Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

MicroRNAs

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...

MicroRNAs

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...

MicroRNAs

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...

Small interfering RNAs (siRNA)

Small interfering RNAs (siRNA)

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...

RNA Stability

RNA Stability

Intact DNA strands can be found in fossils, while scientists sometimes struggle to keep RNA intact under laboratory conditions. The structural variations between RNA and DNA underlie the differences in their stability and longevity. Because DNA is double-stranded, it is inherently more stable. The single-stranded structure of RNA is less stable but also more flexible and can form weak internal bonds. Additionally, most RNAs in the cell are relatively short, while DNA can be up to 250 million...

RNA Stability

RNA Stability

Intact DNA strands can be found in fossils, while scientists sometimes struggle to keep RNA intact under laboratory conditions. The structural variations between RNA and DNA underlie the differences in their stability and longevity. Because DNA is double-stranded, it is inherently more stable. The single-stranded structure of RNA is less stable but also more flexible and can form weak internal bonds. Additionally, most RNAs in the cell are relatively short, while DNA can be up to 250 million...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by

Same author

Argonaute proteins orchestrate Meiotic Sex Chromosome Inactivation and timing of the spermatogenic transcriptional program.

PLoS genetics·2026

Same author

The molecular determinants of PABPC-mediated deadenylation rate.

bioRxiv : the preprint server for biology·2026

Same author

RUNX1+23 Enhancer Marks Erythro-Megakaryocyte Lineages in Early Waves of Hematopoiesis in Human ESC Differentiation.

Blood advances·2026

Same author

Prion-based protein self-assembly tunes mutagenesis to enable rapid adaptation.

Cell·2026

Same author

Genome-wide CG hypomethylation of the <i>Arabidopsis</i> ecotype Cvi linked to structural variation and RNAi at the <i>VIM4</i>-<i>VIM2</i> locus.

Proceedings of the National Academy of Sciences of the United States of America·2026

Same author

CD4+ T Cells Sensitize Quasimesenchymal Breast Tumors Lacking CD73 to Anti-CTLA4 Immune Checkpoint Blockade Therapy.

Cancer research communications·2026

Search research articles

Related Experiment Video

Updated: May 29, 2026

MS2-Affinity Purification Coupled with RNA Sequencing in Gram-Positive Bacteria

MS2-Affinity Purification Coupled with RNA Sequencing in Gram-Positive Bacteria

Published on: February 23, 2021

Weak seed-pairing stability and high target-site abundance decrease the proficiency of lsy-6 and other microRNAs.

David M Garcia¹, Daehyun Baek, Chanseok Shin

¹Whitehead Institute for Biomedical Research, Cambridge, Massachusetts, USA.

Nature Structural & Molecular Biology

|September 13, 2011

Summary

Nematode lsy-6 microRNA (miRNA) and mammalian miR-23 show low gene repression proficiency due to weak seed-pairing stability and high target-site abundance. This finding improves prediction tools for miRNA and small interfering RNA (siRNA) regulation.

More Related Videos

Detection of miRNA Targets in High-throughput Using the 3'LIFE Assay

Detection of miRNA Targets in High-throughput Using the 3'LIFE Assay

Published on: May 25, 2015

Identifying Targets of Human microRNAs with the LightSwitch Luciferase Assay System using 3'UTR-reporter Constructs and a microRNA Mimic in Adherent Cells

Identifying Targets of Human microRNAs with the LightSwitch Luciferase Assay System using 3'UTR-reporter Constructs and a microRNA Mimic in Adherent Cells

Published on: September 28, 2011

Related Experiment Videos

Last Updated: May 29, 2026

MS2-Affinity Purification Coupled with RNA Sequencing in Gram-Positive Bacteria

MS2-Affinity Purification Coupled with RNA Sequencing in Gram-Positive Bacteria

Published on: February 23, 2021

Detection of miRNA Targets in High-throughput Using the 3'LIFE Assay

Detection of miRNA Targets in High-throughput Using the 3'LIFE Assay

Published on: May 25, 2015

Identifying Targets of Human microRNAs with the LightSwitch Luciferase Assay System using 3'UTR-reporter Constructs and a microRNA Mimic in Adherent Cells

Identifying Targets of Human microRNAs with the LightSwitch Luciferase Assay System using 3'UTR-reporter Constructs and a microRNA Mimic in Adherent Cells

Published on: September 28, 2011

Area of Science:

Molecular Biology
Genetics
Bioinformatics

Background:

Most microRNAs (miRNAs) regulate numerous genes, but some exhibit limited proficiency.
The nematode lsy-6 miRNA is known for its low gene repression efficiency.

Purpose of the Study:

To investigate the factors contributing to the low proficiency of lsy-6 miRNA.
To determine if mammalian miRNAs also exhibit low proficiency and identify associated properties.
To enhance computational tools for predicting miRNA and small interfering RNA (siRNA) regulation.

Main Methods:

Recapitulating lsy-6 miRNA function in HeLa cells.
Utilizing reporter assays and array data to analyze miRNA properties.
Expanding the TargetScan algorithm to model miRNA and siRNA proficiencies.

Main Results:

The low proficiency of lsy-6 miRNA was successfully replicated in mammalian cells.
Weak predicted seed-pairing stability (SPS) and high target-site abundance (TA) were identified as key factors for low miRNA proficiency.
These properties also explain differential off-target effects of siRNAs.
The enhanced TargetScan tool showed improved prediction performance for miRNA and siRNA regulation.

Conclusions:

Low miRNA proficiency is linked to weak SPS and high TA.
Understanding these properties can guide the design of more specific siRNAs with reduced off-target activity.
The refined TargetScan tool offers better quantitative prediction of small RNA regulation.