Transposable element fragments in protein-coding regions and their contributions to human functional proteins.
ABSTRACT Transposable elements (TEs) and their contributions to protein-coding regions are of particular interest. Here we searched for TE fragments in Homo sapiens at both the transcript and protein levels. We found evidence in support of TE exonization and its association with alternative splicing. Despite recent findings that long evolutionary times are required to incorporate TE into proteins, we found many functional proteins with translated TE cassettes derived from young TEs. Analyses of two Bcl-family proteins and Alu-encoded segments suggest the coding and functional potential of TE sequences.
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ABSTRACT: Non-coding RNAs from transposable elements of human genome are gaining prominence in modulating transcriptome dynamics. Alu elements, as exonized, edited and antisense components within same transcripts could create novel regulatory switches in response to different transcriptional cues. We provide the first evidence for co-occurrences of these events at transcriptome-wide scale through integrative analysis of data sets across diverse experimental platforms and tissues. This involved the following: (i) positional anchoring of Alu exonization events in the UTRs and CDS of 4663 transcript isoforms from RefSeq mRNAs and (ii) mapping on to them A→I editing events inferred from ∼7 million ESTs from dbEST and antisense transcripts identified from virtual serial analysis of gene expression tags represented in Cancer Genome Anatomy Project next-generation sequencing data sets across 20 tissues. We observed significant enrichment of these events in the 3'UTR as well as positional preference within the embedded Alus. More than 300 genes had co-occurrence of all these events at the exon level and were significantly enriched in apoptosis and lysosomal processes. Further, we demonstrate functional evidence of such dynamic interactions between Alu-mediated events in a time series data from Integrated Personal Omics Profiling during recovery from a viral infection. Such 'single transcript-multiple fate' opportunity facilitated by Alu elements may modulate transcriptional response, especially during stress.Nucleic Acids Research 01/2013; · 8.81 Impact Factor
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ABSTRACT: Transposable elements (TEs) are present in roughly all genomes. These mobile DNA sequences are able to invade genomes and their impact on genome evolution is substantial. The mobility of TEs can induce the appearance of deleterious mutations, gene disruption and chromosome rearrangements, but transposition activity also has positive aspects and the mutational activities of TEs contribute to the genetic diversity of organisms. This short review aims to give a brief overview of the impact TEs may have on animal and plant genome structure and expression, and the relationship between TEs and the stress response of organisms, including insecticide resistance.Gene 08/2012; 509(1):7-15. · 2.20 Impact Factor
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ABSTRACT: Insertion of transposable elements (TEs) into introns can lead to their activation as alternatively spliced cassette exons, an event called exonization. Exonization can enrich the complexity of transcriptomes and proteomes. Previously, we performed a genome-wide computational analysis of Ds exonization events in the monocot Oryza sativa (rice). The insertion patterns of Ds increased the number of transcripts and subsequent protein isoforms, which were determined as interior and C-terminal variants. In this study, these variants were scanned with the PROSITE database in order to identify new functional profiles (domains) that were referred to their reference proteins. The new profiles of the variants were expected to be beneficial for a selective advantage and more than 70% variants achieved this. The new functional profiles could be contributed by an exon-intron junction, an intron alone, an intron-TE junction, or a TE alone. A Ds-inserted intron may yield 167 new profiles on average, while some cases can yield thousands of new profiles, of which C-terminal variants were in major. Additionally, more than 90% of the TE-inserted genes were found to gain novel functional profiles in each intron via exonization. Therefore, new functional profiles yielded by the exonization may occur in many local regions of the reference protein.Evolutionary bioinformatics online 01/2013; 9:417-27. · 1.33 Impact Factor