What is the difference between a DNA transposon and a retrotransposon?

A DNA transposon moves directly as DNA by a cut-and-paste mechanism, whereas a retrotransposon copies itself through an RNA intermediate that is reverse-transcribed and reinserted, so retrotransposons tend to increase in copy number as they spread.

Are mobile elements still active in the human genome?

Yes. While most transposable-element copies are fixed and inactive, a subset of LINE-1, Alu, and SVA elements remains capable of retrotransposition and continues to generate new, individually variable insertions.

Mobile Elements and Transposable Elements

Mobile elements, or transposable elements, are DNA sequences capable of moving or copying themselves to new positions in the genome. They make up a large fraction of human DNA, and their ongoing activity—chiefly through retrotransposition of elements such as Alu, LINE-1, and SVA—is a continuing source of insertional structural variation between individuals.

Definition

Transposable elements are DNA sequences able to change their position within a genome; they are broadly divided into DNA transposons, which move directly as DNA, and retrotransposons, which transpose via reverse transcription of an RNA intermediate and so increase in copy number as they spread.

Scope

This topic covers the major classes of mobile element, the distinction between DNA transposons that move by a cut-and-paste mechanism and retrotransposons that move through an RNA intermediate, and how new insertions contribute to structural variation and genome evolution. It is a reference treatment of mobile-element biology and is not clinical guidance.

Core questions

What are the major classes of transposable element in the human genome?
How do DNA transposons differ mechanistically from retrotransposons?
How do new mobile-element insertions create structural variation between people?
What is the evolutionary and genomic impact of retrotransposon activity?

Key concepts

DNA transposon (cut-and-paste)
Retrotransposon (copy-and-paste via RNA)
LINE-1 (L1) and target-primed reverse transcription
Alu and SVA non-autonomous elements
Endogenous retrovirus (ERV)
Mobile element insertion polymorphism
Insertional structural variation

Mechanisms

Mobile elements propagate by two contrasting routes. DNA transposons excise from one site and reinsert elsewhere through a cut-and-paste reaction catalysed by a transposase, leaving the copy number roughly unchanged. Retrotransposons instead copy themselves: an element is transcribed into RNA, reverse-transcribed, and the new DNA copy is integrated at a fresh location, so each round can add a copy. In humans the autonomous LINE-1 element supplies the machinery for target-primed reverse transcription, which also mobilizes non-autonomous Alu and SVA elements; endogenous retroviruses represent a related, mostly fixed class. New insertions add or interrupt sequence and are detected as a form of structural variation.

Clinical relevance

Mobile-element insertions are one mechanism by which new structural variants arise, and recognizing insertional events is relevant when interpreting genomic data in the health sciences. This entry describes the biology of transposable elements and their insertional activity as a reference matter and is not a basis for individual diagnosis or treatment.

Epidemiology

Transposable elements constitute roughly half of the human genome by sequence, the bulk of it from retrotransposon-derived repeats. Alu elements alone number in the hundreds of thousands of copies and remain among the most active sources of new polymorphic insertions, while LINE-1 supplies the enzymatic activity that drives ongoing retrotransposition; population surveys catalogue insertion polymorphisms that differ among individuals and ancestries.

History

Transposable elements were first recognized by Barbara McClintock in maize, decades before their pervasiveness in mammalian genomes was appreciated. Sequencing of the human genome showed that mobile-element-derived sequence dominates the repeat landscape, and work by Kazazian, Batzer, Deininger, and others established that LINE-1, Alu, and SVA elements remain active, generating new insertions and contributing to both normal variation and, occasionally, disease.

Debates

How large is the ongoing rate of new mobile-element insertions?: Estimates of how often new Alu, LINE-1, and SVA insertions occur per generation vary with the detection method, and quantifying the true rate of active retrotransposition in living populations remains an area of refinement.

Key figures

Barbara McClintock
Haig H. Kazazian
Mark A. Batzer
Prescott L. Deininger
Richard Cordaux

Seminal works

batzer-2002
cordaux-2009
hancks-2016

Frequently asked questions

What is the difference between a DNA transposon and a retrotransposon?: A DNA transposon moves directly as DNA by a cut-and-paste mechanism, whereas a retrotransposon copies itself through an RNA intermediate that is reverse-transcribed and reinserted, so retrotransposons tend to increase in copy number as they spread.
Are mobile elements still active in the human genome?: Yes. While most transposable-element copies are fixed and inactive, a subset of LINE-1, Alu, and SVA elements remains capable of retrotransposition and continues to generate new, individually variable insertions.