Pseudogene is a DNA fragment with high sequence similarity to the corresponding functional gene. Because of accumulation of multiple mutations, pseudogenes have lost their original functions. Previous studies indicated that pseudogenes are dysfunctional relatives of the corresponding functional genes, and are noises in the process of genome evolution. However, with the development of molecular biotechnologies, more and more studies have demonstrated that pseudogenes possess important biologic functions. For example, some pseudogene could regulate the expression of functional genes by competitively binding to the miRNAs, some could produce endogenous small interference RNAs to negatively regulate the expression of functional genes, and some even could encode functional proteins. In this review, we summarize the recent research progresses of pseudogenes through four aspects: the classification, identification, function, and particularly the roles in cancers.
[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, Boychenk
