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Related Concept Videos

piRNA - Piwi-interacting RNAs02:57

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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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RNA interference (RNAi) is a cellular mechanism that inhibits gene expression by suppressing its transcription or activating the RNA degradation process. The mechanism was discovered by Andrew Fire and Craig Mello in 1998 in plants. Today, it is observed in almost all eukaryotes, including protozoa, flies, nematodes, insects, parasites, and mammals. This precise cellular mechanism of gene silencing has been developed into a technique that provides an efficient way to identify and determine the...
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Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
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Enhanced Northern Blot Detection of Small RNA Species in Drosophila Melanogaster
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2L-piRNA: A Two-Layer Ensemble Classifier for Identifying Piwi-Interacting RNAs and Their Function.

Bin Liu1, Fan Yang2, Kuo-Chen Chou3

  • 1School of Computer Science and Technology, Harbin Institute of Technology Shenzhen Graduate School, Shenzhen, Guangdong 518055, China; Key Laboratory of Network Oriented Intelligent Computation, Harbin Institute of Technology Shenzhen Graduate School, Shenzhen, Guangdong 518055, China; Gordon Life Science Institute, Belmont, MA 02478, USA.

Molecular Therapy. Nucleic Acids
|June 19, 2017
PubMed
Summary

This study introduces 2L-piRNA, a computational tool that accurately identifies piwi-interacting RNAs (piRNAs) and distinguishes their function in target mRNA deadenylation using sequence information alone. This advances piRNA research and drug development.

Keywords:
PseKNCcancersmRNA deadenylationnon-coding RNAphysicochemical propertiespiRNAweb server

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Area of Science:

  • Molecular Biology
  • Bioinformatics
  • Genomics

Background:

  • Piwi-interacting RNAs (piRNAs) are small non-coding RNAs crucial for cellular and gene functions, and are implicated in various cancers.
  • Distinguishing piRNAs from other small RNAs and classifying their functional subtypes (e.g., mRNA deadenylation) is vital for biological research and drug development.
  • Existing computational methods lack the capability to address these classification challenges, especially in conjunction.

Purpose of the Study:

  • To develop a computational method for predicting piRNAs based solely on sequence information.
  • To differentiate piRNAs based on their functional role in instructing target mRNA deadenylation.
  • To provide a user-friendly tool for biologists and drug developers to analyze piRNA sequences.

Main Methods:

  • Incorporation of physicochemical properties of nucleotides into the pseudo K-tuple nucleotide composition (PseKNC) model.
  • Development of a two-layer ensemble classifier named 2L-piRNA.
  • The first layer identifies piRNAs versus non-piRNAs; the second layer classifies piRNA function related to mRNA deadenylation.

Main Results:

  • The 2L-piRNA predictor demonstrates high success rates in accurately identifying piRNAs and their functional subtypes.
  • Rigorous cross-validation confirms the efficacy and reliability of the proposed computational method.
  • A web server for 2L-piRNA has been established for easy access by researchers.

Conclusions:

  • The 2L-piRNA tool effectively addresses the need for computational methods to identify piRNAs and classify their functional roles.
  • This predictor offers a valuable resource for advancing basic piRNA research and facilitating drug development.
  • The accessibility of the web server empowers researchers without deep computational expertise to utilize these advanced analyses.