Rapid Evolution of piRNA Pathway in the Teleost Fish: Implication for an Adaptation to Transposon Diversity
Tóm tắt
Từ khóa
Tài liệu tham khảo
Aparicio, 2002, Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes, Science, 297, 1301, 10.1126/science.1072104
Aravin, 2006, A novel class of small RNAs bind to MILI protein in mouse testes, Nature, 442, 203, 10.1038/nature04916
Aravin, 2008, A piRNA pathway primed by individual transposons is linked to de novo DNA methylation in mice, Mol Cell., 31, 785, 10.1016/j.molcel.2008.09.003
Aravin, 2007, Developmentally regulated piRNA clusters implicate MILI in transposon control, Science, 316, 744, 10.1126/science.1142612
Bohne, 2012, Zisupton—a novel superfamily of DNA transposable elements recently active in fish, Mol Biol Evol., 29, 631, 10.1093/molbev/msr208
Carmell, 2007, MIWI2 is essential for spermatogenesis and repression of transposons in the mouse male germline, Dev Cell., 12, 503, 10.1016/j.devcel.2007.03.001
Castillo, 2011, Molecular evolution under increasing transposable element burden in Drosophila: a speed limit on the evolutionary arms race, BMC Evol Biol., 11, 258, 10.1186/1471-2148-11-258
Chen, 2009, Mouse Piwi interactome identifies binding mechanism of Tdrkh Tudor domain to arginine methylated Miwi, Proc Natl Acad Sci U S A., 106, 20336, 10.1073/pnas.0911640106
Chen, 2010, A phylogenomic perspective on the new era of ichthyology, Bioscience, 60, 421, 10.1525/bio.2010.60.6.6
Cheng, 2003, The rice field eel as a model system for vertebrate sexual development, Cytogenet Genome Res., 101, 274, 10.1159/000074348
Chenna, 2003, Multiple sequence alignment with the Clustal series of programs, Nucleic Acids Res., 31, 3497, 10.1093/nar/gkg500
Chuma, 2006, Tdrd1/Mtr-1, a tudor-related gene, is essential for male germ-cell differentiation and nuage/germinal granule formation in mice, Proc Natl Acad Sci U S A., 103, 15894, 10.1073/pnas.0601878103
Coggill, 2008, Identifying protein domains with the Pfam database, Curr Protoc Bioinformatics., 10.1002/0471250953.bi0205s23
Duvernell, 2004, Teleost fish genomes contain a diverse array of L1 retrotransposon lineages that exhibit a low copy number and high rate of turnover, J Mol Evol., 59, 298, 10.1007/s00239-004-2625-8
Eickbush, 2002, Fruit flies and humans respond differently to retrotransposons, Curr Opin Genet Dev., 12, 669, 10.1016/S0959-437X(02)00359-3
Fablet, 2014, Variable expression levels detected in the Drosophila effectors of piRNA biogenesis, Gene, 537, 149, 10.1016/j.gene.2013.11.095
Frost, 2010, MOV10L1 is necessary for protection of spermatocytes against retrotransposons by Piwi-interacting RNAs, Proc Natl Acad Sci U S A., 107, 11847, 10.1073/pnas.1007158107
Furano, 2004, L1 (LINE-1) retrotransposon diversity differs dramatically between mammals and fish, Trends Genet., 20, 9, 10.1016/j.tig.2003.11.006
Girard, 2006, A germline-specific class of small RNAs binds mammalian Piwi proteins, Nature, 442, 199, 10.1038/nature04917
Guindon, 2003, A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood, Syst Biol., 52, 696, 10.1080/10635150390235520
Guindon, 2010, New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0, Syst Biol., 59, 307, 10.1093/sysbio/syq010
Houwing, 2008, Zili is required for germ cell differentiation and meiosis in zebrafish, EMBO J., 27, 2702, 10.1038/emboj.2008.204
Houwing, 2007, A role for Piwi and piRNAs in germ cell maintenance and transposon silencing in Zebrafish, Cell, 129, 69, 10.1016/j.cell.2007.03.026
Huang, 2012, Active transposition in genomes, Annu Rev Genet., 46, 651, 10.1146/annurev-genet-110711-155616
