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Related Concept Videos

Overview of Transposition and Recombination02:13

Overview of Transposition and Recombination

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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...
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LTR Retrotransposons03:08

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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.
The internal coding region of LTR retrotransposons and their mechanism of transposition closely resembles a...
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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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DNA-only Transposons02:57

DNA-only Transposons

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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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Conservative Site-specific Recombination and Phase Variation02:53

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Because the DNA segments are cut and reorganized in a direction-specific manner, site-specific recombination has emerged as an efficient genetic engineering technique. Flippase and Cyclization recombinases or Flp and Cre, respectively, are two members of the tyrosine recombinase family derived from bacteriophages, that are used to mediate site-specific DNA insertions, deletions, and targeted expression of proteins in mammalian cell lines.
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Cis-regulatory Sequences02:02

Cis-regulatory Sequences

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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...
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Related Experiment Video

Updated: Jul 15, 2025

RNA Next-Generation Sequencing and a Bioinformatics Pipeline to Identify Expressed LINE-1s at the Locus-Specific Level
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capTEs enables locus-specific dissection of transcriptional outputs from reference and nonreference transposable

Xuemei Li1, Keying Lu1, Xiao Chen1

  • 1Laboratory of Omics Technology and Bioinformatics, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, Sichuan, 610041, China.

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Transposable elements (TEs) can cause disease, but studying them is hard. A new method, capTEs, uses long-read sequencing to precisely measure individual TE expression and their effects on genes.

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Area of Science:

  • Genomics
  • Molecular Biology
  • Cancer Research

Background:

  • Transposable elements (TEs) are mobile DNA sequences with roles in genome evolution and disease.
  • Aberrant TE activity is linked to various diseases, including cancers.
  • Current methods struggle to accurately measure the expression of individual TEs, especially nonreference insertions.

Purpose of the Study:

  • To develop a novel method for precise, locus-level quantification of transposable element (TE) transcription.
  • To analyze the transcriptional consequences of individual TEs, including nonreference insertions and noncanonical transcripts.
  • To investigate the regulatory roles of TEs in gene expression changes, particularly in cancer.

Main Methods:

  • Introduction of Cas9-assisted profiling TE expression sequencing (capTEs), a long-read targeted RNA sequencing technique.
  • Selective identification of TE-containing transcripts with high TE read percentage (up to 90%).
  • Application of capTEs to human cancer cells to analyze TE expression and its correlation with host gene expression.

Main Results:

  • capTEs enables quantitative analysis of individual TE transcriptional outputs, including nonreference insertions.
  • The method achieved high data yield comparable to whole-transcriptome sequencing.
  • Analysis of human cancer cells revealed distinct regulatory mechanisms for internal and inserted Alu elements in upregulating gene expression.

Conclusions:

  • capTEs is a powerful tool for studying the locus-specific functions of individual TEs.
  • The method facilitates understanding of TEs' roles as both mutagens and regulatory elements in biological and pathogenic processes.
  • Distinct regulatory roles of Alu elements in gene upregulation were identified in cancer cells.