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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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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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Retroviruses have a single-stranded RNA genome that undergoes a special form of replication. Once the retrovirus has entered the host cell, an enzyme called reverse transcriptase synthesizes double-stranded DNA from the retroviral RNA genome. This DNA copy of the genome is then integrated into the host’s genome inside the nucleus via an enzyme called integrase. Consequently, the retroviral genome is transcribed into RNA whenever the host’s genome is transcribed, allowing the...
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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, National Institutes of Health, Bethesda, Maryland, United States.

Medrxiv : the Preprint Server for Health Sciences
|June 26, 2025
PubMed
Summary
This summary is machine-generated.

Retrotransposon expression differs in children with Crohn's disease (CD), particularly in ileal biopsies. Fifteen specific retrotransposon loci were consistently downregulated in CD patients compared to controls, 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 an autoimmune gastrointestinal disorder with complex, partially understood causes.
  • Retrotransposons, mobile genetic elements, are implicated in autoimmune and inflammatory diseases.
  • This study investigates retrotransposon expression in pediatric CD.

Purpose of the Study:

  • To explore and quantify the expression of retrotransposons in children diagnosed with Crohn's disease.
  • To identify specific retrotransposon loci that are differentially expressed in CD ileal and rectal tissues.
  • To validate findings in independent pediatric cohorts.

Main Methods:

  • High-throughput RNA sequencing (RNAseq) was used to analyze retrotransposon expression at the locus level.
  • Ileal and rectal biopsies from treatment-naïve pediatric CD patients and non-IBD controls were analyzed.
  • Expression data was validated using public datasets (GSE57945, GSE117993).

Main Results:

  • Distinct retrotransposon expression patterns were observed between CD patients and controls in ileal biopsies.
  • 118 differentially expressed retrotransposon loci were identified in ileal CD samples (74 LINE-1, 44 HERV).
  • Fifteen retrotransposon loci, including HERV and L1PA types, were consistently downregulated in ileal CD tissues across both datasets.

Conclusions:

  • The retrotransposon transcriptome in pediatric CD ileal biopsies significantly differs from non-IBD controls.
  • Consistent downregulation of 15 retrotransposon loci in CD ileal tissue warrants further investigation into their regulatory roles.
  • These findings may offer new perspectives for developing innovative therapeutic strategies for Crohn's disease.