Huang, 2011, piRNA-associated germline nuage formation and spermatogenesis require MitoPLD profusogenic mitochondrial-surface lipid signaling, Dev Cell., 20, 376, 10.1016/j.devcel.2011.01.004
Huang, 2011, Tdrd1 acts as a molecular scaffold for Piwi proteins and piRNA targets in zebrafish, EMBO J., 30, 3298, 10.1038/emboj.2011.228
Ishizu, 2012, Biology of PIWI-interacting RNAs: new insights into biogenesis and function inside and outside of germlines, Genes Dev., 26, 2361, 10.1101/gad.203786.112
Jurka, 2000, Repbase update: a database and an electronic journal of repetitive elements, Trends Genet., 16, 418, 10.1016/S0168-9525(00)02093-X
Kalmykova, 2005, Argonaute protein PIWI controls mobilization of retrotransposons in the Drosophila male germline, Nucleic Acids Res., 33, 2052, 10.1093/nar/gki323
Kamminga, 2010, Hen1 is required for oocyte development and piRNA stability in zebrafish, EMBO J., 29, 3688, 10.1038/emboj.2010.233
Kirino, 2007, The mouse homolog of HEN1 is a potential methylase for Piwi-interacting RNAs, RNA, 13, 1397, 10.1261/rna.659307
Kirino, 2009, Arginine methylation of Piwi proteins catalysed by dPRMT5 is required for Ago3 and Aub stability, Nat Cell Biol., 11, 652, 10.1038/ncb1872
Kohany, 2006, Annotation, submission and screening of repetitive elements in Repbase: RepbaseSubmitter and Censor, BMC Bioinformatics, 7, 474, 10.1186/1471-2105-7-474
Kolaczkowski, 2011, Recurrent adaptation in RNA interference genes across the Drosophila phylogeny, Mol Biol Evol., 28, 1033, 10.1093/molbev/msq284
Kondrashov, 2002, Selection in the evolution of gene duplications, Genome Biol., 3, 10.1186/gb-2002-3-2-research0008
Kotaja, 2006, Interplay of PIWI/Argonaute protein MIWI and kinesin KIF17b in chromatoid bodies of male germ cells, J Cell Sci., 119, 2819, 10.1242/jcs.03022
Kuramochi-Miyagawa, 2010, MVH in piRNA processing and gene silencing of retrotransposons, Genes Dev., 24, 887, 10.1101/gad.1902110
Lander, 2001, Initial sequencing and analysis of the human genome, Nature, 409, 860, 10.1038/35057062
Le, 2008, An improved general amino acid replacement matrix, Mol Biol Evol., 25, 1307, 10.1093/molbev/msn067
Ma, 2009, GASZ is essential for male meiosis and suppression of retrotransposon expression in the male germline, PLoS Genet., 5, e1000635, 10.1371/journal.pgen.1000635
Malone, 2009, Molecular evolution of piRNA and transposon control pathways in Drosophila, Cold Spring Harb Symp Quant Biol., 74, 225, 10.1101/sqb.2009.74.052
Mathioudakis, 2012, The multiple Tudor domain-containing protein TDRD1 is a molecular scaffold for mouse Piwi proteins and piRNA biogenesis factors, RNA, 18, 2056, 10.1261/rna.034181.112
McFarlane, 2011, Expansion of the Ago gene family in the teleost clade, Dev Genes Evol., 221, 95, 10.1007/s00427-011-0363-7
Mouse Genome Sequencing Consortium, et al, 2002, Initial sequencing and comparative analysis of the mouse genome, Nature, 420, 520, 10.1038/nature01262
Obbard, 2006, Natural selection drives extremely rapid evolution in antiviral RNAi genes, Curr Biol., 16, 580, 10.1016/j.cub.2006.01.065
Price, 2005, De novo identification of repeat families in large genomes, Bioinformatics 21(Suppl., 1), i351, 10.1093/bioinformatics/bti1018
Pride, 2000, SWAAP: a tool for analyzing substitutions and similarity in multiple alignments
Puszyk, 2013, The epigenetic regulator PLZF represses L1 retrotransposition in germ and progenitor cells, EMBO J., 32, 1941, 10.1038/emboj.2013.118
