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Related Concept Videos

MicroRNAs01:22

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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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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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In eukaryotes, transcription and translation are compartmentalized; an mRNA is first synthesized in the nucleus and then selectively transported to the cytoplasm for protein synthesis. Before transport, a pre-mRNA undergoes several steps of post-transcriptional modifications including splicing, 5' capping, and the addition of a poly-adenine tail. Various proteins bind to the pre-mRNA during these modifications. The mRNA transport takes place with the help of multiple proteins playing...
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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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Identifying Targets of Human microRNAs with the LightSwitch Luciferase Assay System using 3'UTR-reporter Constructs and a microRNA Mimic in Adherent Cells
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MicroRNA binding sites in C. elegans 3' UTRs.

Chaochun Liu1, William A Rennie1, Bibekanand Mallick1

  • 1Wadsworth Center; New York State Department of Health; Center for Medical Science; Albany, NY USA.

RNA Biology
|May 16, 2014
PubMed
Summary
This summary is machine-generated.

Researchers developed new bioinformatics tools to predict microRNA (miRNA) targets in C. elegans. These models significantly improve accuracy, aiding the understanding of gene regulation during development.

Keywords:
GO analysisdevelopmental stagemicroRNApredictiontarget binding site

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Area of Science:

  • Genetics and Genomics
  • Developmental Biology
  • Bioinformatics

Background:

  • MicroRNAs (miRNAs) are key post-transcriptional gene regulators.
  • Over 360 miRNAs are identified in Caenorhabditis elegans (C. elegans).
  • Accurate prediction of miRNA targets is crucial for understanding their regulatory roles.

Purpose of the Study:

  • To develop statistical models and bioinformatics tools for predicting miRNA binding sites in C. elegans 3' UTRs.
  • To enable both transcriptome-scale and developmental stage-specific predictions.
  • To improve upon existing algorithms for miRNA target prediction.

Main Methods:

  • Utilized available C. elegans miRNA expression profiles and 3' UTR annotations.
  • Developed statistical models and bioinformatics tools for miRNA binding site prediction.
  • Validated models using Argonaute protein ALG-1 crosslinking immunoprecipitation (CLIP) data.

Main Results:

  • The developed models significantly outperform established algorithms in predicting both seed and seedless miRNA binding sites.
  • Top-ranked predictions show a substantially higher true positive rate, indicating greater likelihood of experimental validation.
  • Gene ontology analysis reveals miRNAs dynamically regulate development, cell cycle, trafficking, and cell signaling.

Conclusions:

  • The new prediction models offer a major improvement for identifying miRNA targets in C. elegans.
  • miRNAs play a significant role in the dynamic regulation of biological processes during C. elegans development.
  • A database and software are available for transcriptome-scale and stage-specific miRNA target predictions.