Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Experiment Videos

PCSD: a plant chromatin state database.

Yue Liu1, Tian Tian1, Kang Zhang1

  • 1State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China.

Nucleic Acids Research
|October 18, 2017
PubMed
Summary
This summary is machine-generated.

Related Concept Videos

You might also read

Related Articles

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

Sort by
Same author

Exogenous porcine blood polypeptide alleviates drought damage in wheat.

BMC plant biology·2026
Same author

EMF2b-1 regulates endosperm cell cycling through PRC2 recruitment in maize.

Genome biology·2026
Same author

The Phase Structure and Properties of Polyurethanes Based on Polycaprolactone Block Copolymers Dangling Side-Chain PEG.

Biomacromolecules·2026
Same author

Evolutionary Changes of <i>GT1</i> Provide Insights Into the Adaptation of Butterflies to Plant Feeding.

Ecology and evolution·2025
Same author

Overexpression of modified Bacillus thuringiensis toxin Cyt2Aa in wheat strongly enhances aphid resistance.

Journal of integrative plant biology·2025
Same author

Chromatin state analysis for regulatory features of JAZ family genes in Arabidopsis thaliana.

Plant science : an international journal of experimental plant biology·2025

This study defines plant chromatin states across multiple species using a Hidden Markov Model, creating a comprehensive Plant Chromatin State Database (PCSD) for epigenomic research.

Area of Science:

  • Plant epigenomics
  • Computational biology
  • Genomics

Background:

  • Genome-wide chromatin state maps are crucial for understanding genome annotation and regulatory activity.
  • Plant epigenomic data is essential for deciphering gene regulation.

Purpose of the Study:

  • To construct a comprehensive Plant Chromatin State Database (PCSD).
  • To integrate and visualize plant chromatin state information.
  • To facilitate comparative epigenomic analyses across species.

Main Methods:

  • Collected public and in-house plant epigenomic data.
  • Applied Hidden Markov Models (HMM) to define chromatin states.
  • Integrated data with Self-Organizing Maps (SOM) and UCSC Genome Browser.

Related Experiment Videos

Main Results:

  • Defined chromatin states across Arabidopsis thaliana, Oryza sativa, and Zea mays genomes.
  • Developed the Plant Chromatin State Database (PCSD) with detailed chromatin state information.
  • Integrated tools for differential analysis, motif discovery, and gene ontology analysis.

Conclusions:

  • The PCSD provides a valuable resource for plant epigenomic research.
  • Facilitates discovery of conserved epigenomic features and causal gene functions.
  • Supports comparative genomics and functional analysis of plant genomes.