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Volumn 30, Issue 14, 2016, Pages 1671-1682

MTAIL-seq reveals dynamic poly(A) tail regulation in oocyte-to-embryo development

Author keywords

Cytoplasmic polyadenylation; Drosophila; Egg activation; Oogenesis; Poly(A) tail; TAIL seq

Indexed keywords

MESSENGER RNA; POLYNUCLEOTIDE ADENYLYLTRANSFERASE; UNCLASSIFIED DRUG; WISPY PROTEIN; DROSOPHILA PROTEIN; POLYADENYLIC ACID; WISPY PROTEIN, DROSOPHILA;

EID: 84979999775     PISSN: 08909369     EISSN: 15495477     Source Type: Journal    
DOI: 10.1101/gad.284802.116     Document Type: Article
Times cited : (124)

References (55)
  • 1
    • 84928987900 scopus 로고    scopus 로고
    • HTSeq—a Python framework to work with high-throughput sequencing data
    • Anders S, Pyl PT, Huber W. 2015. HTSeq—a Python framework to work with high-throughput sequencing data. Bioinformatics 31: 166-169.
    • (2015) Bioinformatics , vol.31 , pp. 166-169
    • Anders, S.1    Pyl, P.T.2    Huber, W.3
  • 3
    • 84862778053 scopus 로고    scopus 로고
    • Ribosome profiling shows that miR-430 reduces translation before causing mRNA decay in zebrafish
    • Bazzini AA, Lee MT, Giraldez AJ. 2012. Ribosome profiling shows that miR-430 reduces translation before causing mRNA decay in zebrafish. Science 336: 233-237.
    • (2012) Science , vol.336 , pp. 233-237
    • Bazzini, A.A.1    Lee, M.T.2    Giraldez, A.J.3
  • 4
    • 34250895717 scopus 로고    scopus 로고
    • Widespread use of poly(A) tail length control to accentuate expression of the yeast transcriptome
    • Beilharz TH, Preiss T. 2007.Widespread use of poly(A) tail length control to accentuate expression of the yeast transcriptome. RNA 13: 982-997.
    • (2007) RNA , vol.13 , pp. 982-997
    • Beilharz, T.H.1    Preiss, T.2
  • 5
    • 26444460263 scopus 로고    scopus 로고
    • An essential cytoplasmic function for the nuclear poly(A) binding protein, PABP2, in poly(A) tail length control and early development in Drosophila
    • Benoit B, Mitou G, Chartier A, Temme C, Zaessinger S, Wahle E, Busseau I, Simonelig M. 2005. An essential cytoplasmic function for the nuclear poly(A) binding protein, PABP2, in poly(A) tail length control and early development in Drosophila. Dev Cell 9: 511-522.
    • (2005) Dev Cell , vol.9 , pp. 511-522
    • Benoit, B.1    Mitou, G.2    Chartier, A.3    Temme, C.4    Zaessinger, S.5    Wahle, E.6    Busseau, I.7    Simonelig, M.8
  • 6
    • 46749084324 scopus 로고    scopus 로고
    • PAPand GLD-2-type poly(A) polymerases are required sequentially in cytoplasmic polyadenylation and oogenesis in Drosophila
    • Benoit P, Papin C, Kwak JE, Wickens M, Simonelig M. 2008. PAPand GLD-2-type poly(A) polymerases are required sequentially in cytoplasmic polyadenylation and oogenesis in Drosophila. Development 135: 1969-1979.
    • (2008) Development , vol.135 , pp. 1969-1979
    • Benoit, P.1    Papin, C.2    Kwak, J.E.3    Wickens, M.4    Simonelig, M.5
  • 7
    • 0022400587 scopus 로고
    • Tudor, a gene required for assembly of the germ plasm in Drosophila melanogaster
    • Boswell RE, Mahowald AP. 1985. tudor, a gene required for assembly of the germ plasm in Drosophila melanogaster. Cell 43: 97-104.
