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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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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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RNA Interference01:23

RNA Interference

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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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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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siRNA - Small Interfering RNAs02:30

siRNA - Small Interfering RNAs

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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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Nucleic Acid Structure01:25

Nucleic Acid Structure

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The pentose sugar in DNA is deoxyribose, while in RNA the pentose sugar is ribose. The difference between the sugars is the presence of the hydroxyl group on the ribose's second carbon and a hydrogen on the deoxyribose's second carbon. The phosphate residue attaches to the hydroxyl group of the 5′ carbon of one sugar and the hydroxyl group of the 3′ carbon of the sugar of the next nucleotide, which forms  a 5′ to 3′ phosphodiester linkage.
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Related Experiment Video

Updated: Jan 15, 2026

Genome-wide Screen for miRNA Targets Using the MISSION Target ID Library
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Genome-wide Screen for miRNA Targets Using the MISSION Target ID Library

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Functional microRNA targeting without seed pairing.

Matthew H Hall1,2,3, Peter Y Wang1,2,3, Thy M Pham1,2,3

  • 1Howard Hughes Medical Institute, Cambridge, MA 02142, USA.

Nucleic Acids Research
|October 16, 2025
PubMed
Summary
This summary is machine-generated.

MicroRNAs (miRNAs) can repress gene expression via 3'-only binding sites, challenging the necessity of seed region pairing. These rare sites demonstrate functional repression, impacting Argonaute protein complex dynamics.

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Related Experiment Videos

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A Complete Pipeline for Isolating and Sequencing MicroRNAs, and Analyzing Them Using Open Source Tools
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Area of Science:

  • Molecular Biology
  • Gene Regulation
  • RNA Biology

Background:

  • MicroRNAs (miRNAs) bind Argonaute (AGO) proteins to guide mRNA targeting for post-transcriptional repression.
  • Canonical miRNA function relies on seed region complementarity (nucleotides 2-7) for mRNA binding and repression.
  • The role of non-canonical binding sites, particularly those lacking seed complementarity, remains less understood.

Purpose of the Study:

  • To investigate the binding and repression capabilities of unusual miRNA binding sites that lack seed complementarity but exhibit extensive pairing in the miRNA 3 egion.
  • To compare the biophysical properties and functional outcomes of 3 extprime-only miRNA binding sites with canonical seed-matched sites.
  • To determine the prevalence and significance of these non-canonical 3 extprime-only sites in endogenous miRNA targeting.

Main Methods:

  • Biophysical characterization of Argonaute-miRNA-mRNA interactions using 3 extprime-only and seed-matched binding sites.
  • Assays to measure binding kinetics (association and dissociation rates) and repression efficiency.
  • Analysis of AGO-miRNA complex conformations induced by different binding site types.

Main Results:

  • 3 extprime-only binding sites demonstrate comparable binding affinity and repression efficacy to top canonical seed-matched sites.
  • Repression by 3 extprime-only sites can be enhanced by minimal additional seed pairing.
  • These sites exhibit slower association/dissociation rates and induce distinct AGO-miRNA complex conformations compared to seed-matched sites.

Conclusions:

  • Seed region complementarity is not strictly required for miRNA binding and repression, nor for accessing the 3 extprime region of the guide RNA.
  • 3 extprime-only sites represent a rare but functional class of miRNA targeting, similar in proportion to other known rare functional sites.
  • Understanding non-canonical miRNA binding expands the known mechanisms of post-transcriptional gene regulation by miRNAs.