[1] |
Balakirev, E.S., Ayala, F.J. Pseudogenes: are they “junk” or functional DNA? Annu. Rev. Genet., 37 (2003),pp. 123-151
|
[2] |
Benovoy, D., Drouin, G. J. Mol. Evol., 62 (2006),pp. 511-522
|
[3] |
Betran, E., Wang, W., Jin, L. et al. Evolution of the phosphoglycerate mutase processed gene in human and chimpanzee revealing the origin of a new primate gene Mol. Biol. Evol., 19 (2002),pp. 654-663
|
[4] |
Bustamante, C.D., Nielsen, R., Hartl, D.L. A maximum likelihood method for analyzing pseudogene evolution: implications for silent site evolution in humans and rodents Mol. Biol. Evol., 19 (2002),pp. 110-117
|
[5] |
Chiefari, E., Iiritano, S., Paonessa, F. et al. Nat. Commun., 1 (2010),p. 40
|
[6] |
Colbert, D.A., Knoll, B.J., Woo, S.L. et al. Differential hormonal responsiveness of the ovalbumin gene and its pseudogenes in the chick oviduct Biochemistry, 19 (1980),pp. 5586-5592
|
[7] |
D'Errico, I., Gadaleta, G., Saccone, C. Pseudogenes in metazoa: origin and features Brief Funct. Genomic Proteomic, 3 (2004),pp. 157-167
|
[8] |
Dierick, H.A., Mercer, J.F., Glover, T.W. Gene, 198 (1997),pp. 37-41
|
[9] |
Ebisuya, M., Yamamoto, T., Nakajima, M. et al. Ripples from neighbouring transcription Nat. Cell. Biol., 10 (2008),pp. 1106-1113
|
[10] |
Elliman, S.J., Wu, I., Kemp, D.M. J. Biol. Chem., 281 (2006),pp. 16-19
|
[11] |
Fischer, J.A., Maniatis, T. Nucleic Acids Res., 13 (1985),pp. 6899-6917
|
[12] |
Fishman, G.I., Eddy, R.L., Shows, T.B. et al. The human connexin gene family of gap junction proteins: distinct chromosomal locations but similar structures Genomics, 10 (1991),pp. 250-256
|
[13] |
Frederiksen, S., Cao, H., Lomholt, B. et al. The rat 5S rRNA bona fide gene repeat maps to chromosome 19q12-->qter and the pseudogene repeat maps to 12q12 Cytogenet. Cell Genet., 76 (1997),pp. 101-106
|
[14] |
Goncalves, I., Duret, L., Mouchiroud, D. Nature and structure of human genes that generate retropseudogenes Genome Res., 10 (2000),pp. 672-678
|
[15] |
Gray, T.A., Wilson, A., Fortin, P.J. et al. Proc. Natl. Acad. Sci. USA, 103 (2006),pp. 12039-12044
|
[16] |
Guo, X., Zhang, Z., Gerstein, M.B. et al. PLoS Comput. Biol., 5 (2009),p. e1000449
|
[17] |
Han, Y.J., Ma, S.F., Yourek, G. et al. FASEB J., 25 (2011),pp. 2305-2312
|
[18] |
Hardison, R.C., , Lacy, E., Maniatis, T. et al. The structure and transcription of four linked rabbit beta-like globin genes Cell, 18 (1979),pp. 1285-1297
|
[19] |
Harrison, P., Kumar, A., Lan, N. et al. A small reservoir of disabled ORFs in the yeast genome and its implications for the dynamics of proteome evolution J. Mol. Biol., 316 (2002),pp. 409-419
|
[20] |
Harrison, P.M., Echols, N., Gerstein, M.B. Nucleic Acids Res., 29 (2001),pp. 818-830
|
[21] |
Harrison, P.M., Milburn, D., Zhang, Z. et al. Nucleic Acids Res., 31 (2003),pp. 1033-1037
|
[22] |
Harrison, P.M., Zheng, D., Zhang, Z. et al. Transcribed processed pseudogenes in the human genome: an intermediate form of expressed retrosequence lacking protein-coding ability Nucleic Acids Res., 33 (2005),pp. 2374-2383
|
[23] |
Harrow, J., Frankish, A., Gonzalez, J.M. et al. GENCODE: the reference human genome annotation for The ENCODE Project Genome Res., 22 (2012),pp. 1760-1774
|
[24] |
Hillier, L.W., Miller, W., Birney, E. et al. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution Nature, 432 (2004),pp. 695-716
|
[25] |
