[1] Jacq C, Miller JR, Brownlee GG. A pseudogene structure in 5S DNA of Xenopus laevis . Cell , 1977, 12(1): 109-120. [2] Proudfoot N. Pseudogenes. Nature , 1980, 286(5776): 840-841. [3] Petrov DA, Hartl DL. Pseudogene evolution and natural selection for a compact genome. J Hered , 2000, 91(3): 221-227. [4] Podlaha O, Zhang JZ. Pseudogenes and their evolution. Chichester: John Wiley & Sons, 2001. [5] Zhou BS, Beidler DR, Cheng YC. Identification of antisense RNA transcripts from a human DNA topoisomeraseⅠ pseudogene 1. Cancer Res , 1992, 52(15): 4280-4285. [6] Korneev SA, Park JH, O'shea M. Neuronal expression of neural nitric oxide synthase (nNOS) protein is suppressed by an antisense RNA transcribed from an NOS pseudogene. J Neurosci , 1999, 19(18): 7711-7720. [7] Tam OH, Aravin AA, Stein P, Girard A, Murchison EP, Cheloufi S, Hodges E, Anger M, Sachidanandam R, Schultz RM, Hannon GJ. Pseudogene-derived small interfering RNAs regulate gene expression in mouse oocytes. Nature , 2008, 453(7194): 534-538. [8] Poliseno L, Salmena L, Zhang JW, Carver B, Haveman WJ, Pandolfi PP. A coding-independent function of gene and pseudogene mRNAs regulates tumour biology. Nature , 2010, 465(7301): 1033-1038. [9] Johnsson P, Ackley A, Vidarsdottir L, Lui WO, Corcoran M, Grandér D, Morris KV. A pseudogene long-noncoding-RNA network regulates PTEN transcription and translation in human cells. Nat Struct Mol Biol , 2013, 20(4): 440-446. [10] Mighell AJ, Smith NR, Robinson PA, Markham AF. Vertebrate pseudogenes. FEBS Lett , 2000, 468(2-3): 109-114. [11] Zhang ZD, Frankish A, Hunt T, Harrow J, Gerstein M. Identification and analysis of unitary pseudogenes: historic and contemporary gene losses in humans and other primates. Genome Biol , 2010, 11(3): R26. [12] Maestre J, Tchenio T, Dhellin O, Heidmann T. mRNA retroposition in human cells: processed pseudogene formation. EMBO J , 1995, 14(24): 6333-6338. [13] D'errico I, Gadaleta G, Saccone C. Pseudogenes in metazoa: origin and features. Brief Funct Genom Proteom , 2004, 3(2): 157-167. [14] Vanin EF. Processed pseudogenes: Characteristics and evolution. Annu Rev Genet , 1985, 19(1): 253-272. [15] Li WH, Gojobori T, Nei M. Pseudogenes as a paradigm of neutral evolution. Nature , 1981, 292(5820): 237-239. [16] Wang W, Zhang JM, Alvarez C, Llopart A, Long MY. The origin of the Jingwei gene and the complex modular structure of its parental gene, Yellow emperor , in Drosophila melanogaster . Mol Biol Evol , 2000, 17(9): 1294-1301. [17] Torrents D, Suyama M, Zdobnov E, Bork P. A genome-wide survey of human pseudogenes. Genome Res , 2003, 13(12): 2559-2567. [18] Li W, Yang W, Wang XJ. Pseudogenes: pseudo or real functional elements? J Genet Genomics , 2013, 40(4): 171-177. [19] Balakirev ES, Ayala FJ. PSEUDOGENES: Are they “Junk” or functional DNA? Annu Rev Genet , 2003, 37(1): 123-151. [20] Betrán E, Wang W, Jin L, Long MY. Evolution of the Phosphoglycerate mutase processed gene in human and chimpanzee revealing the origin of a new primate gene. Mol Biol Evol , 2002, 19(5): 654-663. [21] Zheng DY, Gerstein MB. A computational approach for identifying pseudogenes in the ENCODE regions. Genome Biol , 2006, 7(Suppl. 1): S13. [22] Zheng DY, Frankish A, Baertsch R, Kapranov P, Reymond A, Choo SW, Lu Y, Denoeud F, Antonarakis SE, Snyder M, Ruan YJ, Wei CL, Gingeras TR, Guigó R, Harrow J, Gerstein MB. Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolution. Genome Res , 2007, 17(6): 839-851. [23] Molineris I, Sales G, Bianchi F, Di Cunto F, Caselle M. A new approach for the identification of processed pseudogenes. J Comput Biol , 2010, 17(5): 755-765. [24] Harrow J, Frankish A, Gonzalez JM, Tapanari E, Diekhans M, Kokocinski F, Aken BL, Barrell D, Zadissa A, Searle S, Barnes I, Bignell A, Boychenko V, Hunt T, Kay M, Mukherjee G, Rajan J, Despacio-Reyes G, Saunders G, Steward C, Harte R, Lin M, Howald C, Tanzer A, Derrien T, Chrast J, Walters N, Balasubramanian S, Pei BK, Tress M, Rodriguez JM, Ezkurdia I, Van Baren J, Brent M, Haussler D, Kellis M, Valencia A, Reymond A, Gerstein M, Guigó R, Hubbard TJ. GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res , 2012, 22(9): 1760-1774. [25] Pei BK, Sisu C, Frankish A, Howald C, Habegger L, Mu XJ, Harte R, Balasubramanian S, Tanzer A, Diekhans M, Reymond A, Hubbard TJ, Harrow J, Gerstein MB. The GENCODE pseudogene resource. Genome Biol , 2012, 13(9): R51. [26] Kalyana-Sundaram S, Kumar-Sinha C, Shankar S, Robinson DR, Wu YM, Cao XH, Asangani IA, Kothari V, Prensner JR, Lonigro RJ, Iyer MK, Barrette T, Shanmugam A, Dhanasekaran SM, Palanisamy N, Chinnaiyan AM. Expressed pseudogenes in the transcriptional landscape of human cancers. Cell , 2012, 149(7): 1622-1634. [27] Korneev SA, Kemenes I, Bettini NL, Kemenes G, Staras K, Benjamin PR, O'shea M. Axonal trafficking of an antisense RNA transcribed from a pseudogene is regulated by classical conditioning. Sci Rep , 2013, 3: 1027. [28] Rutnam ZJ, Du WW, Yang WN, Yang XL, Yang BB. The pseudogene TUSC2P promotes TUSC2 function by binding multiple microRNAs. Nat Commun , 2014, 5: 2914. [29] Borrmann L, Wilkening S, Bullerdiek J. The expression of HMGA genes is regulated by their 3 ' UTR. Oncogene , 2001, 20(33): 4537-4541. [30] Chiefari E, Iiritano S, Paonessa F, Le Pera I, Arcidiacono B, Filocamo M, Foti D, Liebhaber SA, Brunetti A. Pseudogene-mediated posttranscriptional silencing of HMGA1 can result in insulin resistance and type 2 diabetes. Nat Commun , 2010, 1: 40. [31] Watanabe T, Totoki Y, Toyoda A, Kaneda M, Kuramochi-Miyagawa S, Obata Y, Chiba H, Kohara Y, Kono T, Nakano T, Surani MA, Sakaki Y, Sasaki H. Endogenous siRNAs from naturally formed dsRNAs regulate transcripts in mouse oocytes. Nature , 2008, 453(7194): 539-543. [32] Chan WL, Yuo CY, Yang WK, Hung SY, Chang YS, Chiu CC, Yeh KT, Huang HD, Chang JG. Transcribed pseudogene ψPPM1K generates endogenous siRNA to suppress oncogenic cell growth in hepatocellular carcinoma. Nucleic Acids Res , 2013, 41(6): 3734-3747. [33] Eichenlaub MP, Ettwiller L. De novo genesis of enhancers in vertebrates. PLoS Biol , 2011, 9(11): e1001188. [34] Dierick HA, Mercer JFB, Glover TW. A phosphoglycerate mutase brain isoform (PGAM1 ) pseudogene is localized within the human Menkes disease gene (ATP7A ). Gene , 1997, 198(1-2): 37-41. [35] Fishman GI, Eddy RL, Shows TB, Rosenthal L, Leinwand LA. The human connexin gene family of gap junction proteins: distinct chromosomal locations but similar structures. Genomics , 1991, 10(1): 250-256. [36] Kandouz M, Bier A, Carystinos GD, Alaoui-Jamali MA, Batist G. Connexin43 pseudogene is expressed in tumor cells and inhibits growth. Oncogene , 2004, 23(27): 4763-4770. [37] Porter KA, Duffy EB, Nyland P, Atianand MK, Sharifi H, Harton JA. The CLRX. 1/NOD24 (NLRP2P) pseudogene codes a functional negative regulator of NF-κB, pyrin-only protein 4. Genes Immun , 2014, 15(6): 392-403. [38] Zheng DY, Gerstein MB. The ambiguous boundary between genes and pseudogenes: the dead rise up, or do they? Trends Genet , 2007, 23(5): 219-224. [39] Han L, Yuan Y, Zheng SY, Yang Y, Li J, Edgerton ME, Diao LX, Xu YX, Verhaak RGW, Liang H. The Pan-Cancer analysis of pseudogene expression reveals biologically and clinically relevant tumour subtypes. Nat Commun , 2014, 5: 3963. [40] Lin H, Shabbir A, Molnar M, Lee T. Stem cell regulatory function mediated by expression of a novel mouse Oct4 pseudogene. Biochem Biophys Res Commun , 2007, 355(1): 111-116. [41] Zhao SD, Yuan QH, Hao HB, Guo YJ, Liu SM, Zhang YM, Wang JL, Liu HJ, Wang FW, Liu K, Ling EA, Hao AJ. Expression of OCT4 pseudogenes in human tumours: lessons from glioma and breast carcinoma. J Pathol , 2011, 223(5): 672-682. [42] Redshaw Z, Strain AJ. Human haematopoietic stem cells express Oct4 pseudogenes and lack the ability to initiate Oct4 promoter-driven gene expression. J Negat Results Biomed , 2010, 9(1): 2. [43] Guo XP, Tang YM. OCT4 pseudogenes present in human leukemia cells. Clin Exp Med , 2012, 12(4): 207-216. [44] Kastler S, Honold L, Luedeke M, Kuefer R, Möller P, Hoegel J, Vogel W, Maier C, Assum G. POU5F1P1, a putative cancer susceptibility gene, is overexpressed in prostatic carcinoma. Prostate , 2010, 70(6): 666-674. [45] Poliseno L. Pseudogenes: Newly discovered players in human cancer. Sci Signal , 2012, 5(242): re5. [46] Wang L, Guo ZY, Zhang R, Xin B, Chen R, Zhao J, Wang T, Wen WH, Jia LT, Yao LB, Yang AG. Pseudogene OCT4-pg4 functions as a natural micro RNA sponge to regulate OCT4 expression by competing for miR-145 in hepatocellular carcinoma. Carcinogenesis , 2013, 34(8): 1773-1781. [47] Prensner JR, Chinnaiyan AM. The emergence of lncRNAs in cancer biology. Cancer Discov , 2011, 1(5): 391-407. [48] Han YJ, Ma SF, Yourek G, Park YD, Garcia JGN. A transcribed pseudogene of MYLK promotes cell proliferation. FASEB J , 2011, 25(7): 2305-2312. [49] Gherman A, Chen PE, Teslovich TM, Stankiewicz P, Withers M, Kashuk CS, Chakravarti A, Lupski JR, Cutler DJ, Katsanis N. Population bottlenecks as a potential major shaping force of human genome architecture. PLoS Genet , 2007, 3(7): e119. [50] Samaan S, Lichner Z, Ding Q, Saleh C, Samuel J, Streutker C, Yousef GM. Kallikreins are involved in an miRNA network that contributes to prostate cancer progression. Biol Chem , 2014, 395(9): 991-1001. [51] Poliseno L, Haimovic A, Christos PJ, Vega YSDMEC, Shapiro R, Pavlick A, Berman RS, Darvishian F, Osman I. Deletion of PTENP1 pseudogene in human melanoma. J Invest Dermatol , 2011, 131(12): 2497-2500. [52] Liu L, Liu Y, Liu JB, Zhai XJ, Wen J, Xie KP, Shen HB, Hu ZB, Fan ZN. Genetic variants in pseudogene E2F3P1 confer risk for HBV-related hepatocellular carcinoma in a Chinese population. J Biomedical Res , 2013, 27(3): 215-219. [53] Pan Y, Sun CQ, Huang MD, Liu Y, Qi FZ, Liu L, Wen J, Liu JB, Xie KP, Ma HX, Hu ZB, Shen HB. A genetic variant in pseudogene E2F3P1 contributes to prognosis of hepatocellular carcinoma. J Biomedical Res , 2014, 28(3): 194-200. [54] Zhang JY, Wang X, Li MX, Han J, Chen B, Wang B, Dai JW. NANOGP8 is a retrogene expressed in cancers. FEBS J , 2006, 273(8): 1723-1730. [55] Jeter CR, Badeaux M, Choy G, Chandra D, Patrawala L, Liu C, Calhoun-Davis T, Zaehres H, Daley GQ, Tang DG. Functional evidence that the self-renewal gene NANOG regulates human tumor development. Stem Cells , 2009, 27(5): 993-1005. [56] Bier A, Oviedo-Landaverde I, Zhao J, Mamane Y, Kandouz M, Batist G. Connexin43 pseudogene in breast cancer cells offers a novel therapeutic target. Mol Cancer Therapeutics , 2009, 8(4): 786-793. [57] Liu Y, Wang ZQ, Li HM, Wu ZP, Wei F, Wang HP. Role of the ERas gene in gastric cancer cells. Oncol Rep , 2013, 30(1): 50-56. [58] Piehler AP, Hellum M, Wenzel JJ, Kaminski E, Haug KB, Kierulf P, Kaminski WE. The human ABC transporter pseudogene family: Evidence for transcription and gene-pseudogene interference. BMC Genomics , 2008, 9: 165. [59] Zou M, Baitei EY, Alzahrani AS, Al-Mohanna F, Farid NR, Meyer B, Shi Y. Oncogenic activation of MAP kinase by BRAF pseudogene in thyroid tumors. Neoplasia , 2009, 11(1): 57-65. [60] Weakley SM, Wang H, Yao QZ, Chen CY. Expression and function of a large non-coding RNA gene XIST in human cancer. World J Surg , 2011, 35(8): 1751-1756. [61] Duret L, Chureau C, Samain S, Weissenbach J, Avner P. The Xist RNA gene evolved in eutherians by pseudogenization of a protein-coding gene. Science , 2006, 312(5780): 1653-1655. |