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Related Concept Videos

MicroRNAs01:22

MicroRNAs

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MicroRNA (miRNA) are short, regulatory RNA transcribed from introns (non-coding regions of a gene) or intergenic regions (stretches of DNA present between genes). Several processing steps are required to form biologically active, mature miRNA. The initial transcript, called primary miRNA (pri-mRNA), base-pairs with itself, forming a stem-loop structure. Within the nucleus, an endonuclease enzyme, called Drosha, shortens the stem-loop structure into hairpin-shaped pre-miRNA. After the pre-miRNA...
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MicroRNA (miRNA) are short, regulatory RNA transcribed from introns—non-coding regions of a gene—or intergenic regions—stretches of DNA present between genes. Several processing steps are required to form biologically active, mature miRNA. The initial transcript, called primary miRNA (pri-mRNA), base-pairs with itself forming a stem-loop structure. Within the nucleus, an endonuclease enzyme, called Drosha, shortens the stem-loop structure into hairpin-shaped pre-miRNA. After...
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Experimental RNAi02:15

Experimental RNAi

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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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RNA interference (RNAi) is a process in which a small non-coding RNA molecule blocks the post-transcriptional expression of a gene by binding to its messenger RNA (mRNA) and preventing the protein from being translated.
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siRNA - Small Interfering RNAs02:30

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Small interfering RNAs, or siRNAs, are short regulatory RNA molecules that can silence genes post-transcriptionally, as well as the transcriptional level in some cases. siRNAs are important for protecting cells against viral infections and silencing transposable genetic elements.
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Biotin-based Pulldown Assay to Validate mRNA Targets of Cellular miRNAs
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miRTarBase 2016: updates to the experimentally validated miRNA-target interactions database.

Chih-Hung Chou1, Nai-Wen Chang2, Sirjana Shrestha3

  • 1Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsinchu, 300, Taiwan.

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|November 22, 2015
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The miRTarBase now includes over 348,000 experimentally validated microRNA-target interactions (MTIs) from CLIP-seq data, significantly expanding its utility for miRNA research. This update enhances understanding of post-transcriptional gene regulation.

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Area of Science:

  • Molecular Biology
  • Genomics
  • Bioinformatics

Background:

  • MicroRNAs (miRNAs) are key regulators of gene expression at the post-transcriptional level.
  • Experimentally validated miRNA-target interactions (MTIs) are crucial for understanding miRNA function.
  • Existing databases require updates to reflect the rapid growth of miRNA research data.

Purpose of the Study:

  • To update and expand the miRTarBase with novel experimentally validated miRNA-target interactions (MTIs).
  • To integrate diverse data types, including Argonaute-miRNA-RNA interactions from CLIP-seq.
  • To provide a comprehensive resource for researchers studying miRNA-mediated gene regulation.

Main Methods:

  • Systematic identification of miRNA-target interactions from 138 CLIP-seq datasets across 21 studies.
  • Inclusion of 7,439 strongly validated MTIs (reporter assays, western blots).
  • Integration of miRNA and gene expression profiles from The Cancer Genome Atlas (TCGA).

Main Results:

  • The updated miRTarBase now contains 348,007 MTIs derived from CLIP-seq data.
  • A total of 7,439 MTIs were strongly validated using reporter assays or western blots.
  • The database has expanded approximately 7-fold since the 2014 update, incorporating data from 4,966 articles.

Conclusions:

  • The enhanced miRTarBase is a more comprehensive and experimentally validated resource for miRNA-target interactions.
  • The integration of TCGA data provides valuable context for the extensive miRNA experimental data.
  • This updated database will facilitate further research into microRNA function and gene regulation.