Hirotsune, S., Yoshida, N., Chen, A. et al. An expressed pseudogene regulates the messenger-RNA stability of its homologous coding gene Nature, 423 (2003),pp. 91-96
|
[26] |
Homma, K., Fukuchi, S., Kawabata, T. et al. Gene, 294 (2002),pp. 25-33
|
[27] |
Jacq, C., Miller, J.R., Brownlee, G.G. Cell, 12 (1977),pp. 109-120
|
[28] |
Jeffs, P., Ashburner, M. Proc. Biol. Sci., 244 (1991),pp. 151-159
|
[29] |
Kalyana-Sundaram, S., Kumar-Sinha, C., Shankar, S. et al. Expressed pseudogenes in the transcriptional landscape of human cancers Cell, 149 (2012),pp. 1622-1634
|
[30] |
Kandouz, M., Bier, A., Carystinos, G.D. et al. Oncogene, 23 (2004),pp. 4763-4770
|
[31] |
Kaneko, S., Aki, I., Tsuda, K. et al. Genetics, 172 (2006),pp. 2421-2429
|
[32] |
Kasschau, K.D., Fahlgren, N., Chapman, E.J. et al. PLoS Biol., 5 (2007),p. e57
|
[33] |
Khachane, A.N., Harrison, P.M. Assessing the genomic evidence for conserved transcribed pseudogenes under selection BMC Genomics, 10 (2009),p. 435
|
[34] |
Khachane, A.N., Harrison, P.M. Strong association between pseudogenization mechanisms and gene sequence length Biology Direct, 4 (2009),p. 38
|
[35] |
Korneev, S.A., Kemenes, I., Bettini, N.L. et al. Axonal trafficking of an antisense RNA transcribed from a pseudogene is regulated by classical conditioning Sci. Rep., 3 (2013),p. 1027
|
[36] |
Korneev, S.A., Park, J.H., O'Shea, M. J. Neurosci., 19 (1999),pp. 7711-7720
|
[37] |
Kunze, N., Yang, G.C., Jiang, Z.Y. et al. Localization of the active type I DNA topoisomerase gene on human chromosome 20q11.2-13.1, and two pseudogenes on chromosomes 1q23-24 and 22q11.2-13.1 Hum. Genet., 84 (1989),pp. 6-10
|
[38] |
Lacy, E., Maniatis, T. The nucleotide sequence of a rabbit beta-globin pseudogene Cell, 21 (1980),pp. 545-553
|
[39] |
Lee, J.S., Brown, G.G., Verma, D.P. Chromosomal arrangement of leghemoglobin genes in soybean Nucleic Acids Res., 11 (1983),pp. 5541-5553
|
[40] |
Lee, J.T. Molecular biology: complicity of gene and pseudogene Nature, 423 (2003),pp. 26-28
|
[41] |
Li, W.H., Gojobori, T., Nei, M. Pseudogenes as a paradigm of neutral evolution Nature, 292 (1981),pp. 237-239
|
[42] |
Lin, H., Shabbir, A., Molnar, M. et al. Biochem. Biophys. Res. Commun., 355 (2007),pp. 111-116
|
[43] |
Lin, M., Pedrosa, E., Shah, A. et al. RNA-Seq of human neurons derived from iPS cells reveals candidate long non-coding RNAs involved in neurogenesis and neuropsychiatric disorders PLoS ONE, 6 (2011),p. e23356
|
[44] |
Liu, Y., Harrison, P.M., Kunin, V. et al. Comprehensive analysis of pseudogenes in prokaryotes: widespread gene decay and failure of putative horizontally transferred genes Genome Biol., 5 (2004),p. R64
|
[45] |
Marques, A.C., Tan, J., Lee, S. et al. Evidence for conserved post-transcriptional roles of unitary pseudogenes and for frequent bifunctionality of mRNAs Genome Biol., 13 (2012),p. R102
|
[46] |
Nishioka, Y., Leder, A., Leder, P. Unusual alpha-globin-like gene that has cleanly lost both globin intervening sequences Proc. Natl. Acad. Sci. USA, 77 (1980),pp. 2806-2809
|
[47] |
Pei, B., Sisu, C., Frankish, A. et al. The GENCODE pseudogene resource Genome Biol., 13 (2012),p. R51
|
[48] |
Petrov, D.A., Lozovskaya, E.R., Hartl, D.L. Nature, 384 (1996),pp. 346-349
|
[49] |
Pink, R.C., Wicks, K., Caley, D.P. et al. Pseudogenes: pseudo-functional or key regulators in health and disease? RNA, 17 (2011),pp. 792-798
|
[50] |
Podlaha, O., Zhang, J. Mol. Biol. Evol., 21 (2004),pp. 2202-2209
|
[51] |
Podlaha, O., Zhang, J.
