-320.
3. Bazzini A.A., Lee M.T., Giraldez A.J. Ribosome profiling shows that miR-430 reduces translation before causing mRNA decay in zebrafish. Science 2012, 336:233-237.
4. Beck A.H., Weng Z., Witten D.M., Zhu S., Foley J.W., Lacroute P., Smith C.L., Tibshirani R., van de Rijn M., Sidow A., West R.B. 3'-end sequencing for expression quantification (3SEQ) from archival tumor samples. PLoS ONE 2010, 5:e8768.
5. Behm-Ansmant I., Rehwinkel J., Doerks T., Stark A., Bork P., Izaurralde E. mRNA degradation by miRNAs and GW182 requires both CCR4:NOT deadenylase and DCP1:DCP2 decapping complexes. Genes Dev. 2006, 20:1885-1898.
6. Beilharz T.H., Preiss T. Widespread use of poly(A) tail length control to accentuate expression of the yeast transcriptome. RNA 2007, 13:982-997.
7. Besse F., Ephrussi A. Translational control of localized mRNAs: restricting protein synthesis in space and time. Nat. Rev. Mol. Cell Biol. 2008, 9:971-980.
8. Béthune J., Artus-Revel C.G., Filipowicz W. Kinetic analysis reveals successive steps leading to miRNA-mediated silencing in mammalian cells. EMBO Rep. 2012, 13:716-723.
9. Bragg L.M., Stone G., Butler M.K., Hugenholtz P., Tyson G.W. Shining a light on dark sequencing: characterising errors in Ion Torrent PGM data. PLoS Comput. Biol. 2013, 9:e1003031.
10. Brawerman G. Eukaryotic messenger RNA. Annu. Rev. Biochem. 1974, 43:621-642.
11. Burns D.M., Richter J.D. CPEB regulation of human cellular senescence, energy metabolism, and p53 mRNA translation. Genes Dev. 2008, 22:3449-3460.
12. Chang H.M., Triboulet R., Thornton J.E., Gregory R.I. A role for the Perlman syndrome exonuclease Dis3l2 in the Lin28-let-7 pathway. Nature 2013, 497:244-248.
13. D'Ambrogio A., Nagaoka K., Richter J.D. Translational control of cell growth and malignancy by the CPEBs. Nat. Rev. Cancer 2013, 13:283-290.
14. Derti A., Garrett-Engele P., Macisaac K.D., Stevens R.C., Sriram S., Chen R., Rohl C.A., Johnson J.M., Babak T. A quantitative atlas of polyadenylation in five mammals. Genome Res. 2012, 22:1173-1183.
15. Dreyfus M., Régnier P. The poly(A) tail of mRNAs: bodyguard in eukaryotes, scavenger in bacteria. Cell 2002, 111:611-613.
16. Du L., Richter J.D. Activity-dependent polyadenylation in neurons. RNA 2005, 11:1340-1347.
17. Elkon R., Ugalde A.P., Agami R. Alternative cleavage and polyadenylation: extent, regulation and function. Nat. Rev. Genet. 2013, 14:496-506.
18. Fu Y., Sun Y., Li Y., Li J., Rao X., Chen C., Xu A. Differential genome-wide profiling of tandem 3' UTRs among human breast cancer and normal cells by high-throughput sequencing. Genome Res. 2011, 21:741-747.
19. Garneau N.L., Wilusz J., Wilusz C.J. The highways and byways of mRNA decay. Nat. Rev. Mol. Cell Biol. 2007, 8:113-126.
20. Giraldez A.J., Mishima Y., Rihel J., Grocock R.J., van Dongen S., Inoue K., Enright A.J., Schier A.F. Zebrafish MiR-430 promotes deadenylation and clearance of maternal mRNAs. Science 2006, 312:75-79.
21. Groisman I., Ivshina M., Marin V., Kennedy N.J., Davis R.J., Richter J.D. Control of cellular senescence by CPEB. Genes Dev. 2006, 20:2701-2712.
22. Guo H., Ingolia N.T., Weissman J.S., Bartel D.P. Mammalian microRNAs predominantly act to decrease target mRNA levels. Nature 2010, 466:835-840.
