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RNA Next-Generation Sequencing and a Bioinformatics Pipeline to Identify Expressed LINE-1s at the Locus-Specific Level
Published on: May 19, 2019
Exonization of the LTR transposable elements in human genome
Jittima Piriyapongsa1, Nalini Polavarapu, Mark Borodovsky
1School of Biology, Georgia Institute of Technology, Atlanta, Georgia 30332, USA. jittima@gatech.edu
BMC Genomics
|August 30, 2007
Summary
Long Terminal Repeat (LTR) retrotransposons contribute to human gene evolution, with some sequences becoming novel exons. This study traces the evolutionary history of an LTR retrotransposon-derived exon in the IL22RA2 gene.
Area of Science:
- Genomics
- Evolutionary Biology
- Molecular Biology
Background:
- Retrotransposons influence the structure and regulation of protein-coding genes.
- Retrotransposon insertion into introns or flanking regions, followed by exon incorporation, is a proposed mechanism for gene evolution.
Purpose of the Study:
- To investigate the role of Long Terminal Repeat (LTR) retrotransposons in human gene evolution.
- To reconstruct the evolutionary history of a specific retrotransposon-derived exon in the Interleukin 22 receptor, alpha 2 (IL22RA2) gene.
Main Methods:
- Computational analysis of LTR retrotransposon distribution in human genes.
- Comparative genomic sequencing and analysis across primate species.
- Experimental approaches to trace the history of LTR exonization.
Main Results:
- LTR retrotransposons are associated with 5.8% of human genes, with some integrated into protein-coding regions.
- Fifty distinct protein-coding exons were found to be exclusively composed of LTR Retrotransposon Sequence (LRTS).
- An alternatively spliced exon in the IL22RA2 gene was identified as originating from a Mammalian apparent LTR retrotransposon (MaLR), inserted ~25 million years ago and recruited as an exon ~14 million years ago.
Conclusions:
- LRTS distribution patterns support their role in human gene evolution, primarily through providing cis-regulatory sequences.
- Direct incorporation of LTR sequences into protein-coding regions occurs less frequently but has been observed.
- The combined computational and experimental approach used for the IL22RA2 gene offers a model for studying transposon-driven gene evolution.
Related Concept Videos
03:08LTR Retrotransposons
LTR retrotransposons are class I transposable elements with long terminal repeats flanking an internal coding region. These elements are less abundant in mammals compared to other class I transposable elements. About 8 percent of human genomic DNA comprises LTR retrotransposons. Some of the common examples of LTR retrotransposons are Ty elements in yeast and Copia elements in Drosophila.
The internal coding region of LTR retrotransposons and their mechanism of transposition closely resembles a...
The internal coding region of LTR retrotransposons and their mechanism of transposition closely resembles a...
03:18Non-LTR Retrotransposons
As the name suggests, non-LTR retrotransposons lack the long terminal repeats characteristic of the LTR retrotransposons. Additionally, both LTR and non-LTR retrotransposons use distinct mechanisms of mobilization. Non-LTR retrotransposons are further divided into two classes - Long interspersed nuclear elements (LINEs) and short interspersed nuclear elements (SINEs), both of which occur abundantly in most mammals, including humans. Some of the active non-LTR retrotransposons in humans are L1...
02:13Overview of Transposition and Recombination
Transposons make up a significant part of genomes of various organisms. Therefore, it is believed that transposition played a major evolutionary role in speciation by changing genome sizes and modifying gene expression patterns. For example, in bacteria, transposition can lead to conferring antibiotic resistance. Movement of transposable elements within the genetic pool of pathogenic bacteria can aid in transfer of antibiotic-resistant genetic elements. In eukaryotes, transposons can carry out...
02:57DNA-only Transposons
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The donor site from where the transposon is excised is either degraded or...
The donor site from where the transposon is excised is either degraded or...
02:32Exon Recombination
The evolution of new genes is critical for speciation. Exon recombination, also known as exon shuffling or domain shuffling, is an important means of new gene formation. It is observed across vertebrates, invertebrates, and in some plants such as potatoes and sunflowers. During exon recombination, exons from the same or different genes recombine and produce new exon-intron combinations, which might evolve into new genes.
Exon shuffling follows “splice frame rules.” Each exon has three reading...
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01:24Transposons
Transposons, or "jumping genes," are small mobile genetic elements (MGEs) that range from 700 to 40,000 base pairs in length. They are found in all organisms and can move within the same chromosome or transfer to different chromosomes. In some cases, transposons can also jump between different host DNA molecules, such as plasmids or viruses, contributing to genetic variability.Barbara McClintock first discovered these mobile genetic elements in the 1940s while studying maize genetics, and she...