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

Cis-regulatory Sequences

Cis-regulatory Sequences

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...

siRNA - Small Interfering RNAs

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...

piRNA - Piwi-interacting RNAs

piRNA - Piwi-interacting RNAs

PIWI-interacting RNAs, or piRNAs, are the most abundant short non-coding RNAs. More than 20,000 genes have been found in humans that code for piRNAs while only 2000 genes have been found for miRNAs. piRNAs can act at the transcriptional and post-transcriptional levels and have a vital role in silencing transposable elements present in germ cells. They are also involved in epigenetic silencing and activation. Previously, they were thought to function only in germ cells but new evidence suggests...

Chromatin Structure and RNA Splicing

Chromatin Structure and RNA Splicing

Position-effect Variegation

Position-effect Variegation

In 1928, a German botanist Emil Heitz observed the moss nuclei with a DNA binding dye. He observed that while some chromatin regions decondense and spread out in the interphase nucleus, others do not. He termed them euchromatin and heterochromatin, respectively. He proposed that the heterochromatin regions reflect a functionally inactive state of the genome. It was later confirmed that heterochromatin is transcriptionally repressed, and euchromatin is transcriptionally active chromatin.

Overview of Transposition and Recombination

Overview of Transposition and Recombination

Transposons make up a significant part of genomes of various organisms. Therefore, it is believed that transposition played a major evolutionary role in speciation by changing genome sizes and modifying gene expression patterns. For example, in bacteria, transposition can lead to conferring antibiotic resistance. Movement of transposable elements within the genetic pool of pathogenic bacteria can aid in transfer of antibiotic-resistant genetic elements. In eukaryotes, transposons can carry out...

You might also read

Related Articles

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

Sort by

Same author

Natural variation in SlGRF10 reveals a role in regulating tomato fruit weight.

Plant physiology·2026

Same author

Unlocking translational control of specialized metabolism in plants through 5'UTR structure.

Science advances·2026

Same author

eQTL Meta-Analysis Reveals Conserved and Population-Specific Regulatory Variation Underlying Nutritional Trait Evolution and Domestication in Tomato.

Advanced science (Weinheim, Baden-Wurttemberg, Germany)·2026

Same author

Population-level super-pangenome reveals genome evolution and empowers precision breeding in watermelon.

Nature genetics·2026

Same author

Genomics Approach Links ROS-Scavenging to Enhanced Lateral Root Development Under Salt Stress in Tomato.

Plant, cell & environment·2026

Same author

Reorganizing the RNA polymerase II complex for replication of an infectious noncoding RNA in vivo.

PLoS pathogens·2026

Search research articles

Related Experiment Video

Updated: Sep 24, 2025

RNA Blot Analysis for the Detection and Quantification of Plant MicroRNAs

RNA Blot Analysis for the Detection and Quantification of Plant MicroRNAs

Published on: July 11, 2020

Dynamically expressed small RNAs, substantially driven by genomic structural variants, contribute to transcriptomic

You Qing^1,2, Yi Zheng^1,2,3, Sizolwenkosi Mlotshwa⁴

¹Beijing Key Laboratory for Agricultural Application and New Technique, College of Plant Science and Technology, Beijing University of Agriculture, Beijing, 102206, China.

The Plant Journal : for Cell and Molecular Biology

|May 6, 2022

Summary

Genomic structural variants (SVs) drive changes in small RNAs (sRNAs), including microRNAs (miRNAs), phased secondary short interfering RNAs (phasiRNAs), and heterochromatic siRNAs (hc-siRNAs), impacting tomato domestication and stress tolerance traits.

Keywords:

Solanum lycopersicum Solanum pimpinellifolium 24-nucleotide hc-siRNA domestication genomic structural variant miRNA phasiRNA tomato

More Related Videos

High-throughput CRISPR Vector Construction and Characterization of DNA Modifications by Generation of Tomato Hairy Roots

High-throughput CRISPR Vector Construction and Characterization of DNA Modifications by Generation of Tomato Hairy Roots

Published on: April 30, 2016

Tomato Root Transformation Followed by Inoculation with Ralstonia Solanacearum for Straightforward Genetic Analysis of Bacterial Wilt Disease

Tomato Root Transformation Followed by Inoculation with Ralstonia Solanacearum for Straightforward Genetic Analysis of Bacterial Wilt Disease

Published on: March 11, 2020

Related Experiment Videos

Last Updated: Sep 24, 2025

RNA Blot Analysis for the Detection and Quantification of Plant MicroRNAs

RNA Blot Analysis for the Detection and Quantification of Plant MicroRNAs

Published on: July 11, 2020

High-throughput CRISPR Vector Construction and Characterization of DNA Modifications by Generation of Tomato Hairy Roots

High-throughput CRISPR Vector Construction and Characterization of DNA Modifications by Generation of Tomato Hairy Roots

Published on: April 30, 2016

Tomato Root Transformation Followed by Inoculation with Ralstonia Solanacearum for Straightforward Genetic Analysis of Bacterial Wilt Disease

Tomato Root Transformation Followed by Inoculation with Ralstonia Solanacearum for Straightforward Genetic Analysis of Bacterial Wilt Disease

Published on: March 11, 2020

Area of Science:

Genomics
Molecular Biology
Plant Science

Background:

Tomato domestication involved extensive selection, with genomic structural variants (SVs) influencing gene expression and traits.
Small RNAs (sRNAs) play crucial roles in gene regulation, but their evolution during crop domestication is not fully understood.

Purpose of the Study:

To comprehensively analyze small RNAs (sRNAs) in diverse tomato accessions.
To investigate the contribution of genomic structural variants (SVs) to the dynamic expression of major sRNA classes during tomato domestication.

Main Methods:

Analysis of small RNA (sRNA) sequencing data from nine representative tomato accessions.
Identification and characterization of microRNAs (miRNAs), phased secondary short interfering RNAs (phasiRNAs), and 24-nucleotide heterochromatic siRNAs (hc-siRNAs).

Main Results:

SVs significantly impact the expression of miRNAs, phasiRNAs, and hc-siRNAs in tomato.
Changes in phasiRNA and hc-siRNA abundance correlate with altered mRNA expression, particularly for stress-tolerance genes.
SVs affect miRNA expression through mechanisms including imprecise processing and alternative selections, impacting less-conserved or low-abundance miRNAs.

Conclusions:

Genomic structural variants (SVs) are key drivers of small RNA (sRNA) evolution during tomato domestication.
Differential selection pressures exist for miRNAs versus phasiRNAs and hc-siRNAs.
This study provides insights into SV-mediated gene regulation and sRNA evolution in crop domestication, offering a resource for tomato sRNA network research.