    • (1985) Cell , vol.43 , pp. 97-104
    • Boswell, R.E.1    Mahowald, A.P.2
  • 8
    • 0037350432 scopus 로고    scopus 로고
    • Orb and a long poly(A) tail are required for efficient oskar translation at the posterior pole of the Drosophila oocyte
    • Castagnetti S, Ephrussi A. 2003. Orb and a long poly(A) tail are required for efficient oskar translation at the posterior pole of the Drosophila oocyte. Development 130: 835-843.
    • (2003) Development , vol.130 , pp. 835-843
    • Castagnetti, S.1    Ephrussi, A.2
  • 9
    • 84896405087 scopus 로고    scopus 로고
    • TAIL-seq: Genome-wide determination of poly(A) tail length and 3′ end modifications
    • Chang H, Lim J, Ha M, Kim VN. 2014. TAIL-seq: genome-wide determination of poly(A) tail length and 3′ end modifications. Mol Cell 53: 1044-1052.
    • (2014) Mol Cell , vol.53 , pp. 1044-1052
    • Chang, H.1    Lim, J.2    Ha, M.3    Kim, V.N.4
  • 10
    • 75149162081 scopus 로고    scopus 로고
    • A novel, noncanonical mechanism of cytoplasmic polyadenylation operates in Drosophila embryogenesis
    • Coll O, Villalba A, Bussotti G, Notredame C, Gebauer F. 2010. A novel, noncanonical mechanism of cytoplasmic polyadenylation operates in Drosophila embryogenesis. Genes Dev 24: 129-134.
    • (2010) Genes Dev , vol.24 , pp. 129-134
    • Coll, O.1    Villalba, A.2    Bussotti, G.3    Notredame, C.4    Gebauer, F.5
  • 11
    • 45849146189 scopus 로고    scopus 로고
    • Wispy, the Drosophila homolog of GLD-2, is required during oogenesis and egg activation
    • Cui J, Sackton KL, Horner VL, Kumar KE, Wolfner MF. 2008. Wispy, the Drosophila homolog of GLD-2, is required during oogenesis and egg activation. Genetics 178: 2017-2029.
    • (2008) Genetics , vol.178 , pp. 2017-2029
    • Cui, J.1    Sackton, K.L.2    Horner, V.L.3    Kumar, K.E.4    Wolfner, M.F.5
  • 12
    • 84885475499 scopus 로고    scopus 로고
    • Cytoplasmic polyadenylation is a major mRNA regulator during oogenesis and egg activation in Drosophila
    • Cui J, Sartain CV, Pleiss JA, Wolfner MF. 2013. Cytoplasmic polyadenylation is a major mRNA regulator during oogenesis and egg activation in Drosophila. Dev Biol 383: 121-131.
    • (2013) Dev Biol , vol.383 , pp. 121-131
    • Cui, J.1    Sartain, C.V.2    Pleiss, J.A.3    Wolfner, M.F.4
  • 13
    • 84875413008 scopus 로고    scopus 로고
    • Translational control of cell growth and malignancy by the CPEBs
    • D’Ambrogio A, Nagaoka K, Richter JD. 2013. Translational control of cell growth and malignancy by the CPEBs. Nat Rev Cancer 13: 283-290.
    • (2013) Nat Rev Cancer , vol.13 , pp. 283-290
    • D’Ambrogio, A.1    Nagaoka, K.2    Richter, J.D.3
  • 15
    • 24044462931 scopus 로고    scopus 로고
    • Activity-dependent polyadenylation in neurons
    • Du L, Richter JD. 2005. Activity-dependent polyadenylation in neurons. RNA 11: 1340-1347.
    • (2005) RNA , vol.11 , pp. 1340-1347
    • Du, L.1    Richter, J.D.2
  • 16
    • 84902497730 scopus 로고    scopus 로고
    • Poly(A)-binding proteins: Structure, domain organization, and activity regulation
    • Eliseeva IA, Lyabin DN, Ovchinnikov LP. 2013. Poly(A)-binding proteins: structure, domain organization, and activity regulation. Biochemistry (Mosc) 78: 1377-1391.
