pseudogenes

Summary

Summary: Genes bearing close resemblance to known genes at different loci, but rendered non-functional by additions or deletions in structure that prevent normal transcription or translation. When lacking introns and containing a poly-A segment near the downstream end (as a result of reverse copying from processed nuclear RNA into double-stranded DNA), they are called processed genes.

Top Publications

  1. Alexander R, Fang G, Rozowsky J, Snyder M, Gerstein M. Annotating non-coding regions of the genome. Nat Rev Genet. 2010;11:559-71 pubmed publisher
    ..Finally, one can relate functional genomics annotations to conserved units and measures of conservation derived from comparative sequence analysis. ..
  2. Cui J, Das S, Smith T, Samuelson J. Trichomonas transmembrane cyclases result from massive gene duplication and concomitant development of pseudogenes. PLoS Negl Trop Dis. 2010;4:e782 pubmed publisher
    ..With the goal of beginning to understand why some Trichomonas genes are present in so many copies, we characterized here a family of approximately 123 Trichomonas genes that encode transmembrane adenylyl cyclases (TMACs)...
  3. Muro E, Andrade Navarro M. Pseudogenes as an alternative source of natural antisense transcripts. BMC Evol Biol. 2010;10:338 pubmed publisher
    ..To support this we identified human pseudogenes with a trans-NAT to the parental gene in their antisense strand by analysis of the database of expressed ..
  4. Salmena L, Poliseno L, Tay Y, Kats L, Pandolfi P. A ceRNA hypothesis: the Rosetta Stone of a hidden RNA language?. Cell. 2011;146:353-8 pubmed publisher
    Here, we present a unifying hypothesis about how messenger RNAs, transcribed pseudogenes, and long noncoding RNAs "talk" to each other using microRNA response elements (MREs) as letters of a new language...
  5. Muro E, Mah N, Andrade Navarro M. Functional evidence of post-transcriptional regulation by pseudogenes. Biochimie. 2011;93:1916-21 pubmed publisher
    b>Pseudogenes have been mainly considered as functionless evolutionary relics since their discovery in 1977...
  6. Molineris I, Sales G, Bianchi F, Di Cunto F, Caselle M. A new approach for the identification of processed pseudogenes. J Comput Biol. 2010;17:755-65 pubmed publisher
    Processed pseudogenes are DNA sequences generated through reverse transcription (RT) and retrotransposition of mature mRNAs...
  7. Baele G, Van de Peer Y, Vansteelandt S. Modelling the ancestral sequence distribution and model frequencies in context-dependent models for primate non-coding sequences. BMC Evol Biol. 2010;10:244 pubmed publisher
    ..Further, these assumptions are shown to change across different datasets, making the search for an adequate model for a given dataset quite challenging. ..
  8. Kuo C, Ochman H. The extinction dynamics of bacterial pseudogenes. PLoS Genet. 2010;6: pubmed publisher
    b>Pseudogenes are usually considered to be completely neutral sequences whose evolution is shaped by random mutations and chance events...
  9. Vaughn C, Robles J, Swensen J, Miller C, Lyon E, Mao R, et al. Clinical analysis of PMS2: mutation detection and avoidance of pseudogenes. Hum Mutat. 2010;31:588-93 pubmed publisher
    ..four mismatch repair genes associated with Lynch syndrome, is greatly complicated by the presence of numerous pseudogenes. We used a modification of a long-range PCR method to evaluate PMS2 in 145 clinical samples...

More Information

Publications62

  1. Khachane A, Harrison P. Strong association between pseudogenization mechanisms and gene sequence length. Biol Direct. 2009;4:38 pubmed publisher
    b>Pseudogenes arise from the decay of gene copies following either RNA-mediated duplication (processed pseudogenes) or DNA-mediated duplication (nonprocessed pseudogenes)...
  2. McDonell L, Drouin G. The abundance of processed pseudogenes derived from glycolytic genes is correlated with their expression level. Genome. 2012;55:147-51 pubmed publisher
    The abundance of processed pseudogenes in different vertebrate species is known to be proportional to the length of their oogenesis...
