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Related Concept Videos

Conserved Binding Sites01:49

Conserved Binding Sites

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Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
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Many proteins form complexes to carry out their functions, making protein-protein interactions (PPIs) essential for an organism's survival. Most PPIs are stabilized by numerous weak noncovalent chemical forces. The physical shape of the interfaces determines the way two proteins interact. Many globular proteins have closely-matching shapes on their surfaces, which form a large number of weak bonds. Additionally, many PPIs occur between two helices or between a surface cleft and a...
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Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
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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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Related Experiment Video

Updated: Oct 8, 2025

Exploring Sequence Space to Identify Binding Sites for Regulatory RNA-Binding Proteins
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Predicting sequence and structural features of effective piRNA target binding sites.

Garima Singh1, Bibekanand Mallick1

  • 1RNAi and Functional Genomics Lab., Department of Life Science, National Institute of Technology Rourkela, Rourkela, India.

Journal of Molecular Recognition : JMR
|January 3, 2022
PubMed
Summary

Identifying Piwi-interacting RNA (piRNA) targets is improved by analyzing CLIP-Seq data. New features, including AU enrichment and 3'UTR localization, enhance piRNA target prediction accuracy.

Keywords:
3′ untranslated region3′UTR5′ untranslated region5′UTRCDSPiwi-interacting RNAcoding sequencemRNAtarget

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Area of Science:

  • Molecular Biology
  • Genomics
  • RNA Biology

Background:

  • Piwi-interacting RNA (piRNA) target identification traditionally relies on seed region base pairing, often leading to inaccurate predictions.
  • Cross-linking immunoprecipitation (CLIP) coupled with sequencing (CLIP-Seq) offers a more precise method for identifying PIWI-clade targets by pinpointing RNA-binding sites.

Purpose of the Study:

  • To analyze piRNA-target CLIP-Seq datasets to uncover additional characteristic features of piRNA targets.
  • To identify sequence and structural features that enhance the accuracy of piRNA target site predictions.

Main Methods:

  • Analysis of piRNA-target CLIP-Seq datasets, comparing immunoprecipitated (IP+) and non-immunoprecipitated (IP-) target sets.
  • Examination of sequence composition (AU enrichment) and structural features (minimal folding energy - MFE) around target sites.
  • Evaluation of target site localization within mRNA transcripts (e.g., 3'UTR).

Main Results:

  • Significant AU enrichment was observed in and around target sites of the IP+ set compared to the IP- set.
  • Lower MFE thresholds and higher miRanda scores were associated with validated piRNA targets.
  • A majority of piRNA target sites were found to reside within the 3' untranslated region (3'UTR).

Conclusions:

  • The study identified key sequence and structural features, such as AU enrichment and 3'UTR localization, that improve piRNA target prediction.
  • These findings enhance the accuracy of identifying potential piRNA targets, aiding in the understanding of their functional roles.
  • The results suggest that 3'UTRs are preferential targets for piRNAs, similar to microRNA targets.