Effect of the Transposable Element Environment of Human Genes on Gene Length and Expression

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dc.contributor.authorJjingo, Daudi
dc.contributor.authorHuda, Ahsan
dc.contributor.authorGundapuneni, Madhumati
dc.contributor.authorMariño-Ramǐrez, Leonardo
dc.contributor.authorJordan, I. King
dc.date.accessioned2018-12-17T14:26:27Z
dc.date.accessioned2021-12-21T08:58:53Z
dc.date.available2018-12-17T14:26:27Z
dc.date.available2021-12-21T08:58:53Z
dc.date.issued2011-02-28
dc.descriptionPublished by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.en_US
dc.description.abstractIndependent lines of investigation have documented effects of both transposable elements (TEs) and gene length (GL) on gene expression. However, TE gene fractions are highly correlated with GL, suggesting that they cannot be considered independently. We evaluated the TE environment of human genes and GL jointly in an attempt to tease apart their relative effects. TE gene fractions and GL were compared with the overall level of gene expression and the breadth of expression across tissues. GL is strongly correlated with overall expression level but weakly correlated with the breadth of expression, confirming the selection hypothesis that attributes the compactness of highly expressed genes to selection for economy of transcription. However, TE gene fractions overall, and for the L1 family in particular, show stronger anti-correlations with expression level than GL, indicating that GL may not be the most important target of selection for transcriptional economy. These results suggest a specific mechanism, removal of TEs, by which highly expressed genes are selectively tuned for efficiency. MIR elements are the only family of TEs with gene fractions that show a positive correlation with tissue-specific expression, suggesting that they may provide regulatory sequences that help to control human gene expression. Consistent with this notion, MIR fractions are relatively enriched close to transcription start sites and associated with expression in specific sets of related tissues. Our results confirm the overall relevance of the TE environment to gene expression and point to distinct mechanisms by which different TE families may contribute to gene regulation.en_US
dc.identifier.citationDaudi Jjingo, Ahsan Huda, Madhumati Gundapuneni, Leonardo Mariño-Ramírez, I. King Jordan; Effect of the Transposable Element Environment of Human Genes on Gene Length and Expression, Genome Biology and Evolution, Volume 3, 1 January 2011, Pages 259–271, https://doi.org/10.1093/gbe/evr015en_US
dc.identifier.issn1759-6653
dc.identifier.urihttps://hdl.handle.net/20.500.11951/640
dc.language.isoenen_US
dc.publisherOxford University Pressen_US
dc.subjectGene Transposable element and gene lengthen_US
dc.subjectGene transposable element and gene expressionen_US
dc.subjectGene expressionen_US
dc.subjectGene regulationen_US
dc.subjectGene selection hypothesisen_US
dc.subjectGenomic design hypothesisen_US
dc.titleEffect of the Transposable Element Environment of Human Genes on Gene Length and Expressionen_US
dc.typeArticleen_US
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