23. Henriksson N., Nilsson P., Wu M., Song H., Virtanen A. Recognition of adenosine residues by the active site of poly(A)-specific ribonuclease. J.Biol. Chem. 2010, 285:163-170.
24. Heo I., Ha M., Lim J., Yoon M.J., Park J.E., Kwon S.C., Chang H., Kim V.N. Mono-uridylation of pre-microRNA as a key step in the biogenesis of group II let-7 microRNAs. Cell 2012, 151:521-532.
25. Hoque M., Ji Z., Zheng D., Luo W., Li W., You B., Park J.Y., Yehia G., Tian B. Analysis of alternative cleavage and polyadenylation by 3' region extraction and deep sequencing. Nat. Methods 2013, 10:133-139.
26. Huntzinger E., Izaurralde E. Gene silencing by microRNAs: contributions of translational repression and mRNA decay. Nat. Rev. Genet. 2011, 12:99-110.
27. Jan C.H., Friedman R.C., Ruby J.G., Bartel D.P. Formation, regulation and evolution of Caenorhabditis elegans 3'UTRs. Nature 2011, 469:97-101.
28. Kojima S., Sher-Chen E.L., Green C.B. Circadian control of mRNA polyadenylation dynamics regulates rhythmic protein expression. Genes Dev. 2012, 26:2724-2736.
29. Lackner D.H., Beilharz T.H., Marguerat S., Mata J., Watt S., Schubert F., Preiss T., Bähler J. A network of multiple regulatory layers shapes gene expression in fission yeast. Mol. Cell. 2007, 26:145-155.
30. Ledergerber C., Dessimoz C. Base-calling for next-generation sequencing platforms. Brief. Bioinform. 2011, 12:489-497.
31. Lubas M., Damgaard C.K., Tomecki R., Cysewski D., Jensen T.H., Dziembowski A. Exonuclease hDIS3L2 specifies an exosome-independent 3'-5' degradation pathway of human cytoplasmic mRNA. EMBO J. 2013, 32:1855-1868.
32. Malecki M., Viegas S.C., Carneiro T., Golik P., Dressaire C., Ferreira M.G., Arraiano C.M. The exoribonuclease Dis3L2 defines a novel eukaryotic RNA degradation pathway. EMBO J. 2013, 32:1842-1854.
33. Mangone M., Manoharan A.P., Thierry-Mieg D., Thierry-Mieg J., Han T., Mackowiak S.D., Mis E., Zegar C., Gutwein M.R., Khivansara V., et al. The landscape of C. elegans 3'UTRs. Science 2010, 329:432-435.
34. Martin G., Gruber A.R., Keller W., Zavolan M. Genome-wide analysis of pre-mRNA 3' end processing reveals a decisive role of human cleavage factor I in the regulation of 3'UTR length. Cell Rep. 2012, 1:753-763.
35. Meijer H.A., Bushell M., Hill K., Gant T.W., Willis A.E., Jones P., de Moor C.H. A novel method for poly(A) fractionation reveals a large population of mRNAs with a short poly(A) tail in mammalian cells. Nucleic Acids Res. 2007, 35:e132.
36. Mendez R., Richter J.D. Translational control by CPEB: a means to the end. Nat. Rev. Mol. Cell Biol. 2001, 2:521-529.
37. Morozov I.Y., Jones M.G., Gould P.D., Crome V., Wilson J.B., Hall A.J., Rigden D.J., Caddick M.X. mRNA 3' tagging is induced by nonsense-mediated decay and promotes ribosome dissociation. Mol. Cell. Biol. 2012, 32:2585-2595.
38. Mullen T.E., Marzluff W.F. Degradation of histone mRNA requires oligouridylation followed by decapping and simultaneous degradation of the mRNA both 5' to 3' and 3' to 5'. Genes Dev. 2008, 22:50-65.
39. Norbury C.J. Cytoplasmic RNA: a case of the tail wagging the dog. Nat. Rev. Mol. Cell Biol. 2013, 14:643-653.
40. Novoa I., Gallego J., Ferreira P.G., Mendez R. Mitotic cell-cycle progression is regulated by CPEB1 and CPEB4-dependent translational control. Nat. Cell Biol. 2010, 12:447-456.