  3. Pei B, Sisu C, Frankish A, Howald C, Habegger L, Mu X, et al. The GENCODE pseudogene resource. Genome Biol. 2012;13:R51 pubmed publisher
    b>Pseudogenes have long been considered as nonfunctional genomic sequences...
  4. Wang K, Chang H. Molecular mechanisms of long noncoding RNAs. Mol Cell. 2011;43:904-14 pubmed publisher
    ..As new lncRNAs are being discovered at a rapid pace, the molecular mechanisms of lncRNAs are likely to be enriched and diversified. ..
  5. Singh N, George A, Sharma R, Singla S, Palta P, Manik R, et al. Characterization of POU5F1 (OCT4) gene and its promoter in buffalo ESC-like cells identifies multiple transcription start sites and expression of four pseudogenes. Gene. 2012;491:165-72 pubmed publisher
    ..In addition, we identified expression of four pseudogenes in buffalo ESC-like cells...
  6. Raha D, Wang Z, Moqtaderi Z, Wu L, Zhong G, Gerstein M, et al. Close association of RNA polymerase II and many transcription factors with Pol III genes. Proc Natl Acad Sci U S A. 2010;107:3639-44 pubmed publisher
    ..These results indicate that, contrary to previous expectations, polymerases can often work with one another to globally coordinate gene expression. ..
  7. Cui J, Pan Y, Zhang Y, Jones G, Zhang S. Progressive pseudogenization: vitamin C synthesis and its loss in bats. Mol Biol Evol. 2011;28:1025-31 pubmed publisher
    ..We also suggest that the evolution of bat GULO genes can be a good model to study genetic processes associated with loss-of-function...
  8. Harrow J, Frankish A, Gonzalez J, Tapanari E, Diekhans M, Kokocinski F, et al. GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res. 2012;22:1760-74 pubmed publisher
    ..GENCODE 7 is publicly available from gencodegenes.org and via the Ensembl and UCSC Genome Browsers. ..
  9. Wang L, Si W, Yao Y, Tian D, Araki H, Yang S. Genome-wide survey of pseudogenes in 80 fully re-sequenced Arabidopsis thaliana accessions. PLoS ONE. 2012;7:e51769 pubmed publisher
    b>Pseudogenes (?s), including processed and non-processed ?s, are ubiquitous genetic elements derived from originally functional genes in all studied genomes within the three kingdoms of life...
  10. Dhahbi J, Spindler S, Atamna H, Boffelli D, Mote P, Martin D. 5'-YRNA fragments derived by processing of transcripts from specific YRNA genes and pseudogenes are abundant in human serum and plasma. Physiol Genomics. 2013;45:990-8 pubmed publisher
    ..Many of the YRNAs from which these fragments are derived were previously annotated only as pseudogenes, or predicted informatically...
  11. McEntee G, Minguzzi S, O Brien K, Ben Larbi N, Loscher C, Ó Fágáin C, et al. The former annotated human pseudogene dihydrofolate reductase-like 1 (DHFRL1) is expressed and functional. Proc Natl Acad Sci U S A. 2011;108:15157-62 pubmed publisher
    ..Although the presence of a number of intronless DHFR pseudogenes has been known since the 1980s, it was assumed that none of these were expressed or functional...
  12. Thibaud Nissen F, Ouyang S, Buell C. Identification and characterization of pseudogenes in the rice gene complement. BMC Genomics. 2009;10:317 pubmed publisher
    ..ssp. japonica cv. Nipponbare) is the product of a semi-automated pipeline that does not explicitly predict pseudogenes. As such, it is likely to mis-annotate pseudogenes as functional genes...
  13. Jiang P, Josue J, Li X, Glaser D, Li W, Brand J, et al. Major taste loss in carnivorous mammals. Proc Natl Acad Sci U S A. 2012;109:4956-61 pubmed publisher
    ..These data provide strong support for the view that loss of taste receptor function in mammals is widespread and directly related to feeding specializations...
