Integrative epigenomic mapping defines four main chromatin states in Arabidopsis

Roudier, François; Ahmed, Ikhlak; Bérard, Caroline; Sarazin, Alexis; Mary‐Huard, Tristan; Cortijo, Sandra; Bouyer, Daniel; Caillieux, Erwann; Duvernois-Berthet, Evelyne; Al-Shikhley, Liza; Giraut, Laurène; Despres, Barbara; Drevensek, Stéphanie; Barneche, Frédy; Dèrozier, Sandra; Brunaud, Véronique; Aubourg, Santiago P.; Schnittger, Arp; Bowler, Chris; Martin‐Magniette, Marie‐Laure; Robin, Stéphane; Caboche, Michel; Colot, Vincent

doi:10.1038/emboj.2011.103

Cited by 596 publications

(721 citation statements)

References 71 publications

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“…Following quality control, enriched domains and marked genes were identified (see Methods). A good overlap was found between previously published data (Oh et al 2008;Roudier et al 2011) and the genes detected as marked by H3K4me3 or H3K27me3 in the present work, with estimated specificity and sensitivity values ranging from 84 to 94% and from 76 to 93%, respectively. RNA-seq analysis was also performed to determine mRNA abundance in the same samples.…”

Section: Resultssupporting

confidence: 72%

Profiling spatial enrichment of chromatin marks suggests an additional epigenomic dimension in gene regulation

Chica

Szarzyńska

Chen-Min-Tao

et al. 2013

Frontiers in Life Science

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Post-translational modifications of histones are important components of chromatin-level control of genome activity in eukaryotes. In order to clarify the biological function of chromatin marks, classification methods have been developed that partition genomic regions based on their chromatin composition. Spatial enrichment of histone modifications over genes is one of the many epigenomic dimensions that reflect the impact of chromatin dynamics on gene regulation. Using a clustering approach, we have classified genes according to their H3K27me3 and H3K4me3 marking in Arabidopsis leaves and find that multiple spatial profiles with specific functional properties can be distinguished in both cases. In particular, we show that different profiles specify distinct levels of gene expression. In addition, we find that genes with different H3K27me3 profiles can be distinguished by the length of their first intron and that the length of the first exon is an important parameter that shapes the distinct H3K4me3 profiles. Finally, we suggest that profile height could be quantitatively used to estimate the relative abundance of cells in which a gene is marked, and potentially expressed, within a tissue.

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Section: Resultssupporting

confidence: 72%

Profiling spatial enrichment of chromatin marks suggests an additional epigenomic dimension in gene regulation

Chica

Szarzyńska

Chen-Min-Tao

et al. 2013

Frontiers in Life Science

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“…S7). By hybridizing the immunoprecipitated DNA to a whole-genome tiling array (ChIP-chip 14 ), we identified 851 genes bound by NLP7 in the presence of nitrate (Supplementary Data 1). Gene Ontology (GO) term analysis revealed a significant enrichment for genes involved in N-metabolism and related metabolic pathways, such as the oxidative pentose-phosphate (OPP) pathway, sulphur-and carbon-metabolism, as well as genes involved in hormone metabolism and in transport (Fig.…”

Section: Resultsmentioning

confidence: 99%

Nuclear retention of the transcription factor NLP7 orchestrates the early response to nitrate in plants

et al. 2013

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Nitrate is both an important nutrient and a signalling molecule for plants. Although several components of the nitrate signalling pathway have been identified, their hierarchical organization remains unclear. Here we show that the localization of NLP7, a member of the RWP-RK transcription factor family, is regulated by nitrate via a nuclear retention mechanism. Genome-wide analyses revealed that NLP7 binds and modulates a majority of known nitrate signalling and assimilation genes. Our findings indicate that plants, like fungi and mammals, rely on similar nuclear retention mechanisms to instantaneously respond to the availability of key nutrients.

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“…Second, the tails of the histone proteins that constitute the nucleosomes can be subjected to post‐translational modifications, such as acetylation, methylation, ubiquitination, phosphorylation, and glycosylation. Histone marks have either a repressive or an activating effect on gene expression, and usually colocalize to define specific chromatin states that determine gene activity (Roudier et al., 2011; Sequeira‐Mendes et al., 2014). Active genes are usually marked with H3K4me3, H2Bub, H3K9ac, and H3K36me3, while repressed genes are marked with H3K27me3 and H2Aub.…”

Section: The Role Of Chromatin Modifications In Somatic Embryogenesismentioning

confidence: 99%

A transcriptional view on somatic embryogenesis

2017

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Somatic embryogenesis is a form of induced plant cell totipotency where embryos develop from somatic or vegetative cells in the absence of fertilization. Somatic embryogenesis can be induced in vitro by exposing explants to stress or growth regulator treatments. Molecular genetics studies have also shown that ectopic expression of specific embryo‐ and meristem‐expressed transcription factors or loss of certain chromatin‐modifying proteins induces spontaneous somatic embryogenesis. We begin this review with a general description of the major developmental events that define plant somatic embryogenesis and then focus on the transcriptional regulation of this process in the model plant Arabidopsis thaliana (arabidopsis). We describe the different somatic embryogenesis systems developed for arabidopsis and discuss the roles of transcription factors and chromatin modifications in this process. We describe how these somatic embryogenesis factors are interconnected and how their pathways converge at the level of hormones. Furthermore, the similarities between the developmental pathways in hormone‐ and transcription‐factor‐induced tissue culture systems are reviewed in the light of our recent findings on the somatic embryo‐inducing transcription factor BABY BOOM.

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Integrative epigenomic mapping defines four main chromatin states in Arabidopsis

Cited by 596 publications

References 71 publications

Profiling spatial enrichment of chromatin marks suggests an additional epigenomic dimension in gene regulation

Profiling spatial enrichment of chromatin marks suggests an additional epigenomic dimension in gene regulation

Nuclear retention of the transcription factor NLP7 orchestrates the early response to nitrate in plants

A transcriptional view on somatic embryogenesis

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