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Related Concept Videos

piRNA - Piwi-interacting RNAs02:57

piRNA - Piwi-interacting RNAs

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PIWI-interacting RNAs, or piRNAs, are the most abundant short non-coding RNAs. More than 20,000 genes have been found in humans that code for piRNAs while only 2000 genes have been found for miRNAs. piRNAs can act at the transcriptional and post-transcriptional levels and have a vital role in silencing transposable elements present in germ cells. They are also involved in epigenetic silencing and activation. Previously, they were thought to function only in germ cells but new evidence suggests...
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Overview of Transposition and Recombination02:13

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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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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.
The donor site from where the transposon is excised is either degraded or...
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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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LTR Retrotransposons03:08

LTR Retrotransposons

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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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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: May 30, 2025

Real-Time Quantification of the Effects of IS200/IS605 Family-Associated TnpB on Transposon Activity
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FishPi: a bioinformatic prediction tool to link piRNA and transposable elements.

Alice M Godden1, Benjamin Rix2, Simone Immler2

  • 1School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK. alice.godden@uea.ac.uk.

Mobile DNA
|January 28, 2025
PubMed
Summary

FishPi is a new tool that links piRNAs (Piwi-interacting RNAs) with their complementary transposable element (TE) targets. This helps researchers understand how piRNAs regulate genome stability and gene expression.

Keywords:
EvolutionPiRNAsTransposonsZebrafish

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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Piwi-interacting RNAs (piRNAs) are small non-coding RNAs crucial for genome defense against transposable elements (TEs).
  • Understanding piRNA-TE interactions is key to comprehending genome maintenance and gene regulation.
  • Existing tools have limitations in linking piRNAs to their specific TE targets across diverse species.

Purpose of the Study:

  • To develop a user-friendly tool, FishPi, for predicting piRNA-TE interactions.
  • To facilitate the analysis of piRNA complementarity with TEs in various genomes.
  • To enhance the study of piRNA function in genome stability.

Main Methods:

  • FishPi analyzes piRNA sequences against reference TEs, focusing on the seed region for complementarity.
  • The tool allows user customization of parameters such as piRNA orientation and mismatches.
  • It processes individual piRNAs or lists in FASTA format and generates scored piRNA-TE match reports.

Main Results:

  • FishPi successfully predicts piRNA-TE pairings for zebrafish, medaka, and tilapia genomes.
  • The software identifies TE types, counts them, and records genomic loci of interactions.
  • A graphical user interface (GUI) simplifies input and report generation for piRNA-TE interactions.

Conclusions:

  • FishPi provides valuable insights into genome mobility by identifying piRNA-TE interactions.
  • The tool aids in understanding the biological roles of piRNAs in genome maintenance.
  • FishPi's adaptability to new genomes broadens the interpretation of piRNA functionality for the research community.