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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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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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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, 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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Retroviral CRISPR/Cas9-Mediated Gene Targeting for the Study of Th17 Differentiation in Vitro
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Distinct Retrotransposon Transcriptome in Pediatric Crohn's Disease.

Qing Chen1, Colton McNinch2, Eve May1

  • 1Clinical Microbiome Unit, Laboratory of Host Immunity and Microbiome, Division of Intramural Research, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, United States.

Inflammatory Bowel Diseases
|September 19, 2025
PubMed
Summary
This summary is machine-generated.

Retrotransposon expression in the ileum of children with Crohn's disease (CD) differs significantly from healthy controls. Fifteen specific retrotransposon loci were consistently downregulated in pediatric CD patients, suggesting potential therapeutic targets.

Keywords:
gene expressionhuman endogenous retrovirusesinflammatory bowel diseaselong interspersed nuclear element-1

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Area of Science:

  • Genomics
  • Molecular Biology
  • Immunology

Background:

  • Crohn's disease (CD) is a complex autoimmune disorder affecting the gastrointestinal tract.
  • The precise mechanisms underlying CD pathogenesis remain incompletely understood.
  • Retrotransposons, mobile genetic elements, are implicated in inflammatory and autoimmune diseases.

Purpose of the Study:

  • To investigate the expression patterns of retrotransposons in pediatric patients diagnosed with Crohn's disease.
  • To compare retrotransposon expression between treatment-naïve children with CD and non-inflammatory bowel disease (IBD) controls.

Main Methods:

  • High-throughput RNA sequencing (RNAseq) was employed for locus-level expression analysis of LINE, SINE, and LTR-retrotransposons (human endogenous retroviruses - HERVs).
  • Analysis was conducted on ileal and rectal biopsies from pediatric CD patients and age-matched controls.
  • Findings were validated using public datasets (GSE57945 and GSE117993).

Main Results:

  • Distinct retrotransposon expression profiles were observed between CD patients and controls in ileal biopsies, with less pronounced differences in rectal biopsies.
  • A total of 118 differentially expressed retrotransposon loci were identified in the ileum (27 upregulated, 91 downregulated), including LINE-1 and HERV elements.
  • Fifteen retrotransposon loci, such as HERV9N-int and L1PA4, were consistently downregulated in the ileum of CD patients across both analyzed datasets.

Conclusions:

  • The retrotransposon transcriptome in pediatric CD patients shows significant alterations, particularly in the ileum.
  • Consistent downregulation of 15 specific retrotransposon loci in pediatric CD ileal biopsies warrants further investigation into their regulatory roles.
  • These findings may offer novel insights for developing targeted therapeutic strategies for Crohn's disease.