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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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lncRNA - Long Non-coding RNAs02:39

lncRNA - Long Non-coding RNAs

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In humans, more than 80% of the genome gets transcribed. However, only around 2% of the genome codes for proteins. The remaining part produces non-coding RNAs which includes ribosomal RNAs, transfer RNAs, telomerase RNAs, and regulatory RNAs, among other types. A large number of regulatory non-coding RNAs have been classified into two groups depending upon their length – small non-coding RNAs, such as microRNA, which are less than 200 nucleotides in length, and long non-coding RNA...
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Related Experiment Video

Updated: Mar 29, 2026

MicroRNA Amplification and Recognition through Locked-nucleic-acid In situ Hybridization as a Novel Detection and Quantification Method
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MicroRNA Amplification and Recognition through Locked-nucleic-acid In situ Hybridization as a Novel Detection and Quantification Method

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DIANA-LncBase v2: indexing microRNA targets on non-coding transcripts.

Maria D Paraskevopoulou1, Ioannis S Vlachos2, Dimitra Karagkouni3

  • 1DIANA-Lab, Department of Computer & Communication Engineering, University of Thessaly, 382 21, Volos, Greece Hellenic Pasteur Institute, 127 Vasilissis Sofias Avenue, 11521, Athens, Greece mparaskevopoulou@inf.uth.gr.

Nucleic Acids Research
|November 28, 2015
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Summary

Long non-coding RNAs (lncRNAs) regulate gene expression by interacting with microRNAs (miRNAs). The updated LncBase v2 database significantly expands experimentally supported miRNA:lncRNA interactions and predicted binding sites across diverse cell types.

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Area of Science:

  • * Molecular Biology
  • * Genomics
  • * Bioinformatics

Background:

  • * MicroRNAs (miRNAs) are key post-transcriptional regulators of gene expression.
  • * Long non-coding RNAs (lncRNAs) have emerged as crucial regulators interacting with miRNAs.
  • * LncRNAs can act as miRNA sponges, adding complexity to gene regulation.

Purpose of the Study:

  • * To present LncBase v2, an enhanced database of miRNA:lncRNA interactions.
  • * To provide a comprehensive resource for experimentally supported and predicted interactions.
  • * To facilitate the study of cell type-specific miRNA:lncRNA regulatory networks.

Main Methods:

  • * Manual curation of publications and analysis of 153 AGO CLIP-Seq libraries for experimental interactions.
  • * In silico prediction of miRNA targets on lncRNAs using the DIANA-microT algorithm.
  • * Integration of lncRNA expression data from over 6 billion RNA-Seq reads.

Main Results:

  • * LncBase v2 contains over 70,000 experimentally supported miRNA:lncRNA interactions, a 14-fold increase from v1.
  • * Millions of predicted miRNA binding sites with conservation metrics are available.
  • * Cell type-specific interaction data for 66 cell types and 36 tissues (human and mouse) are included.

Conclusions:

  • * LncBase v2 offers a significantly expanded and detailed resource for miRNA:lncRNA interactions.
  • * The database supports research into lncRNA-mediated gene regulation and its cellular context.
  • * LncBase v2 is a valuable tool for investigating the complex interplay between lncRNAs and miRNAs.