  14. Xue J, Liu Y, Li L, Wang B, Qiu Y. The complete mitochondrial genome sequence of the hornwort Phaeoceros laevis: retention of many ancient pseudogenes and conservative evolution of mitochondrial genomes in hornworts. Curr Genet. 2010;56:53-61 pubmed publisher
    ..There are 11 pseudogenes in this genome, and nine of them are shared with the other fully sequenced hornwort chondriome from Megaceros ..
  15. Terai G, Yoshizawa A, Okida H, Asai K, Mituyama T. Discovery of short pseudogenes derived from messenger RNAs. Nucleic Acids Res. 2010;38:1163-71 pubmed publisher
    ..Here, we report that the human genome contains many previously unidentified short pseudogenes generated by retrotransposition of mRNAs...
  16. Banaei Moghaddam A, Meier K, Karimi Ashtiyani R, Houben A. Formation and expression of pseudogenes on the B chromosome of rye. Plant Cell. 2013;25:2536-44 pubmed publisher
    ..Phenotypes and effects associated with the presence of Bs might be explained by the activity of B-located pseudogenes. We propose a model for the evolution of B-located pseudogenes.
  17. Liu Y, Zheng D, Balasubramanian S, Carriero N, Khurana E, Robilotto R, et al. Comprehensive analysis of the pseudogenes of glycolytic enzymes in vertebrates: the anomalously high number of GAPDH pseudogenes highlights a recent burst of retrotrans-positional activity. BMC Genomics. 2009;10:480 pubmed publisher
    b>Pseudogenes provide a record of the molecular evolution of genes...
  18. Wen Y, Zheng L, Qu L, Ayala F, Lun Z. Pseudogenes are not pseudo any more. RNA Biol. 2012;9:27-32 pubmed publisher
    Recent significant progress toward understanding the function of pseudogenes in protozoa (Trypanosoma brucei), metazoa (mouse) and plants, make it pertinent to provide a brief overview on what has been learned about this fascinating ..
  19. Kalyana Sundaram S, Kumar Sinha C, Shankar S, Robinson D, Wu Y, Cao X, et al. Expressed pseudogenes in the transcriptional landscape of human cancers. Cell. 2012;149:1622-34 pubmed publisher
    ..representing 13 cancer and normal tissue types, and observe a surprisingly prevalent, genome-wide expression of pseudogenes that could be categorized as ubiquitously expressed or lineage and/or cancer specific...
  20. Chiefari E, Iiritano S, Paonessa F, Le Pera I, Arcidiacono B, Filocamo M, et al. Pseudogene-mediated posttranscriptional silencing of HMGA1 can result in insulin resistance and type 2 diabetes. Nat Commun. 2010;1:40 pubmed publisher
    Processed pseudogenes are non-functional copies of normal genes that arise by a process of mRNA retrotransposition. The human genome contains thousands of pseudogenes; however, knowledge regarding their biological role is limited...
  21. Wolff J, Shearman D, Brooks R, Ballard J. Selective enrichment and sequencing of whole mitochondrial genomes in the presence of nuclear encoded mitochondrial pseudogenes (numts). PLoS ONE. 2012;7:e37142 pubmed publisher
    ..1) led to the identification of a numt sequence in the reference sequence. This unexpected result further highlights the need of a reliable and accessible strategy to eliminate this source of error. ..
  22. Rogers H, Griffiths Jones S. Mitochondrial pseudogenes in the nuclear genomes of Drosophila. PLoS ONE. 2012;7:e32593 pubmed publisher
    Mitochondrial pseudogenes in nuclear chromosomes (numts) have been detected in the genomes of a diverse range of eukaryotic species...
  23. Sellam A, Hogues H, Askew C, Tebbji F, van het Hoog M, Lavoie H, et al. Experimental annotation of the human pathogen Candida albicans coding and noncoding transcribed regions using high-resolution tiling arrays. Genome Biol. 2010;11:R71 pubmed publisher
    ..In summary, we provide a comprehensive expression atlas that covers relevant C. albicans pathogenic developmental stages in addition to the discovery of new ORF and non-coding genetic elements. ..
