Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Overview of Transposition and Recombination02:13

Overview 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...
Transposons01:24

Transposons

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...
Non-LTR Retrotransposons03:18

Non-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...
DNA-only Transposons02:57

DNA-only Transposons

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.
The donor site from where the transposon is excised is either degraded or...
LTR Retrotransposons03:08

LTR 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...
piRNA - Piwi-interacting RNAs02:57

piRNA - Piwi-interacting RNAs

PIWI-interacting RNAs, or piRNAs, are the most abundant short non-coding RNAs. More than 20,000 genes have been found in humans that code for piRNAs while only 2000 genes have been found for miRNAs. piRNAs can act at the transcriptional and post-transcriptional levels and have a vital role in silencing transposable elements present in germ cells. They are also involved in epigenetic silencing and activation. Previously, they were thought to function only in germ cells but new evidence suggests...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Applying Artificial Intelligence Technologies to Detect Pancreatic Ductal Adenocarcinoma Using Routine Laboratory Tests: A Pilot Study with the Aid of Machine Learning Suitable for a Small Data Analysis.

Internal medicine (Tokyo, Japan)·2026
Same author

Genetic and environmental regulation of early heading in photoperiod-insensitive rice: impacts on heading synchrony, premature heading, and tiller development lag.

Breeding science·2026
Same author

Independent Origin of Phenol Non-responsive Phenotype Caused By Phr1 Variation During Domestication of Asian and African Rice.

Rice (New York, N.Y.)·2026
Same author

Accurate detections of the heterozygous SNPs with rice genomic data and prediction of de novo spontaneous mutation rate.

Plant methods·2025
Same author

Two Stabiliser loci suppress Tam3 transposition without compromising transposase production in Antirrhinum.

Plant physiology·2025
Same author

Haplotype shifts in the lipid-related OsGELP gene family underpin rice adaptation to high latitudes.

Scientific reports·2025

Related Experiment Video

Updated: Jul 9, 2026

Real-Time Quantification of the Effects of IS200/IS605 Family-Associated TnpB on Transposon Activity
04:04

Real-Time Quantification of the Effects of IS200/IS605 Family-Associated TnpB on Transposon Activity

Published on: January 20, 2023

Rice transposable elements are characterized by various methylation environments in the genome.

Miwako Takata1, Akihiro Kiyohara, Atsuko Takasu

  • 1Laboratory of Plant Breeding, Graduate School of Agriculture, Hokkaido University, Sapporo 060-8589, Japan. miwako-takata@taiho.co.jp

BMC Genomics
|December 21, 2007
PubMed
Summary

Transposable elements (TEs) in rice genomes are linked to specific DNA methylation patterns in their surrounding DNA. These methylation environments are characteristic features of particular TE families, not correlated with copy number or conservation.

More Related Videos

Immunostaining for DNA Modifications: Computational Analysis of Confocal Images
09:42

Immunostaining for DNA Modifications: Computational Analysis of Confocal Images

Published on: September 7, 2017

In Vitro Selection of Engineered Transcriptional Repressors for Targeted Epigenetic Silencing
10:44

In Vitro Selection of Engineered Transcriptional Repressors for Targeted Epigenetic Silencing

Published on: May 5, 2023

Related Experiment Videos

Last Updated: Jul 9, 2026

Real-Time Quantification of the Effects of IS200/IS605 Family-Associated TnpB on Transposon Activity
04:04

Real-Time Quantification of the Effects of IS200/IS605 Family-Associated TnpB on Transposon Activity

Published on: January 20, 2023

Immunostaining for DNA Modifications: Computational Analysis of Confocal Images
09:42

Immunostaining for DNA Modifications: Computational Analysis of Confocal Images

Published on: September 7, 2017

In Vitro Selection of Engineered Transcriptional Repressors for Targeted Epigenetic Silencing
10:44

In Vitro Selection of Engineered Transcriptional Repressors for Targeted Epigenetic Silencing

Published on: May 5, 2023

Area of Science:

  • Genomics
  • Epigenetics
  • Plant Biology

Background:

  • Transposable elements (TEs) are extensively targeted by DNA methylation, but their genomic methylation context remains poorly understood.
  • The rice genome harbors diverse TE families with varied genomic distributions and characteristics.
  • Investigating DNA methylation around TEs in rice and its wild relatives is crucial for understanding genome regulation.

Purpose of the Study:

  • To investigate the DNA methylation states surrounding 12 transposable element families in cultivated and wild rice strains.
  • To determine if specific methylation patterns are associated with different TE families and their genomic locations.
  • To explore the relationship between TE characteristics (e.g., class, distribution) and their methylation environments.

Main Methods:

  • Utilized transposon display (TD) to analyze DNA methylation patterns in nine rice genomic DNA samples.
  • Examined 12 distinct transposable element families, including class I and class II elements.
  • Assessed methylation degrees in sequences flanking TEs across different rice strains.

Main Results:

  • Transposable element families exhibited differential chromosomal distributions, from centromeric to euchromatic regions.
  • TEs were embedded in flanking sequences with varying methylation degrees, consistent across rice strains for each TE.
  • Class I elements were generally in highly methylated regions, while class II elements showed diverse methylation levels.
  • Some TE families displayed methylation degrees lower than the genomic average, with distance-dependent methylation changes observed in two families.

Conclusions:

  • Rice transposable element families are characterized by distinct surrounding DNA methylation states.
  • TE copy number and conservation are unlikely to correlate with the degree of DNA methylation.
  • This study establishes a link between transposable elements and specific, characteristic methylation environments within the genome.