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Related Concept Videos

DNA-only Transposons02:57

DNA-only Transposons

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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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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, 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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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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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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Epigenetic changes alter the physical structure of the DNA without changing the genetic sequence and often regulate whether genes are turned on or off. This regulation ensures that each cell produces only proteins necessary for its function. For example, proteins that promote bone growth are not produced in muscle cells. Epigenetic mechanisms play an essential role in healthy development. Conversely, precisely regulated epigenetic mechanisms are disrupted in diseases like cancer.
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Transposon age and non-CG methylation.

Zhengming Wang1, David C Baulcombe2

  • 1Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK.

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|March 8, 2020
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Summary

Epigenetic silencing of transposable elements (TEs) involves small RNA-directed DNA methylation (RdDM) and RNA-independent pathways. In tomato and Arabidopsis, chromodomain DNA methyltransferases (CMTs) silence younger LTR transposons in distal chromatin, suggesting a novel silencing progression.

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Area of Science:

  • Epigenetics
  • Plant Molecular Biology
  • Genomics

Background:

  • Transposable elements (TEs) are silenced primarily through small RNA-directed DNA methylation (RdDM).
  • Maintenance of TE silencing involves both RdDM and RNA-independent mechanisms, including DNA methyltransferases MET1 and CMTs.
  • Existing models predict decreased RdDM involvement with increasing TE age.

Purpose of the Study:

  • To investigate the age-dependent patterns of TE silencing mechanisms in tomato and Arabidopsis.
  • To propose a revised model for epigenetic silencing progression in gene-rich distal chromatin.

Main Methods:

  • Analysis of DNA methylation patterns and small RNA populations in tomato and Arabidopsis.
  • Comparative analysis of silencing mechanisms targeting different age groups of long terminal repeat (LTR) transposons.
  • Bioinformatic and molecular biology approaches to assess TE silencing dynamics.

Main Results:

  • Contrary to expectations, younger LTR transposons in distal chromatin of tomato and Arabidopsis are silenced by CMTs, not RdDM.
  • TEs targeted by RdDM are older than those silenced by CMTs in these species.
  • Evidence suggests a dynamic progression of epigenetic silencing mechanisms.

Conclusions:

  • A novel model for epigenetic silencing is proposed: initial RdDM establishment, followed by RNA-independent maintenance via CMTs, and subsequent secondary RdDM.
  • This progression in gene-rich distal chromatin influences the transcriptome via cis or trans regulatory effects.
  • The findings reveal a complex interplay of epigenetic mechanisms in maintaining genome stability and regulating gene expression.