  24. Khachane A, Harrison P. Assessing the genomic evidence for conserved transcribed pseudogenes under selection. BMC Genomics. 2009;10:435 pubmed publisher
    Transcribed pseudogenes are copies of protein-coding genes that have accumulated indicators of coding-sequence decay (such as frameshifts and premature stop codons), but nonetheless remain transcribed...
  25. Ambady S, Malcuit C, Kashpur O, Kole D, Holmes W, Hedblom E, et al. Expression of NANOG and NANOGP8 in a variety of undifferentiated and differentiated human cells. Int J Dev Biol. 2010;54:1743-54 pubmed publisher
    ..of expressed transcripts in several cell types detected a NANOG pseudogene, NANOGP8, one of only two NANOG pseudogenes with the potential of encoding a similar size protein to embryonic NANOG (eNANOG)...
  26. Schrider D, Costello J, Hahn M. All human-specific gene losses are present in the genome as pseudogenes. J Comput Biol. 2009;16:1419-27 pubmed publisher
    ..As the fate of gene losses is still unclear, we identified gene losses through a method that does not require pseudogenes to identify human-specific gene losses...
  27. Zhang Z, 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:R26 pubmed publisher
    Unitary pseudogenes are a class of unprocessed pseudogenes without functioning counterparts in the genome. They constitute only a small fraction of annotated pseudogenes in the human genome...
  28. Van den Broeke A, Van Poucke M, Marcos Carcavilla A, Hugot K, Hayes H, Bertaud M, et al. Characterization of the ovine ribosomal protein SA gene and its pseudogenes. BMC Genomics. 2010;11:179 pubmed publisher
    ..species, RPSA is a member of a multicopy gene family consisting of one full length functional gene and several pseudogenes. Therefore, for studies on RPSA related pathways/pathologies, it is important to characterize the whole family ..
  29. Uchino K, Hirano G, Hirahashi M, Isobe T, Shirakawa T, Kusaba H, et al. Human Nanog pseudogene8 promotes the proliferation of gastrointestinal cancer cells. Exp Cell Res. 2012;318:1799-807 pubmed publisher
    ..These data suggest that NanogP8 is involved in GI cancer development in a fraction of patients, in whom it presumably acts by supporting CSC proliferation. ..
  30. de Groot N, Heijmans C, de Groot N, Doxiadis G, Otting N, Bontrop R. The chimpanzee Mhc-DRB region revisited: gene content, polymorphism, pseudogenes, and transcripts. Mol Immunol. 2009;47:381-9 pubmed publisher
    ..In addition, the limited amount of allelic variation observed at the various Patr-DRB genes is in agreement with the fact that chimpanzees experienced a selective sweep that may have been caused by an ancient retroviral infection. ..
  31. Feng Y, Chien K, Chen H, Chiu C. Pseudogene recoding revealed from proteomic analysis of salmonella serovars. J Proteome Res. 2012;11:1715-9 pubmed publisher
    ..to investigate the proteome of host-adapted Salmonella serovars, which are characteristic of accumulation of pseudogenes. Interestingly, a few annotated pseudogenes were indeed able to express peptides downstream of the inactivation ..
  32. Holford M, Khurana E, Cheung K, Gerstein M. Using semantic web rules to reason on an ontology of pseudogenes. Bioinformatics. 2010;26:i71-8 pubmed publisher
    ..We have built a knowledge base of human pseudogenes, extending the existing SO framework to incorporate additional attributes...
  33. Raboin M, Timko A, Howe D, Felix M, Denver D. Evolution of Caenorhabditis mitochondrial genome pseudogenes and Caenorhabditis briggsae natural isolates. Mol Biol Evol. 2010;27:1087-96 pubmed publisher
    ..and encode little noncoding DNA outside of the "AT" region, the accumulation of mitochondrial pseudogenes and other types of noncoding DNA has been observed in a growing number of animal groups...