Reuter, 2009, Loss of the Mili-interacting Tudor domain-containing protein-1 activates transposons and alters the Mili-associated small RNA profile, Nat Struct Mol Biol., 16, 639, 10.1038/nsmb.1615
Schartl, 2013, The genome of the platyfish, Xiphophorus maculatus, provides insights into evolutionary adaptation and several complex traits, Nat Genet., 45, 567, 10.1038/ng.2604
Schwede, 2003, SWISS-MODEL: an automated protein homology-modeling server, Nucleic Acids Res., 31, 3381, 10.1093/nar/gkg520
Simkin, 2013, Recurrent and recent selective sweeps in the piRNA pathway, Evolution, 67, 1081, 10.1111/evo.12011
Siomi, 1994, Essential role for KH domains in RNA binding: impaired RNA binding by a mutation in the KH domain of FMR1 that causes fragile X syndrome, Cell, 77, 33, 10.1016/0092-8674(94)90232-1
Song, 2004, Crystal structure of Argonaute and its implications for RISC slicer activity, Science, 305, 1434, 10.1126/science.1102514
Swanson, 2001, Positive Darwinian selection drives the evolution of several female reproductive proteins in mammals, Proc Natl Acad Sci U S A., 98, 2509, 10.1073/pnas.051605998
Tamura, 2011, MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods, Mol Biol Evol., 28, 2731, 10.1093/molbev/msr121
Tarailo-Graovac, 2009, Using RepeatMasker to identify repetitive elements in genomic sequences, Curr Protoc Bioinformatics., 10.1002/0471250953.bi0410s25
Tian, 2011, Structural basis for piRNA 2′-O-methylated 3′-end recognition by Piwi PAZ (Piwi/Argonaute/Zwille) domains, Proc Natl Acad Sci U S A., 108, 903, 10.1073/pnas.1017762108
Vagin, 2009, Proteomic analysis of murine Piwi proteins reveals a role for arginine methylation in specifying interaction with Tudor family members, Genes Dev., 23, 1749, 10.1101/gad.1814809
Valverde, 2008, Structure and function of KH domains, FEBS J., 275, 2712, 10.1111/j.1742-4658.2008.06411.x
Vermaak, 2005, Positive selection drives the evolution of rhino, a member of the heterochromatin protein 1 family in Drosophila, PLoS Genet., 1, 96, 10.1371/journal.pgen.0010009
Volff, 2005, Genome evolution and biodiversity in teleost fish, Heredity (Edinb), 94, 280, 10.1038/sj.hdy.6800635
Volff, 2003, Diversity of retrotransposable elements in compact pufferfish genomes, Trends Genet., 19, 674, 10.1016/j.tig.2003.10.006
Watanabe, 2011, MITOPLD is a mitochondrial protein essential for nuage formation and piRNA biogenesis in the mouse germline, Dev Cell., 20, 364, 10.1016/j.devcel.2011.01.005
Whitfield, 1993, Rapid sequence evolution of the mammalian sex-determining gene SRY, Nature, 364, 713, 10.1038/364713a0
Xiol, 2012, A role for Fkbp6 and the chaperone machinery in piRNA amplification and transposon silencing, Mol Cell., 47, 970, 10.1016/j.molcel.2012.07.019
Yang, 2007, PAML 4: phylogenetic analysis by maximum likelihood, Mol Biol Evol., 24, 1586, 10.1093/molbev/msm088
Yang, 2005, Bayes empirical Bayes inference of amino acid sites under positive selection, Mol Biol Evol., 22, 1107, 10.1093/molbev/msi097
Zhang, 2004, Evolution of DMY, a newly emergent male sex-determination gene of medaka fish, Genetics, 166, 1887, 10.1534/genetics.166.4.1887
Zhang, 1998, Positive Darwinian selection after gene duplication in primate ribonuclease genes, Proc Natl Acad Sci U S A., 95, 3708, 10.1073/pnas.95.7.3708
Zheng, 2010, Mouse MOV10L1 associates with Piwi proteins and is an essential component of the Piwi-interacting RNA (piRNA) pathway, Proc Natl Acad Sci U S A., 107, 11841, 10.1073/pnas.1003953107
Zhou, 2001, Differential genome duplication and fish diversity, Rev Fish Biol Fish., 11, 331, 10.1023/A:1021395506705