PuSH - Publikationsserver des Helmholtz Zentrums München

Export: TXT Text RIS Endnote (RIS) BIB BibTeX
Omony, J. ; Nussbaumer, T. ; Gutzat, R.*

DNA methylation analysis in plants: review of computational tools and future perspectives.

Brief. Bioinform. 21, 906-918 (2020)
Verlagsversion Postprint Forschungsdaten DOI PMC
Open Access Gold
Genome-wide DNA methylation studies have quickly expanded due to advances in next-generation sequencing techniques along with a wealth of computational tools to analyze the data. Most of our knowledge about DNA methylation profiles, epigenetic heritability and the function of DNA methylation in plants derives from the model species Arabidopsis thaliana. There are increasingly many studies on DNA methylation in plants-uncovering methylation profiles and explaining variations in different plant tissues. Additionally, DNA methylation comparisons of different plant tissue types and dynamics during development processes are only slowly emerging but are crucial for understanding developmental and regulatory decisions. Translating this knowledge from plant model species to commercial crops could allow the establishment of new varieties with increased stress resilience and improved yield. In this review, we provide an overview of the most commonly applied bioinformatics tools for the analysis of DNA methylation data (particularly bisulfite sequencing data). The performances of a selection of the tools are analyzed for computational time and agreement in predicted methylated sites for A. thaliana, which has a smaller genome compared to the hexaploid bread wheat. The performance of the tools was benchmarked on five plant genomes. We give examples of applications of DNA methylation data analysis in crops (with a focus on cereals) and an outlook for future developments for DNA methylation status manipulations and data integration.
Impact Factor
Scopus SNIP
Web of Science
Times Cited
Scopus
Cited By
Altmetric
8.990
2.126
2
6
Tags
Anmerkungen
Besondere Publikation
Auf Hompepage verbergern

Zusatzinfos bearbeiten
Eigene Tags bearbeiten
Privat
Eigene Anmerkung bearbeiten
Privat
Auf Publikationslisten für
Homepage nicht anzeigen
Als besondere Publikation
markieren
Publikationstyp Artikel: Journalartikel
Dokumenttyp Review
Schlagwörter Epigenomics ; Epigenetics ; Bisulfite Sequencing ; Dna Methylation ; Plants ; Differentially Methylated Regions; Transgenerational Epigenetic Inheritance; Gene-expression; Cpg Islands; Quality-control; Reveals; Regions; Sequence; Insights; Patterns; Accurate
Sprache englisch
Veröffentlichungsjahr 2020
Prepublished im Jahr 2019
HGF-Berichtsjahr 2019
ISSN (print) / ISBN 1467-5463
e-ISSN 1477-4054
Zeitschrift Briefings in Bioinformatics
Quellenangaben Band: 21, Heft: 3, Seiten: 906-918 Artikelnummer: , Supplement: ,
Verlag Oxford University Press
Verlagsort Great Clarendon St, Oxford Ox2 6dp, England
Begutachtungsstatus Peer reviewed
Institut(e) Research Unit Plant Genome and Systems Biology (PGSB)
Institute of Network Biology (INET)
Institute of Environmental Medicine (IEM)
POF Topic(s) 30202 - Environmental Health
30203 - Molecular Targets and Therapies
Forschungsfeld(er) Environmental Sciences
Allergy
PSP-Element(e) G-503500-002
G-506400-001
G-503400-001
DOI 10.1093/bib/bbz039
WOS ID WOS:000537509700012
PubMed ID 31220217
Erfassungsdatum 2019-04-23
[➜Korrektur melden]