|
[52] |
Poliseno, L. Pseudogenes: newly discovered players in human cancer Sci. Signal., 5 (2012),p. re5
|
[53] |
Poliseno, L., Salmena, L., Zhang, J. et al. A coding-independent function of gene and pseudogene mRNAs regulates tumour biology Nature, 465 (2010),pp. 1033-1038
|
[54] |
Proudfoot, N. Pseudogenes Nature, 286 (1980),pp. 840-841
|
[55] |
Proudfoot, N.J., Maniatis, T. The structure of a human alpha-globin pseudogene and its relationship to alpha-globin gene duplication Cell, 21 (1980),pp. 537-544
|
[56] |
Singh, N., George, A., Sharma, R. et al. Gene, 491 (2012),pp. 165-172
|
[57] |
Sudbrak, R., Reinhardt, R., Hennig, S. et al. Comparative and evolutionary analysis of the rhesus macaque extended MHC class II region Immunogenetics, 54 (2003),pp. 699-704
|
[58] |
Svensson, O., Arvestad, L., Lagergren, J. Genome-wide survey for biologically functional pseudogenes PLoS Comput. Biol., 2 (2006),p. e46
|
[59] |
Tam, O.H., Aravin, A.A., Stein, P. et al. Pseudogene-derived small interfering RNAs regulate gene expression in mouse oocytes Nature, 453 (2008),pp. 534-538
|
[60] |
Taniguchi, Y., Katsumata, Y., Koido, S. et al. Cloning, sequencing, and chromosomal localization of two tandemly arranged human pseudogenes for the proliferating cell nuclear antigen (PCNA) Mamm. Genome, 7 (1996),pp. 906-908
|
[61] |
Tonner, P., Srinivasasainagendra, V., Zhang, S. et al. Detecting transcription of ribosomal protein pseudogenes in diverse human tissues from RNA-seq data BMC Genomics, 13 (2012),p. 412
|
[62] |
Torrents, D., Suyama, M., Zdobnov, E. et al. A genome-wide survey of human pseudogenes Genome Res., 13 (2003),pp. 2559-2567
|
[63] |
Vanin, E.F. Processed pseudogenes: characteristics and evolution Annu. Rev. Genet., 19 (1985),pp. 253-272
|
[64] |
Wang, W., Zhang, J., Alvarez, C. et al. Mol. Biol. Evol., 17 (2000),pp. 1294-1301
|
[65] |
Watanabe, T., Totoki, Y., Toyoda, A. et al. Endogenous siRNAs from naturally formed dsRNAs regulate transcripts in mouse oocytes Nature, 453 (2008),pp. 539-543
|
[66] |
Willecke, K., Jungbluth, S., Dahl, E. et al. Six genes of the human connexin gene family coding for gap junctional proteins are assigned to four different human chromosomes Eur. J. Cell Biol., 53 (1990),pp. 275-280
|
[67] |
Zhang, Z., Carriero, N., Gerstein, M. Comparative analysis of processed pseudogenes in the mouse and human genomes Trends Genet., 20 (2004),pp. 62-67
|
[68] |
Zhang, Z.D., Frankish, A., Hunt, T. et al. Identification and analysis of unitary pseudogenes: historic and contemporary gene losses in humans and other primates Genome Biol., 11 (2010),p. R26
|
[69] |
Zhang, Z., Gerstein, M. Large-scale analysis of pseudogenes in the human genome Curr. Opin. Genet. Dev., 14 (2004),pp. 328-335
|
[70] |
Zhang, Z., Harrison, P., Gerstein, M. Identification and analysis of over 2000 ribosomal protein pseudogenes in the human genome Genome Res., 12 (2002),pp. 1466-1482
|
[71] |
Zhang, Z., Harrison, P.M., Liu, Y. et al. Millions of years of evolution preserved: a comprehensive catalog of the processed pseudogenes in the human genome Genome Res., 13 (2003),pp. 2541-2558
|
[72] |
Zheng, D., Gerstein, M.B. The ambiguous boundary between genes and pseudogenes: the dead rise up, or do they? Trends Genet., 23 (2007),pp. 219-224
|
[73] |
Zhou, B.S., Beidler, D.R., Cheng, Y.C. Identification of antisense RNA transcripts from a human DNA topoisomerase I pseudogene Cancer Res., 52 (1992),pp. 4280-4285
|