    • (2013) Biochemistry (Mosc) , vol.78 , pp. 1377-1391
    • Eliseeva, I.A.1    Lyabin, D.N.2    Ovchinnikov, L.P.3
  • 17
    • 82455179428 scopus 로고    scopus 로고
    • Shining light on Drosophila oogenesis: Live imaging of egg development
    • He L, Wang XB, Montell DJ. 2011. Shining light on Drosophila oogenesis: live imaging of egg development. Curr Opin Genet Dev 21: 612-619.
    • (2011) Curr Opin Genet Dev , vol.21 , pp. 612-619
    • He, L.1    Wang, X.B.2    Montell, D.J.3
  • 18
    • 0035931276 scopus 로고    scopus 로고
    • Male contributions to egg production: The role of accessory gland products and sperm in Drosophila melanogaster
    • Heifetz Y, Tram U, Wolfner MF. 2001. Male contributions to egg production: the role of accessory gland products and sperm in Drosophila melanogaster. Proc Biol Sci 268: 175-180.
    • (2001) Proc Biol Sci , vol.268 , pp. 175-180
    • Heifetz, Y.1    Tram, U.2    Wolfner, M.F.3
  • 19
    • 40849098573 scopus 로고    scopus 로고
    • Transitioning from egg to embryo: Triggers and mechanisms of egg activation
    • Horner VL, Wolfner MF. 2008. Transitioning from egg to embryo: triggers and mechanisms of egg activation. Dev Dyn 237: 527-544.
    • (2008) Dev Dyn , vol.237 , pp. 527-544
    • Horner, V.L.1    Wolfner, M.F.2
  • 20
    • 61449172037 scopus 로고    scopus 로고
    • Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
    • Huang daW, Sherman BT, Lempicki RA. 2009. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 4: 44-57.
    • (2009) Nat Protoc , vol.4 , pp. 44-57
    • Huang, D.1    Sherman, B.T.2    Lempicki, R.A.3
  • 21
    • 62549134121 scopus 로고    scopus 로고
    • Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling
    • Ingolia NT, Ghaemmaghami S, Newman JR, Weissman JS. 2009. Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science 324: 218-223.
    • (2009) Science , vol.324 , pp. 218-223
    • Ingolia, N.T.1    Ghaemmaghami, S.2    Newman, J.R.3    Weissman, J.S.4
  • 22
    • 33749662940 scopus 로고    scopus 로고
    • Opposing polymerase-deadenylase activities regulate cytoplasmic polyadenylation
    • Kim JH, Richter JD. 2006. Opposing polymerase-deadenylase activities regulate cytoplasmic polyadenylation. Mol Cell 24: 173-183.
    • (2006) Mol Cell , vol.24 , pp. 173-183
    • Kim, J.H.1    Richter, J.D.2
  • 23
    • 0029028583 scopus 로고
    • Translational regulation of oskar mRNA by Bruno, an ovarian RNA-binding protein, is essential
    • Kim-Ha J, Kerr K, Macdonald PM. 1995. Translational regulation of oskar mRNA by Bruno, an ovarian RNA-binding protein, is essential. Cell 81: 403-412.
    • (1995) Cell , vol.81 , pp. 403-412
    • Kim-Ha, J.1    Kerr, K.2    Macdonald, P.M.3
  • 24
    • 84865647770 scopus 로고    scopus 로고
    • Protein phosphorylation changes reveal new candidates in the regulation of egg activation and early embryogenesis in D. Melanogaster
    • Krauchunas AR, Horner VL, Wolfner MF. 2012. Protein phosphorylation changes reveal new candidates in the regulation of egg activation and early embryogenesis in D. melanogaster. Dev Biol 370: 125-134.
