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Non-LTR Retrotransposons

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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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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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DNA-only transposons are called autonomous transposons since they code for the enzyme transposase that is required for the transposition mechanism. Insertion of transposons can alter gene functions in multiple ways. They can mutate the gene, alter gene expression by introducing a novel promoter or insulator sequence, introduce new splice sites, and change the mRNA transcripts produced, or remodel chromatin structure.
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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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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...
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Retroviruses and retrotransposons both insert copies of their genetic elements into the genome of the host cell. Thus, the viral genes are passed on when the host genome is replicated or translated. A typical retroviral DNA sequence contains 3-4 genes that encode the different proteins required for its structural assembly and function as a molecular parasite. This DNA is transcribed into a single mRNA, which is very similar in structure to conventional mRNAs, i.e., it is capped at the 5’...
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Human Retrotransposons and Effective Computational Detection Methods for Next-Generation Sequencing Data.

Haeun Lee1, Jun Won Min2, Seyoung Mun3,4

  • 1Department of Bioconvergence Engineering, Dankook University, Yongin 16890, Korea.

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|October 27, 2022
PubMed
Summary
This summary is machine-generated.

Retrotransposons, mobile genetic elements, contribute to genetic diversity and disease. This review details next-generation sequencing technologies and computational methods for detecting retrotransposon insertions in the human genome.

Keywords:
computational toolsnext-generation sequencing (NGS)retrotransposonstransposable elements

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Analysis of LINE-1 Retrotransposition at the Single Nucleus Level
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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Transposable elements (TEs) are mobile DNA sequences.
  • Retrotransposons, unlike DNA transposons, replicate via a "copy and paste" mechanism.
  • Active retrotransposons like LINE-1, Alu, and SVA elements influence primate genetic diversity and can cause genetic disorders.

Purpose of the Study:

  • To review recent advances in next-generation sequencing (NGS) technologies for detecting retrotransposon-mediated structural variations (SVs).
  • To discuss computational approaches for identifying retrotransposon insertions using NGS data.
  • To provide researchers with insights into studying transposable elements and their role in the human genome.

Main Methods:

  • Review of current next-generation sequencing (NGS) technologies.
  • Analysis of computational methods for detecting retrotransposon insertions.
  • Synthesis of existing literature on transposable elements and structural variations.

Main Results:

  • NGS technologies offer new perspectives for detecting retrotransposon-mediated SVs, particularly insertions.
  • Various computational tools have been developed to precisely identify insertions and deletions in the human genome.
  • The review covers both NGS technologies and computational strategies for retrotransposon discovery.

Conclusions:

  • Understanding retrotransposon insertions is crucial for comprehending genetic diversity and disease.
  • Effective computational methods combined with NGS enable precise detection of retrotransposon activity.
  • This review serves as a guide for researchers investigating transposable elements in the human genome.