  34. Lafontaine I, Dujon B. Origin and fate of pseudogenes in Hemiascomycetes: a comparative analysis. BMC Genomics. 2010;11:260 pubmed publisher
    b>Pseudogenes are ubiquitous genetic elements that derive from functional genes after mutational inactivation...
  35. Brosch M, Saunders G, Frankish A, Collins M, Yu L, Wright J, et al. Shotgun proteomics aids discovery of novel protein-coding genes, alternative splicing, and "resurrected" pseudogenes in the mouse genome. Genome Res. 2011;21:756-67 pubmed publisher
    ..We also report nine processed pseudogenes that have unique peptide hits, demonstrating, for the first time, that they are not just transcribed but are ..
  36. van der Klift H, Tops C, Bik E, Boogaard M, Borgstein A, Hansson K, et al. Quantification of sequence exchange events between PMS2 and PMS2CL provides a basis for improved mutation scanning of Lynch syndrome patients. Hum Mutat. 2010;31:578-87 pubmed publisher
    ..Four of these (21%) are lying in the region with frequent sequence transfer and are missed or called incorrectly as homozygous with several PSV-based mutation detection methods. ..
  37. Malik A, Shahni R, Rodriguez de Ledesma A, Laftah A, Cunningham P. Mitochondrial DNA as a non-invasive biomarker: accurate quantification using real time quantitative PCR without co-amplification of pseudogenes and dilution bias. Biochem Biophys Res Commun. 2011;412:1-7 pubmed publisher
    ..genome is duplicated in the nuclear genome, many commonly used MtDNA primers co-amplify homologous pseudogenes found in the nuclear genome; (2) use of regions from genes such as ?-actin and 18S rRNA which are repetitive ..
  38. Jeter C, Badeaux M, Choy G, Chandra D, Patrawala L, Liu C, et al. Functional evidence that the self-renewal gene NANOG regulates human tumor development. Stem Cells. 2009;27:993-1005 pubmed publisher
    ..Thus, our results demonstrate that NANOG, a cell-fate regulatory molecule known to be important for ESC self-renewal, also plays a novel role in tumor development. ..
  39. Arroyo J, Hoffmann F, Good S, Opazo J. INSL4 pseudogenes help define the relaxin family repertoire in the common ancestor of placental mammals. J Mol Evol. 2012;75:73-8 pubmed publisher
    ..Here we identified INSL4 pseudogenes in two laurasiatherian, (alpaca and dolphin) and one xenarthran (armadillo) species...
  40. Proudhon C, Duffié R, Ajjan S, Cowley M, Iranzo J, Carbajosa G, et al. Protection against de novo methylation is instrumental in maintaining parent-of-origin methylation inherited from the gametes. Mol Cell. 2012;47:909-20 pubmed publisher
    ..Here we provide evidence that protection against de novo methylation acts as an equal major pivot, at implantation and throughout life...
  41. Kim S, Bachvaroff T, Handy S, Delwiche C. Dynamics of actin evolution in dinoflagellates. Mol Biol Evol. 2011;28:1469-80 pubmed publisher
    ..Several potential pseudogenes were found (approximately 10% of all sequences depending on species) with incomplete open reading frames due to ..
  42. Kerr K. A cryptic, intergeneric cytochrome c oxidase I pseudogene in tyrant flycatchers (family: Tyrannidae). Genome. 2010;53:1103-9 pubmed publisher
    Nuclear mitochondrial pseudogenes, or "numts", are nonfunctional copies of mitochondrial genes that have been translocated to the nuclear genome...
  43. Shanahan M, Tanabe H, Ouellette A. Strain-specific polymorphisms in Paneth cell ?-defensins of C57BL/6 mice and evidence of vestigial myeloid ?-defensin pseudogenes. Infect Immun. 2011;79:459-73 pubmed publisher
    ..Both mouse genome assemblies contain conserved ?-defensin pseudogenes that are closely related to functional myeloid ?-defensin genes in the rat, suggesting that the neutrophil ?-..
