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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...
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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...
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Next-generation sequencing technologies have created large genomic databases of a variety of animals and plants. Ever since the human genome project was completed, scientists studied the genome of primates, mammals, and other phylogenetically distant living beings. Such large-scale  studies have provided new insights into the evolutionary relationship between organisms.
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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.
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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. 
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The seminal work of Ohno in 1970 popularized the idea of gene duplication and divergence. DNA sequence comparison studies reveal that a large portion of the genes in bacteria, archaebacteria, and eukaryotes was  generated by gene duplication and divergence, indicating its critical role in evolution.
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A knowledgebase of the human Alu repetitive elements.

Izaskun Mallona1, Mireia Jordà1, Miguel A Peinado1

  • 1Institute of Predictive and Personalized Medicine of Cancer (IMPPC) and Health Research Institute Germans Trias i Pujol (IGTP), Can Ruti Campus. Ctra. de Can Ruti, camí de les escoles, s/n, 08916 Badalona, Spain.

Journal of Biomedical Informatics
|February 2, 2016
PubMed
Summary

Human Alu elements, abundant retrotransposons, play roles in genome regulation and disease. This study introduces an ontology-based knowledgebase to analyze Alu element function and genetic context, overcoming conventional research challenges.

Keywords:
AluKnowledgebaseOntologyRepetitive element

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Alu elements are abundant human retrotransposons implicated in genome regulation, compartmentalization, and disease pathology.
  • Studying Alu elements' genomic regulatory roles is challenging due to technical and analytical limitations of conventional methods.

Purpose of the Study:

  • To develop an ontology-based semantic method for querying a human Alu knowledgebase.
  • To integrate functional and genetic information of Alu elements within their genomic context.

Main Methods:

  • Leveraged Sequence Ontology (SO) and Gene Ontology (GO) to build a knowledgebase for human Alus.
  • Utilized Web Ontology Language (OWL) and Semantic Web Rule Language (SWRL) for data modeling.
  • Stored information on Alu elements, including closest genes/transcripts, GO annotations, chromatin states, and transcription factor binding sites.

Main Results:

  • Demonstrated the utility of the ontology by evaluating epigenetic states of Alu repeats near gene promoters in relation to transcriptional activity.
  • The knowledgebase effectively links Alu elements to functional and genetic data.

Conclusions:

  • The proposed ontology-based approach provides a novel framework for studying Alu element functions and genomic roles.
  • The easily extendable ontology serves as a scaffold for incorporating new experimental data, facilitating research into Alu-mediated genomic regulation and disease.