Evaluating the protein coding potential of exonized transposable element sequences

Piriyapongsa, Jittima; Rutledge, Mark T.; Patel, Sanil; Borodovsky, Mark; Jordan, I. King

doi:10.1186/1745-6150-2-31

Cited by 38 publications

(31 citation statements)

References 58 publications

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“…The remaining five exons were in coding regions, including two that introduced premature termination codons. This distribution is consistent with the hypothesis that most functional Alu exonization events do not contribute to the proteome but may play a role in regulating gene expression [46],[47]. Similar to the finding by a recent study of species-specific exons [48], we observed an excess of Alu-derived internal exons in 5′-UTR as compared to 3′-UTR.…”

Section: Resultssupporting

confidence: 92%

Diverse Splicing Patterns of Exonized Alu Elements in Human Tissues

et al. 2008

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Exonization of Alu elements is a major mechanism for birth of new exons in primate genomes. Prior analyses of expressed sequence tags show that almost all Alu-derived exons are alternatively spliced, and the vast majority of these exons have low transcript inclusion levels. In this work, we provide genomic and experimental evidence for diverse splicing patterns of exonized Alu elements in human tissues. Using Exon array data of 330 Alu-derived exons in 11 human tissues and detailed RT-PCR analyses of 38 exons, we show that some Alu-derived exons are constitutively spliced in a broad range of human tissues, and some display strong tissue-specific switch in their transcript inclusion levels. Most of such exons are derived from ancient Alu elements in the genome. In SEPN1, mutations of which are linked to a form of congenital muscular dystrophy, the muscle-specific inclusion of an Alu-derived exon may be important for regulating SEPN1 activity in muscle. Realtime qPCR analysis of this SEPN1 exon in macaque and chimpanzee tissues indicates human-specific increase in its transcript inclusion level and muscle specificity after the divergence of humans and chimpanzees. Our results imply that some Alu exonization events may have acquired adaptive benefits during the evolution of primate transcriptomes.

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Section: Resultssupporting

confidence: 92%

Diverse Splicing Patterns of Exonized Alu Elements in Human Tissues

et al. 2008

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“…TE-related genes were detected using hmmsearch50 v3.1b2 (trusted cutoff) using 137 identified TE-related domains51.…”

Section: Methodsmentioning

confidence: 99%

The pangenome of an agronomically important crop plant Brassica oleracea

et al. 2016

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There is an increasing awareness that as a result of structural variation, a reference sequence representing a genome of a single individual is unable to capture all of the gene repertoire found in the species. A large number of genes affected by presence/absence and copy number variation suggest that it may contribute to phenotypic and agronomic trait diversity. Here we show by analysis of the Brassica oleracea pangenome that nearly 20% of genes are affected by presence/absence variation. Several genes displaying presence/absence variation are annotated with functions related to major agronomic traits, including disease resistance, flowering time, glucosinolate metabolism and vitamin biosynthesis.

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“…It has been shown that the choice of sequence similarity search methods to detect TE–derived sequences strongly influences the estimate of TE-cassettes that can be identified in protein coding regions [46] . Hidden Markov model based searches followed by BLAST methods (tBLASTx → tBLASTn → BLASTx → BLASTp → BLASTn) and RepeatMasker are more sensitive in identifying exonized TEs.…”

Section: Methodsmentioning

confidence: 99%

Transcriptional Activity, Chromosomal Distribution and Expression Effects of Transposable Elements in Coffea Genomes

et al. 2013

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Plant genomes are massively invaded by transposable elements (TEs), many of which are located near host genes and can thus impact gene expression. In flowering plants, TE expression can be activated (de-repressed) under certain stressful conditions, both biotic and abiotic, as well as by genome stress caused by hybridization. In this study, we examined the effects of these stress agents on TE expression in two diploid species of coffee, Coffea canephora and C. eugenioides, and their allotetraploid hybrid C. arabica. We also explored the relationship of TE repression mechanisms to host gene regulation via the effects of exonized TE sequences. Similar to what has been seen for other plants, overall TE expression levels are low in Coffea plant cultivars, consistent with the existence of effective TE repression mechanisms. TE expression patterns are highly dynamic across the species and conditions assayed here are unrelated to their classification at the level of TE class or family. In contrast to previous results, cell culture conditions per se do not lead to the de-repression of TE expression in C. arabica. Results obtained here indicate that differing plant drought stress levels relate strongly to TE repression mechanisms. TEs tend to be expressed at significantly higher levels in non-irrigated samples for the drought tolerant cultivars but in drought sensitive cultivars the opposite pattern was shown with irrigated samples showing significantly higher TE expression. Thus, TE genome repression mechanisms may be finely tuned to the ideal growth and/or regulatory conditions of the specific plant cultivars in which they are active. Analysis of TE expression levels in cell culture conditions underscored the importance of nonsense-mediated mRNA decay (NMD) pathways in the repression of Coffea TEs. These same NMD mechanisms can also regulate plant host gene expression via the repression of genes that bear exonized TE sequences.

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Evaluating the protein coding potential of exonized transposable element sequences

Cited by 38 publications

References 58 publications

Diverse Splicing Patterns of Exonized Alu Elements in Human Tissues

Diverse Splicing Patterns of Exonized Alu Elements in Human Tissues

The pangenome of an agronomically important crop plant Brassica oleracea

Transcriptional Activity, Chromosomal Distribution and Expression Effects of Transposable Elements in Coffea Genomes

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