  44. Tonner P, Srinivasasainagendra V, Zhang S, Zhi D. Detecting transcription of ribosomal protein pseudogenes in diverse human tissues from RNA-seq data. BMC Genomics. 2012;13:412 pubmed publisher
    Ribosomal proteins (RPs) have about 2000 pseudogenes in the human genome. While anecdotal reports for RP pseudogene transcription exists, it is unclear to what extent these pseudogenes are transcribed...
  45. Vieira F, Rozas J. Comparative genomics of the odorant-binding and chemosensory protein gene families across the Arthropoda: origin and evolutionary history of the chemosensory system. Genome Biol Evol. 2011;3:476-90 pubmed publisher
    ..evolution of the OBP and CSP gene families is highly dynamic, with a high number of gains and losses of genes, pseudogenes, and independent origins of subfamilies...
  46. Wicker T, Mayer K, Gundlach H, Martis M, Steuernagel B, Scholz U, et al. Frequent gene movement and pseudogene evolution is common to the large and complex genomes of wheat, barley, and their relatives. Plant Cell. 2011;23:1706-18 pubmed publisher
    ..in detail 50 genes from chromosome 1H for which BAC sequences were available, we found that many represent pseudogenes that resulted from transposable element activity and double-strand break repair...
  47. Ganster C, Wernstedt A, Kehrer Sawatzki H, Messiaen L, Schmidt K, Rahner N, et al. Functional PMS2 hybrid alleles containing a pseudogene-specific missense variant trace back to a single ancient intrachromosomal recombination event. Hum Mutat. 2010;31:552-60 pubmed publisher
    ..N775S of so far unknown functional significance, we assessed the H1-carrier frequency in 164 colorectal cancer patients. So far, we found no indication that the variant plays a major role with regard to cancer susceptibility. ..
  48. Voorter C, Lauterbach N, Tilanus M. Inactivation of a functional HLA-A gene: a 4-kb deletion turns HLA-A*24 into a pseudogene. Hum Immunol. 2010;71:1197-202 pubmed publisher
    ..Although different repeat sequences are present in the region both inside and outside the deletion, no evidence points to a retrotransposon mechanism. The detected partial deletion of HLA-A turns this functional gene into a pseudogene. ..
  49. Sen K, Podder S, Ghosh T. Insights into the genomic features and evolutionary impact of the genes configuring duplicated pseudogenes in human. FEBS Lett. 2010;584:4015-8 pubmed publisher
    b>Pseudogenes, regarded as 'genomic fossils', are DNA sequences resembling functional genes in perspective of sequence homology but completely non-functional...
  50. Williams D, Slayden R, Amin A, Martinez A, Pittman T, Mira A, et al. Implications of high level pseudogene transcription in Mycobacterium leprae. BMC Genomics. 2009;10:397 pubmed publisher
    The Mycobacterium leprae genome has less than 50% coding capacity and 1,133 pseudogenes. Preliminary evidence suggests that some pseudogenes are expressed...
  51. Guo X, Zhang Z, Gerstein M, Zheng D. Small RNAs originated from pseudogenes: cis- or trans-acting?. PLoS Comput Biol. 2009;5:e1000449 pubmed publisher
    b>Pseudogenes are significant components of eukaryotic genomes, and some have acquired novel regulatory roles...
  52. Kanber D, Berulava T, Ammerpohl O, Mitter D, Richter J, Siebert R, et al. The human retinoblastoma gene is imprinted. PLoS Genet. 2009;5:e1000790 pubmed publisher
    ..The imprinting of two components of the same pathway indicates that there has been strong evolutionary selection for maternal inhibition of cell proliferation. ..
  53. Zhao S, Yuan Q, Hao H, Guo Y, Liu S, Zhang Y, et al. Expression of OCT4 pseudogenes in human tumours: lessons from glioma and breast carcinoma. J Pathol. 2011;223:672-82 pubmed publisher
    ..By using RT-PCR and sequencing analysis, three OCT4 pseudogenes, viz...