    • (2012) Dev Biol , vol.370 , pp. 125-134
    • Krauchunas, A.R.1    Horner, V.L.2    Wolfner, M.F.3
  • 25
    • 84902326037 scopus 로고    scopus 로고
    • Widespread changes in the posttranscriptional landscape at the Drosophila oocyte-to-embryo transition
    • Kronja I, Yuan B, Eichhorn SW, Dzeyk K, Krijgsveld J, Bartel DP, Orr-Weaver TL. 2014. Widespread changes in the posttranscriptional landscape at the Drosophila oocyte-to-embryo transition. Cell Rep 7: 1495-1508.
    • (2014) Cell Rep , vol.7 , pp. 1495-1508
    • Kronja, I.1    Yuan, B.2    Eichhorn, S.W.3    Dzeyk, K.4    Krijgsveld, J.5    Bartel, D.P.6    Orr-Weaver, T.L.7
  • 27
    • 84946476579 scopus 로고    scopus 로고
    • Regulation and function of maternal gene products during the maternal-to-zygotic transition in Drosophila
    • Laver JD, Marsolais AJ, Smibert CA, Lipshitz HD. 2015. Regulation and function of maternal gene products during the maternal-to-zygotic transition in Drosophila. Curr Top Dev Biol 113: 43-84.
    • (2015) Curr Top Dev Biol , vol.113 , pp. 43-84
    • Laver, J.D.1    Marsolais, A.J.2    Smibert, C.A.3    Lipshitz, H.D.4
  • 28
    • 80053194792 scopus 로고    scopus 로고
    • Base-calling for next-generation sequencing platforms
    • Ledergerber C, Dessimoz C. 2011. Base-calling for next-generation sequencing platforms. Brief Bioinform 12: 489-497.
    • (2011) Brief Bioinform , vol.12 , pp. 489-497
    • Ledergerber, C.1    Dessimoz, C.2
  • 30
    • 79961123152 scopus 로고    scopus 로고
    • RSEM: Accurate transcript quantification fromRNA-seq data with or without a reference genome
    • Li B, Dewey CN. 2011. RSEM: accurate transcript quantification fromRNA-seq data with or without a reference genome. BMC Bioinformatics 12: 323.
    • (2011) BMC Bioinformatics , vol.12 , pp. 323
    • Li, B.1    Dewey, C.N.2
  • 32
    • 36148973188 scopus 로고    scopus 로고
    • A novel method for poly(A) fractionation reveals a large population of mRNAs with a short poly(A) tail in mammalian cells
    • Meijer HA, Bushell M, Hill K, Gant TW, Willis AE, Jones P, de Moor CH. 2007. 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 35: e132.
    • (2007) Nucleic Acids Res , vol.35
    • Meijer, H.A.1    Bushell, M.2    Hill, K.3    Gant, T.W.4    Willis, A.E.5    Jones, P.6    De Moor, C.H.7
  • 33
    • 0035404265 scopus 로고    scopus 로고
    • Translational control by CPEB: A means to the end
    • Mendez R, Richter JD. 2001. Translational control by CPEB: a means to the end. Nat Rev Mol Cell Biol 2: 521-529.
    • (2001) Nat Rev Mol Cell Biol , vol.2 , pp. 521-529
    • Mendez, R.1    Richter, J.D.2
  • 34
    • 84886404826 scopus 로고    scopus 로고
    • Cytoplasmic RNA: A case of the tail wagging the dog
    • Norbury CJ. 2013. Cytoplasmic RNA: a case of the tail wagging the dog. Nat Rev Mol Cell Biol 14: 643-653.
    • (2013) Nat Rev Mol Cell Biol , vol.14 , pp. 643-653
    • Norbury, C.J.1
  • 35
    • 77951978351 scopus 로고    scopus 로고
    • Mitotic cell-cycle progression is regulated by CPEB1 and CPEB4-dependent translational control
    • Novoa I, Gallego J, Ferreira PG, Mendez R. 2010. Mitotic cell-cycle progression is regulated by CPEB1 and CPEB4-dependent translational control. Nat Cell Biol 12: 447-456.
