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Overview of Transposition and Recombination

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...

DNA-only Transposons

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 Retrotransposons

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...

Cis-regulatory Sequences

Cis-regulatory Sequences

Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...

Cis-regulatory Sequences

Cis-regulatory Sequences

Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...

Transposons

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...

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Related Experiment Video

Updated: May 9, 2026

Describing a Transcription Factor Dependent Regulation of the MicroRNA Transcriptome

Describing a Transcription Factor Dependent Regulation of the MicroRNA Transcriptome

Published on: June 15, 2016

Regulatory transposable elements in the encyclopedia of DNA elements.

Alan Y Du^1,2, Jason D Chobirko³, Xiaoyu Zhuo^1,2

¹Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA.

Nature Communications

|August 31, 2024

Summary

Transposable elements (TEs) significantly shape the human genome, contributing to regulatory elements and transcription factor binding. These DNA sequences play a crucial role in genome evolution and function.

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Published on: January 20, 2023

Area of Science:

Genomics
Molecular Biology
Evolutionary Biology

Background:

Transposable elements (TEs) constitute approximately 50% of the human genome.
The precise impact of TEs on genome evolution, particularly the regulatory genome, is not fully understood.

Purpose of the Study:

To conduct a comprehensive analysis of TE contributions to the human regulatory genome using ENCODE4 data.
To investigate the evolutionary origins and functional impact of TE-derived cis-regulatory elements (cCREs).

Main Methods:

Leveraged ENCODE4 data to identify and characterize TE-derived candidate cis-regulatory elements (cCREs).
Analyzed transcription factor (TF) motif composition and evolutionary conservation within TE-derived cCREs.
Assessed the regulatory activity and functional significance of TE-derived cCREs using MPRA and GWAS data.

Main Results:

Identified 236,181 TE-derived cCREs, representing approximately 25% of human cCREs.
Found that over 90% of these TE-derived cCREs are lineage-specific since the human-mouse divergence.
Demonstrated that TEs contribute significantly to transcription factor binding site turnover and exhibit functional similarities to non-TE cCREs.

Conclusions:

Transposable elements have played a substantial role in shaping the human regulatory landscape.
TE-derived regulatory elements are evolutionarily dynamic and functionally relevant.
This study provides a comprehensive view of TEs' impact on genome evolution and gene regulation.