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Related Concept Videos

MicroRNAs01:22

MicroRNAs

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...
MicroRNAs01:22

MicroRNAs

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 ends...
MicroRNAs01:22

MicroRNAs

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 ends...
Experimental RNAi02:15

Experimental RNAi

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...
RNA Interference01:23

RNA Interference

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.
This process occurs naturally in cells, often through the activity of genomically-encoded microRNAs. Researchers can take advantage of this mechanism by introducing synthetic RNAs to deactivate specific genes for research or therapeutic purposes. For example, RNAi could be used...
siRNA - Small Interfering RNAs02:30

siRNA - Small Interfering RNAs

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.
In the cytoplasm, siRNA is processed from a double-stranded RNA, which comes from either endogenous DNA transcription or exogenous sources like a virus. This double-stranded RNA is then cleaved by the ATP-dependent...

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Related Experiment Video

Updated: Jun 29, 2026

RNA Blot Analysis for the Detection and Quantification of Plant MicroRNAs
14:41

RNA Blot Analysis for the Detection and Quantification of Plant MicroRNAs

Published on: July 11, 2020

Selection and mutation on microRNA target sequences during rice evolution.

Xingyi Guo1, Yijie Gui, Yu Wang

  • 1Institute of Crop Science & Institute of Bioinformatics, Zhejiang University, Hangzhou 310029, PR China. bioinplant@zju.edu.cn

BMC Genomics
|October 4, 2008
PubMed
Summary
This summary is machine-generated.

MicroRNA (miRNA) binding sites in rice are conserved by purifying selection, with nucleotide mutations driving their gain and loss during evolution. This study analyzed miRNA targets in duplicated genes to understand their co-evolution.

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Last Updated: Jun 29, 2026

RNA Blot Analysis for the Detection and Quantification of Plant MicroRNAs
14:41

RNA Blot Analysis for the Detection and Quantification of Plant MicroRNAs

Published on: July 11, 2020

Identifying Mutations by High Resolution Melting in a TILLING Population of Rice
06:10

Identifying Mutations by High Resolution Melting in a TILLING Population of Rice

Published on: September 2, 2019

mirMachine: A One-Stop Shop for Plant miRNA Annotation
06:16

mirMachine: A One-Stop Shop for Plant miRNA Annotation

Published on: May 1, 2021

Area of Science:

  • Plant molecular biology
  • Evolutionary genetics

Background:

  • MicroRNAs (miRNAs) regulate gene expression post-transcriptionally by targeting messenger RNAs (mRNAs).
  • Analyzing the evolution of miRNA binding sites helps elucidate the co-evolutionary dynamics between miRNAs and their targets.
  • Understanding these evolutionary processes in plants is crucial for comprehending gene regulation.

Purpose of the Study:

  • To investigate the evolution of miRNA binding sites in plants.
  • To analyze miRNA-targeted duplicated gene pairs from a whole genome duplication (WGD) event in rice (O. sativa).
  • To conduct a population genetics study of experimentally validated miRNA binding sites in rice.

Main Methods:

  • Comparative analysis of miRNA-targeted duplicated gene pairs from a rice WGD event.
  • Computational prediction of miRNA targets among duplicate genes.
  • Sequence substitution analysis to compare substitution rates in binding sites versus flanking regions.
  • Phylogenetic analysis and separation of conserved versus rice-specific miRNAs.
  • Population genetics analysis of miRNA binding sites and flanking regions in cultivated and wild rice populations.

Main Results:

  • Of 1,331 duplicate gene pairs, 41 genes (29 pairs) were predicted as miRNA targets.
  • Synonymous substitution rates were significantly lower in miRNA binding sites compared to flanking regions.
  • 17 out of 29 pairs showed only one paralog targeted by a miRNA, indicating gain or loss of binding sites post-WGD.
  • The estimated gain/loss rate of miRNA binding sites was 3.0 x 10^-9 per year, primarily due to nucleotide mutations (70.6%).
  • No segregating sites were found in six miRNA binding sites in rice populations, contrasting with SNPs in flanking regions.

Conclusions:

  • Conserved miRNA binding sites are maintained by purifying selection, which eliminates deleterious alleles.
  • Nucleotide mutations are the primary drivers for the gain and loss of miRNA binding sites throughout evolution.
  • Molecular evolution and population genetics data support the role of selection in maintaining miRNA binding site integrity.