    • (2010) Nat Cell Biol , vol.12 , pp. 447-456
    • Novoa, I.1    Gallego, J.2    Ferreira, P.G.3    Mendez, R.4
  • 36
    • 38849190013 scopus 로고    scopus 로고
    • A combinatorial code for CPE-mediated translational control
    • Pique M, Lopez JM, Foissac S, Guigo R, Mendez R. 2008. A combinatorial code for CPE-mediated translational control. Cell 132: 434-448.
    • (2008) Cell , vol.132 , pp. 434-448
    • Pique, M.1    Lopez, J.M.2    Foissac, S.3    Guigo, R.4    Mendez, R.5
  • 37
    • 62549110472 scopus 로고    scopus 로고
    • Mutations in the chromosomal passenger complex and the condensin complex differentially affect synaptonemal complex disassembly and metaphase I configuration in Drosophila female meiosis
    • Resnick TD, Dej KJ, Xiang Y, Hawley RS, Ahn C, Orr-Weaver TL. 2009. Mutations in the chromosomal passenger complex and the condensin complex differentially affect synaptonemal complex disassembly and metaphase I configuration in Drosophila female meiosis. Genetics 181: 875-887.
    • (2009) Genetics , vol.181 , pp. 875-887
    • Resnick, T.D.1    Dej, K.J.2    Xiang, Y.3    Hawley, R.S.4    Ahn, C.5    Orr-Weaver, T.L.6
  • 38
    • 34249908103 scopus 로고    scopus 로고
    • CPEB: A life in translation
    • Richter JD. 2007. CPEB: a life in translation. Trends Biochem Sci 32: 279-285.
    • (2007) Trends Biochem Sci , vol.32 , pp. 279-285
    • Richter, J.D.1
  • 39
    • 84909644283 scopus 로고    scopus 로고
    • Normalization of RNA-seq data using factor analysis of control genes or samples
    • Risso D, Ngai J, Speed TP, Dudoit S. 2014. Normalization of RNA-seq data using factor analysis of control genes or samples. Nat Biotechnol 32: 896-902.
    • (2014) Nat Biotechnol , vol.32 , pp. 896-902
    • Risso, D.1    Ngai, J.2    Speed, T.P.3    Dudoit, S.4
  • 40
    • 0028604498 scopus 로고
    • Coordinate initiation of Drosophila development by regulated polyadenylation of maternal messenger RNAs
    • Salles FJ, Lieberfarb ME, Wreden C, Gergen JP, Strickland S. 1994. Coordinate initiation of Drosophila development by regulated polyadenylation of maternal messenger RNAs. Science 266: 1996-1999.
    • (1994) Science , vol.266 , pp. 1996-1999
    • Salles, F.J.1    Lieberfarb, M.E.2    Wreden, C.3    Gergen, J.P.4    Strickland, S.5
  • 41
    • 0032864002 scopus 로고    scopus 로고
    • Assaying the polyadenylation state of mRNAs
    • Salles FJ, Richards WG, Strickland S. 1999. Assaying the polyadenylation state of mRNAs. Methods 17: 38-45.
    • (1999) Methods , vol.17 , pp. 38-45
    • Salles, F.J.1    Richards, W.G.2    Strickland, S.3
  • 42
    • 0028226530 scopus 로고
    • The 3′-untranslated regions of c-mos and cyclin mRNAsstimulate translation by regulating cytoplasmic polyadenylation
    • Sheets MD, Fox CA, Hunt T, VandeWoude G, Wickens M. 1994. The 3′-untranslated regions of c-mos and cyclin mRNAsstimulate translation by regulating cytoplasmic polyadenylation. Genes Dev 8: 926-938.
    • (1994) Genes Dev , vol.8 , pp. 926-938
    • Sheets, M.D.1    Fox, C.A.2    Hunt, T.3    Vandewoude, G.4    Wickens, M.5
  • 43
    • 84897571308 scopus 로고    scopus 로고
    • Poly(A)-tail profiling reveals an embryonic switch in translational control
    • Subtelny AO, Eichhorn SW, Chen GR, Sive H, Bartel DP. 2014. Poly(A)-tail profiling reveals an embryonic switch in translational control. Nature 508: 66-71.