41. Ozsolak F., Kapranov P., Foissac S., Kim S.W., Fishilevich E., Monaghan A.P., John B., Milos P.M. Comprehensive polyadenylation site maps in yeast and human reveal pervasive alternative polyadenylation. Cell 2010, 143:1018-1029.
42. Piqué M., López J.M., Foissac S., Guigó R., Méndez R. A combinatorial code for CPE-mediated translational control. Cell 2008, 132:434-448.
43. Rissland O.S., Norbury C.J. Decapping is preceded by 3' uridylation in a novel pathway of bulk mRNA turnover. Nat. Struct. Mol. Biol. 2009, 16:616-623.
44. Rissland O.S., Mikulasova A., Norbury C.J. Efficient RNA polyuridylation by noncanonical poly(A) polymerases. Mol. Cell. Biol. 2007, 27:3612-3624.
45. Sallés F.J., Richards W.G., Strickland S. Assaying the polyadenylation state of mRNAs. Methods 1999, 17:38-45.
46. Schmidt M.J., West S., Norbury C.J. The human cytoplasmic RNA terminal U-transferase ZCCHC11 targets histone mRNAs for degradation. RNA 2011, 17:39-44.
47. Schwanhäusser B., Busse D., Li N., Dittmar G., Schuchhardt J., Wolf J., Chen W., Selbach M. Global quantification of mammalian gene expression control. Nature 2011, 473:337-342.
48. Sement F.M., Ferrier E., Zuber H., Merret R., Alioua M., Deragon J.M., Bousquet-Antonelli C., Lange H., Gagliardi D. Uridylation prevents 3' trimming of oligoadenylated mRNAs. Nucleic Acids Res. 2013, 41:7115-7127.
49. Shen B., Goodman H.M. Uridine addition after microRNA-directed cleavage. Science 2004, 306:997.
50. Shepard P.J., Choi E.A., Lu J., Flanagan L.A., Hertel K.J., Shi Y. Complex and dynamic landscape of RNA polyadenylation revealed by PAS-Seq. RNA 2011, 17:761-772.
51. Tani H., Mizutani R., Salam K.A., Tano K., Ijiri K., Wakamatsu A., Isogai T., Suzuki Y., Akimitsu N. Genome-wide determination of RNA stability reveals hundreds of short-lived noncoding transcripts in mammals. Genome Res. 2012, 22:947-956.
52. Udagawa T., Swanger S.A., Takeuchi K., Kim J.H., Nalavadi V., Shin J., Lorenz L.J., Zukin R.S., Bassell G.J., Richter J.D. Bidirectional control of mRNA translation and synaptic plasticity by the cytoplasmic polyadenylation complex. Mol. Cell 2012, 47:253-266.
53. Viswanathan P., Chen J., Chiang Y.C., Denis C.L. Identification of multiple RNA features that influence CCR4 deadenylation activity. J.Biol. Chem. 2003, 278:14949-14955.
54. Wang Z., Gerstein M., Snyder M. RNA-Seq: a revolutionary tool for transcriptomics. Nat. Rev. Genet. 2009, 10:57-63.
55. Weill L., Belloc E., Bava F.A., Méndez R. Translational control by changes in poly(A) tail length: recycling mRNAs. Nat. Struct. Mol. Biol. 2012, 19:577-585.
56. Whiteford N., Skelly T., Curtis C., Ritchie M.E., Löhr A., Zaranek A.W., Abnizova I., Brown C. Swift: primary data analysis for the Illumina Solexa sequencing platform. Bioinformatics 2009, 25:2194-2199.
57. Wilkening S., Pelechano V., Järvelin A.I., Tekkedil M.M., Anders S., Benes V., Steinmetz L.M. An efficient method for genome-wide polyadenylation site mapping and RNA quantification. Nucleic Acids Res. 2013, 41:e65.
58. Wu L., Fan J., Belasco J.G. MicroRNAs direct rapid deadenylation of mRNA. Proc. Natl Acad. Sci. USA 2006, 103:4034-4039.
59. Yoon O.K., Brem R.B. Noncanonical transcript forms in yeast and their regulation during environmental stress. RNA 2010, 16:1256-1267.