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Related Concept Videos

Non-LTR Retrotransposons03:18

Non-LTR Retrotransposons

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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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Nuclear Localization Signals and Import01:46

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Proteins targeted to the nucleus carry short stretches of amino acid sequences called the nuclear localization signal or NLS. Classical nuclear localization signals are of two types: monopartite and bipartite NLS. Monopartite classical NLS (cNLS) consists of a single cluster of 4-8 amino acids. Bipartite cNLS consists of two clusters of  2-3 amino acids and a 9-12 residue long proline-rich linker bridging the two clusters. Signal clusters are rich in positively charged amino acids such as...
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Retroviruses02:33

Retroviruses

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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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Chromatin Position Affects Gene Expression02:35

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Chromatin is the massive complex of DNA and proteins packaged inside the nucleus. The complexity of chromatin folding and how it is packaged inside the nucleus greatly influences  access to genetic information. Generally, the nucleus' periphery is considered transcriptionally repressive, while the cell's interior is considered a transcriptionally active area. 
Topologically Associated Domains (TADs)
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Regulated mRNA Transport

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In eukaryotes, transcription and translation are compartmentalized; an mRNA is first synthesized in the nucleus and then selectively transported to the cytoplasm for protein synthesis. Before transport, a pre-mRNA undergoes several steps of post-transcriptional modifications including splicing, 5' capping, and the addition of a poly-adenine tail. Various proteins bind to the pre-mRNA during these modifications. The mRNA transport takes place with the help of multiple proteins playing...
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Updated: Aug 19, 2025

Analysis of LINE-1 Retrotransposition at the Single Nucleus Level
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Analysis of LINE-1 Retrotransposition at the Single Nucleus Level

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Generalized nuclear localization of retroelement transcripts.

Simanti Das1, Amanda E Jones1, John M Abrams2

  • 1Department of Cell Biology, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.

Mobile DNA
|December 2, 2022
PubMed
Summary
This summary is machine-generated.

Retrotransposon RNAs, including LINE-1s and Alus, are predominantly found in the cell nucleus. This conserved nuclear localization across different elements and species suggests a potential adaptive role for the host or the elements themselves.

Keywords:
DevelopmentLINE-1Nuclear localizationRNARNA-sequencingRetroelementsRetrotransposition

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Area of Science:

  • Genomics
  • Molecular Biology
  • Epigenetics

Background:

  • Human genomes contain retrotransposable elements like LINE-1s, Alus, and SVAs, which can cause disease through mobilization and insertional mutagenesis.
  • Accumulation of retrotransposition intermediates in the cytoplasm can trigger inflammatory responses.
  • Previous studies showed conflicting data regarding the subcellular localization of LINE-1 and Alu RNAs.

Purpose of the Study:

  • To comprehensively analyze the subcellular localization patterns of retroelement RNAs.
  • To compare retroelement RNA localization with that of protein-coding genes.
  • To investigate the conservation and dynamics of retroelement RNA localization.

Main Methods:

  • Utilized a comprehensive and unbiased approach to analyze retroelement RNA localization.
  • Employed common cell lines and publicly available RNA-sequencing datasets from subcellular fractions.
  • Developed a customized analytic pipeline for comparing localization patterns.

Main Results:

  • Demonstrated a generalized pattern of nuclear localization for retroelement RNAs, conserved across different retroelement classes (LINE-1s, Alus, SVAs) and evolutionary ages.
  • Observed preferential nuclear enrichment of retroelement transcripts consistently in cell lines, in vivo, and across species.
  • Found that retroelement RNA localization patterns are dynamic and change during development, as evidenced in zebrafish embryos.

Conclusions:

  • The consistent nuclear retention of retroelement transcripts suggests they are not re-imported or degraded in the cytoplasm.
  • This pronounced nuclear localization may hold adaptive significance for either the host, the retroelements, or both.
  • Further research is warranted to elucidate the functional implications of this nuclear localization.