    • (2014) Nature , vol.508 , pp. 66-71
    • Subtelny, A.O.1    Eichhorn, S.W.2    Chen, G.R.3    Sive, H.4    Bartel, D.P.5
  • 44
    • 70350023619 scopus 로고    scopus 로고
    • The maternal-to-zygotic transition: A play in two acts
    • Tadros W, Lipshitz HD. 2009. The maternal-to-zygotic transition: a play in two acts. Development 136: 3033-3042.
    • (2009) Development , vol.136 , pp. 3033-3042
    • Tadros, W.1    Lipshitz, H.D.2
  • 47
    • 33845737053 scopus 로고    scopus 로고
    • The Drosophila PNG kinase complex regulates the translation of cyclin B
    • Vardy L, Orr-Weaver TL. 2007. The Drosophila PNG kinase complex regulates the translation of cyclin B. DevCell 12: 157-166.
    • (2007) Devcell , vol.12 , pp. 157-166
    • Vardy, L.1    Orr-Weaver, T.L.2
  • 48
    • 60549117666 scopus 로고    scopus 로고
    • Regulation of Cyclin A protein in meiosis and early embryogenesis
    • Vardy L, Pesin JA, Orr-Weaver TL. 2009. Regulation of Cyclin A protein in meiosis and early embryogenesis. Proc Natl Acad Sci 106: 1838-1843.
    • (2009) Proc Natl Acad Sci , vol.106 , pp. 1838-1843
    • Vardy, L.1    Pesin, J.A.2    Orr-Weaver, T.L.3
  • 49
    • 84863950214 scopus 로고    scopus 로고
    • Developmental control of oocyte maturation and egg activation in metazoan models
    • Von Stetina JR, Orr-Weaver TL. 2011. Developmental control of oocyte maturation and egg activation in metazoan models. Cold Spring Harb Perspect Biol 3: a005553.
    • (2011) Cold Spring Harb Perspect Biol , vol.3
    • Von Stetina, J.R.1    Orr-Weaver, T.L.2
  • 50
    • 0030200219 scopus 로고    scopus 로고
    • The biochemistry of polyadenylation
    • Wahle E, Keller W. 1996. The biochemistry of polyadenylation. Trends Biochem Sci 21: 247-250.
    • (1996) Trends Biochem Sci , vol.21 , pp. 247-250
    • Wahle, E.1    Keller, W.2
  • 52
    • 84861911071 scopus 로고    scopus 로고
    • Translational control by changes in poly(A) tail length: Recycling mRNAs
    • Weill L, Belloc E, Bava FA, Mendez R. 2012. Translational control by changes in poly(A) tail length: recycling mRNAs. Nat Struct Mol Biol 19: 577-585.
    • (2012) Nat Struct Mol Biol , vol.19 , pp. 577-585
    • Weill, L.1    Belloc, E.2    Bava, F.A.3    Mendez, R.4
  • 54
    • 1842507194 scopus 로고    scopus 로고
    • PKA-R1 spatially restricts Oskar expression for Drosophila embryonic patterning
    • Yoshida S, Muller HA, Wodarz A, Ephrussi A. 2004. PKA-R1 spatially restricts Oskar expression for Drosophila embryonic patterning. Development 131: 1401-1410.
    • (2004) Development , vol.131 , pp. 1401-1410
    • Yoshida, S.1    Muller, H.A.2    Wodarz, A.3    Ephrussi, A.4
  • 55
    • 84901196875 scopus 로고    scopus 로고
    • Sizing up the poly(A) tail: Insights from deep sequencing
    • Zheng D, Tian B. 2014. Sizing up the poly(A) tail: insights from deep sequencing. Trends Biochem Sci 39: 255-257.
    • (2014) Trends Biochem Sci , vol.39 , pp. 255-257
    • Zheng, D.1    Tian, B.2


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