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Patterns of gene duplication and intron loss in the ENCODE regions suggest a confounding factor

Chatterji, Sourav and Pachter, Lior (2007) Patterns of gene duplication and intron loss in the ENCODE regions suggest a confounding factor. Genomics, 90 (1). pp. 44-48. ISSN 0888-7543. PMCID PMC2034525. doi:10.1016/j.ygeno.2007.03.008. https://resolver.caltech.edu/CaltechAUTHORS:20170307-130932831

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Abstract

The exon–intron structure of eukaryotic genes allows for phenomena such as alternative splicing, nonsense-mediated decay, and regulation through untranslated regions. However, the evolution of the exon structure of genes is not well elucidated because of limited and phylogenetically sparse data sets. In this study, we use the phylogenetically diverse sequencing of the ENCODE regions to study gene structure evolution in mammalian genomes. This first phylogenetically diverse study of gene structure changes offers insights into the mode and tempo of mammalian gene structure evolution. The genes undergoing structure changes appear to be moderately to highly expressed in germline cells and show levels of selection similar to those of other ENCODE genes. Patterns of gene duplication of the affected genes are more complex than expected. The number of sampled genomes is sufficiently dense to infer that certain gene duplications happened after intron loss. Thus, although gene duplication is highly correlated with intron loss, we conclude that structural changes in genes are not necessarily due to a loss of constraint following gene duplication as previously suggested.


Item Type:Article
Related URLs:
URLURL TypeDescription
http://dx.doi.org/10.1016/j.ygeno.2007.03.008DOIArticle
http://www.sciencedirect.com/science/article/pii/S0888754307000675PublisherArticle
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2034525/PubMed CentralArticle
ORCID:
AuthorORCID
Pachter, Lior0000-0002-9164-6231
Additional Information:© 2007 Elsevier. Received 29 November 2006, Accepted 22 March 2007, Available online 11 May 2007. We thank Colin Dewey for providing Mercator maps of the ENCODE regions. We also thank the GENCODE and HAVANA teams for organizing the EGASP workshop during which we began work on this project. S.C. and L.P. were partially funded by NIH Grants R01:HG02632-1 and U01:HG003150-01.
Funders:
Funding AgencyGrant Number
NIHR01 HG02632-1
NIHU01 HG003150-01
Subject Keywords:Gene evolution; Exon–intron structure; Intron loss; Gene duplication; Gene structure evolution; Mammalian genome evolution; ENCODE
Issue or Number:1
PubMed Central ID:PMC2034525
DOI:10.1016/j.ygeno.2007.03.008
Record Number:CaltechAUTHORS:20170307-130932831
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20170307-130932831
Official Citation:Sourav Chatterji, Lior Pachter, Patterns of gene duplication and intron loss in the ENCODE regions suggest a confounding factor, Genomics, Volume 90, Issue 1, July 2007, Pages 44-48, ISSN 0888-7543, http://dx.doi.org/10.1016/j.ygeno.2007.03.008. (http://www.sciencedirect.com/science/article/pii/S0888754307000675)
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:74857
Collection:CaltechAUTHORS
Deposited By: George Porter
Deposited On:07 Mar 2017 21:29
Last Modified:15 Nov 2021 16:28

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