Skip Navigation

Nucleic Acids Research 2005 33(8):2374-2383; doi:10.1093/nar/gki531
This Article
Right arrow Full Text Freely available
Right arrow Print PDF (379K) Freely available
Right arrow Screen PDF (389K) Freely available
Right arrow Supplementary Material
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in ISI Web of Science
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Search for citing articles in:
ISI Web of Science (34)
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Harrison, P. M.
Right arrow Articles by Gerstein, M.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Harrison, P. M.
Right arrow Articles by Gerstein, M.
Related Collections
Right arrow Computational methods
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Published online 28 April 2005

© The Author 2005. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oupjournals.org

Article

Transcribed processed pseudogenes in the human genome: an intermediate form of expressed retrosequence lacking protein-coding ability

Paul M. Harrison*, Deyou Zheng1, Zhaolei Zhang3, Nicholas Carriero2 and Mark Gerstein1,2

Department of Biology, McGill University Stewart Biology Building, 1205 Dr. Penfield Avenue, Montreal, Quebec, Canada H3A 1B1 1Department of Molecular Biophysics and Biochemistry, Yale University New Haven, CT, USA 2Department of Computer Science, Yale University New Haven, CT, USA 3Banting and Best Department of Medical Research, University of Toronto Toronto, Ontario, Canada

*To whom correspondence should be addressed. Tel: +1 514 398 6420; Fax: +1 514 398 5069; Email: paul.harrison{at}mcgill.ca

Received January 19, 2005. Revised March 14, 2005. Accepted April 4, 2005.

Pseudogenes, in the case of protein-coding genes, are gene copies that have lost the ability to code for a protein; they are typically identified through annotation of disabled, decayed or incomplete protein-coding sequences. Processed pseudogenes (P{Psi}gs) are made through mRNA retrotransposition. There is overwhelming genomic evidence for thousands of human P{Psi}gs and also dozens of human processed genes that comprise complete retrotransposed copies of other genes. Here, we survey for an intermediate entity, the transcribed processed pseudogene (TP{Psi}g), which is disabled but nonetheless transcribed. TP{Psi}gs may affect expression of paralogous genes, as observed in the case of the mouse makorin1-p1 TP{Psi}g. To elucidate their role, we identified human TP{Psi}gs by mapping expressed sequences onto P{Psi}gs and, reciprocally, extracting TP{Psi}gs from known mRNAs. We consider only those P{Psi}gs that are homologous to either non-mammalian eukaryotic proteins or protein domains of known structure, and require detection of identical coding-sequence disablements in both the expressed and genomic sequences. Oligonucleotide microarray data provide further expression verification. Overall, we find 166–233 TP{Psi}gs (~4–6% of P{Psi}gs). Proteins/transcripts with the highest numbers of homologous TP{Psi}gs generally have many homologous P{Psi}gs and are abundantly expressed. TP{Psi}gs are significantly over-represented near both the 5' and 3' ends of genes; this suggests that TP{Psi}gs can be formed through gene–promoter co-option, or intrusion into untranslated regions. However, roughly half of the TP{Psi}gs are located away from genes in the intergenic DNA and thus may be co-opting cryptic promoters of undesignated origin. Furthermore, TP{Psi}gs are unlike other P{Psi}gs and processed genes in the following ways: (i) they do not show a significant tendency to either deposit on or originate from the X chromosome; (ii) only 5% of human TP{Psi}gs have potential orthologs in mouse. This latter finding indicates that the vast majority of TP{Psi}gs is lineage specific. This is likely linked to well-documented extensive lineage-specific SINE/LINE activity. The list of TP{Psi}gs is available at: http://www.biology.mcgill.ca/faculty/harrison/tppg/bppg.tov (or) http:pseudogene.org.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Plant Physiol.Home page
C. Zou, M. D. Lehti-Shiu, F. Thibaud-Nissen, T. Prakash, C. R. Buell, and S.-H. Shiu
Evolutionary and Expression Signatures of Pseudogenes in Arabidopsis and Rice
Plant Physiology, September 1, 2009; 151(1): 3 - 15.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
Z. D. Zhang, P. Cayting, G. Weinstock, and M. Gerstein
Analysis of Nuclear Receptor Pseudogenes in Vertebrates: How the Silent Tell Their Stories
Mol. Biol. Evol., January 1, 2008; 25(1): 131 - 143.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
D. V. Babushok, K. Ohshima, E. M. Ostertag, X. Chen, Y. Wang, P. K. Mandal, N. Okada, C. S. Abrams, and H. H. Kazazian Jr.
A novel testis ubiquitin-binding protein gene arose by exon shuffling in hominoids
Genome Res., August 1, 2007; 17(8): 1129 - 1138.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
M. B. Gerstein, C. Bruce, J. S. Rozowsky, D. Zheng, J. Du, J. O. Korbel, O. Emanuelsson, Z. D. Zhang, S. Weissman, and M. Snyder
What is a gene, post-ENCODE? History and updated definition
Genome Res., June 1, 2007; 17(6): 669 - 681.
[Abstract] [Full Text] [PDF]

