Genome-wide profiling of H3K4me3 and H3K27me3 modifications during and after vernalization in Brachypodium

Vernalization, the requirement of long-term exposure to low environmental temperature for flowering, is a typical epigenetic phenomenon in plants. Histone modifications have been analyzed for key vernalization genes, but genome-wide regulation remains unclear. Here, we performed global analysis of histone 3 lysine 4 (H3K4me3) and 27 (H3K27me3) trimethylation with Chromatin Immunoprecipitation-Sequencing (ChIP-Seq) during and after vernalization to obtain complete view of histone modification fluctuation both on whole genome scale and for single genes, even different regions of genes. The critical role of H3K27me3 was revealed. During vernalization H3K27me3 regulation concentrated on a few biological processes, with two essential environmental responses, transcription regulation and anti-stress reactions, being main targets, as indicated by change pattern and GO analysis. The regulation of H3K4me3, however, showed no obvious focus. For gene expression, H3K27me3 is involved in multiple trends of control. H3K4me3, however, mainly focuses on unidirectional regulation. After vernalization most of H3K27me3 changes were kept, but relatively small proportion of H3K4me3 changes could be maintained, as shown by multiple-level analysis, suggesting the active role of H3K27me3 in epigenetic memory. Vernalization-induced histone modification changes were uncovered for VRN3, a gene integrating vernalization/photoperiod signals, suggesting its regulation role at epigenetic level. Memory-related genes were genome-widely identified and a high proportion of them showed quantitative response to vernalization-treatment, suggesting broad existence of this mechanism. Our studies shed new light on epigenetic role of H3K27me3 and VRN3 in vernalization, revealed mechanism underlying epigenetic memory, which helps us to further understand vernalization, a mechanism with great potential in agriculture.

Dataset features

Information

Specifications

Application:	ChIP-seq analysis
Number of samples:	7
Release date:	May 22 2018
Last update date:	Aug 21 2018
Access:	Public
Dataset link	Genome-wide profiling of H3K4me3 and H3K27me3 modifications during and after vernalization in Brachypodium

Experimental Protocol

Examination of 2 different histone modifications (H3K4me3 and H3K27me3) in 3 differently vernalized Brachypodium seedlings (V0,V30 and V30N). And another one H3K4me3 sequencing in non-vernalized seedlings (H3K4me3_V0_2) is the biological replication.

Repositories

GEO

GSE93140

ENA

SRP096034

BioProject

PRJNA360125

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Contact

Qing Huan