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

Next-generation Sequencing

Next-generation Sequencing

The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
Next-Generation Sequencing Methods
Although all next-generation methods use different technologies, they all share a set of standard features....

Plant Breeding and Biotechnology

Plant Breeding and Biotechnology

Crop cultivation has a long history in human civilization, with records showing the cultivation of cereal plants beginning at around 8000 BC. This early plant breeding was developed primarily to provide a steady supply of food.

Genomics

Genomics

Genomics is the science of genomes: it is the study of all the genetic material of an organism. In humans, the genome consists of information carried in 23 pairs of chromosomes in the nucleus, as well as mitochondrial DNA. In genomics, both coding and non-coding DNA is sequenced and analyzed. Genomics allows a better understanding of all living things, their evolution, and their diversity. It has a myriad of uses: for example, to build phylogenetic trees, to improve productivity and...

Synthetic Biology

Synthetic Biology

Synthetic biology is an interdisciplinary science that involves using principles from disciplines such as engineering, molecular biology, cell biology, and systems biology. It involves remodeling existing organisms from nature or constructing completely new synthetic organisms for applications such as protein or enzyme production, bioremediation, value-added macromolecule production, and the addition of desirable traits to crops, to name a few.
Golden rice
Golden rice is a genetically modified...

You might also read

Related Articles

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

Sort by

Same author

6mA DNA methylation dynamics during chloroplast development in Agave angustifolia Haw.

Planta·2026

Same author

ROS and autophagy in plant stress responses: adaptive partners in survival.

Plant physiology and biochemistry : PPB·2025

Same author

Parallel DLD microfluidics for chloroplast isolation and sorting.

Lab on a chip·2025

Same author

Beyond the surface: the plant secretome as a bridge between the cell and its environment.

Planta·2025

Same author

Chlorophyll deficiency in Agave angustifolia Haw.: unveiling the impact on secondary metabolite production.

Planta·2024

Same author

Protocol for Generating Arabidopsis thaliana Cell Suspension Cultures Under Different Light Conditions.

Methods in molecular biology (Clifton, N.J.)·2024

Search research articles

Related Experiment Video

Updated: Jan 19, 2026

Obtaining High-Quality Transcriptome Data from Cereal Seeds by a Modified Method for Gene Expression Profiling

Obtaining High-Quality Transcriptome Data from Cereal Seeds by a Modified Method for Gene Expression Profiling

Published on: May 21, 2020

DNA Methylation and Transcriptomic Next-Generation Technologies in Cereal Genomics.

Cynthia G Soto-Cardinault¹, Fátima Duarte-Aké¹, Clelia De-la-Peña¹

¹Unidad de Biotecnología, Centro de Investigación Científica de Yucatán, Mérida, Yucatán, Mexico.

Methods in Molecular Biology (Clifton, N.J.)

|September 22, 2019

Summary

This study presents a bioinformatics protocol using RNA sequencing (RNA-seq) to identify genes potentially regulated by DNA methylation. The method highlights low-expressed genes as candidates for methylation analysis.

Keywords:

Bioinformatics Bisulfite technique Cereals Genome methylation Transcriptome expression

More Related Videos

Targeted DNA Methylation Analysis by Next-generation Sequencing

Targeted DNA Methylation Analysis by Next-generation Sequencing

Published on: February 24, 2015

Determination of DNA Methylation of Imprinted Genes in Arabidopsis Endosperm

Determination of DNA Methylation of Imprinted Genes in Arabidopsis Endosperm

Published on: January 28, 2011

Related Experiment Videos

Last Updated: Jan 19, 2026

Obtaining High-Quality Transcriptome Data from Cereal Seeds by a Modified Method for Gene Expression Profiling

Obtaining High-Quality Transcriptome Data from Cereal Seeds by a Modified Method for Gene Expression Profiling

Published on: May 21, 2020

Targeted DNA Methylation Analysis by Next-generation Sequencing

Targeted DNA Methylation Analysis by Next-generation Sequencing

Published on: February 24, 2015

Determination of DNA Methylation of Imprinted Genes in Arabidopsis Endosperm

Determination of DNA Methylation of Imprinted Genes in Arabidopsis Endosperm

Published on: January 28, 2011

Area of Science:

Genomics
Epigenetics
Bioinformatics

Background:

DNA methylation plays a crucial role in gene regulation.
RNA sequencing (RNA-seq) provides insights into gene expression levels.
Integrating these techniques can reveal methylation-mediated gene expression.

Purpose of the Study:

To describe a bioinformatics protocol for analyzing RNA-seq data.
To identify candidate genes whose expression is potentially regulated by DNA methylation.
To facilitate further validation using bisulfite assays.

Main Methods:

Utilizing RNA sequencing (RNA-seq) data.
Applying bioinformatics analysis to gene expression levels.
Identifying genes with low expression in specific conditions or developmental stages as candidates.

Main Results:

A protocol for analyzing RNA-seq data to find methylation-mediated gene candidates is described.
The method focuses on identifying genes with reduced expression.
Candidate genes are suitable for subsequent bisulfite assay validation.

Conclusions:

The described bioinformatics protocol effectively integrates RNA-seq data for identifying potential DNA methylation targets.
This approach aids in discovering genes regulated by epigenetic mechanisms.
It provides a foundation for targeted bisulfite analysis of candidate genes.