Home page
 Genome ResHome page
D. Zheng, A. Frankish, R. Baertsch, P. Kapranov, A. Reymond, S. W. Choo, Y. Lu, F. Denoeud, S. E. Antonarakis, M. Snyder, et al.
Pseudogenes in the ENCODE regions: Consensus annotation, analysis of transcription, and evolution
Genome Res., June 1, 2007; 17(6): 839 - 851.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
S. O. Sassi, E. L. Braun, and S. A. Benner
The Evolution of Seminal Ribonuclease: Pseudogene Reactivation or Multiple Gene Inactivation Events?
Mol. Biol. Evol., April 1, 2007; 24(4): 1012 - 1024.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
J. E. Karro, Y. Yan, D. Zheng, Z. Zhang, N. Carriero, P. Cayting, P. Harrrison, and M. Gerstein
Pseudogene.org: a comprehensive database and comparison platform for pseudogene annotation
Nucleic Acids Res., January 12, 2007; 35(suppl_1): D55 - D60.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
D. R. Hoen, K. C. Park, N. Elrouby, Z. Yu, N. Mohabir, R. K. Cowan, and T. E. Bureau
Transposon-Mediated Expansion and Diversification of a Family of ULP-like Genes
Mol. Biol. Evol., June 1, 2006; 23(6): 1254 - 1268.
[Abstract] [Full Text] [PDF]

Home page
 Clin. Cancer Res.Home page
B. C.K. Wong, K.C. A. Chan, A. T.C. Chan, S.-F. Leung, L. Y.S. Chan, K. C.K. Chow, and Y.M. D. Lo
Reduced Plasma RNA Integrity in Nasopharyngeal Carcinoma Patients
Clin. Cancer Res., April 15, 2006; 12(8): 2512 - 2516.
[Abstract] [Full Text] [PDF]

Home page
 GeneticsHome page
S. Kaneko, I. Aki, K. Tsuda, K. Mekada, K. Moriwaki, N. Takahata, and Y. Satta
Origin and Evolution of Processed Pseudogenes That Stabilize Functional Makorin1 mRNAs in Mice, Primates and Other Mammals
Genetics, April 1, 2006; 172(4): 2421 - 2429.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
N. Vinckenbosch, I. Dupanloup, and H. Kaessmann
Evolutionary fate of retroposed gene copies in the human genome
PNAS, February 28, 2006; 103(9): 3220 - 3225.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
S. J. Elliman, I. Wu, and D. M. Kemp
Adult Tissue-specific Expression of a Dppa3-derived Retrogene Represents a Postnatal Transcript of Pluripotent Cell Origin
J. Biol. Chem., January 6, 2006; 281(1): 16 - 19.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
A. S. Hinrichs, D. Karolchik, R. Baertsch, G. P. Barber, G. Bejerano, H. Clawson, M. Diekhans, T. S. Furey, R. A. Harte, F. Hsu, et al.
The UCSC Genome Browser Database: update 2006
Nucleic Acids Res., January 1, 2006; 34(suppl_1): D590 - D598.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.