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High-resolution mapping of H4K16 and H3K23 acetylation reveals conserved and unique distribution patterns and functions in Arabidopsis and rice

ABSTRACT: We generated genome-wide high-resolution maps of H4K16ac and H3K23ac in Arabidopsis thaliana and Oryza sativa.

ORGANISM(S): Arabidopsis thaliana Oryza sativa

PROVIDER: GSE69426 | GEO | 2015/12/01

SECONDARY ACCESSION(S): PRJNA285469

REPOSITORIES: GEO

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High-resolution mapping of H4K16 and H3K23 acetylation reveals conserved and unique distribution patterns in Arabidopsis and rice.

Project description:Histone acetylation and deacetylation are key epigenetic gene regulatory mechanisms that play critical roles in eukaryotes. Acetylation of histone 4 lysine 16 (H4K16ac) is implicated in many cellular processes. However, its biological function and relationship with transcription are largely unexplored in plants. We generated first genome-wide high-resolution maps of H4K16ac in Arabidopsis thaliana and Oryza sativa. We showed that H4K16ac is preferentially enriched around the transcription start sites and positively correlates with gene expression levels. Co-existence of H4K16ac and H3K23ac is correlated with high gene expression levels, suggesting a potentially combinatorial effect of H4K16ac and H3K23ac histone 3 lysine 23 acetylation on gene expression. Our data further revealed that while genes enriched with both H4K16ac and H3K23ac are ubiquitously expressed, genes enriched with only H4K16ac or H3K23ac showed significantly distinct expression patterns in association with particular developmental stages. Unexpectedly, and unlike in Arabidopsis, there are significant levels of both H4K16ac and H3K23ac in the lowly expressed genes in rice. Furthermore, we found that H4K16ac-enriched genes are associated with different biological processes in Arabidopsis and rice, suggesting a potentially species-specific role of H4K16ac in plants. Together, our genome-wide profiling reveals the conserved and unique distribution patterns of H4K16ac and H3K23ac in Arabidopsis and rice and provides a foundation for further understanding their function in plants.

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Profile of H4K16 acetylation in undifferentiated ES cells [Illumina BeadArray data]

Project description:Level of H4K16ac on highest and lowest expressed genes in undifferentiated ES cells

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Gain and loss of H4K16 acetylation during ES cell differentiation [NimbleGen ChIP-chip]

Project description:H4K16ac is gained on hox loci and lost on pluripotency genes upon differentiation ChIP on chip over hox loxi and pluripotency genes for H4K16ac in undifferentiated ES cells and after 3 days of retinoic acid treatment

2013-08-23 | E-GEOD-43099 | biostudies-arrayexpress

Gain and loss of H4K16 acetylation during ES cell differentiation [Agilent arrays]

Project description:Genome wide gain and loss of H4K16ac upon differentiation correlated with changes in expression.

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Profile of H4K16 acetylation in undifferentiated ES cells [Illumina BeadArray data]

Project description:Level of H4K16ac on highest and lowest expressed genes in undifferentiated ES cells 3 biological replicates in undifferentiated ES cells

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Gain and loss of H4K16 acetylation during ES cell differentiation [NimbleGen ChIP-chip]

Project description:H4K16ac is gained on hox loci and lost on pluripotency genes upon differentiation

2013-08-23 | GSE43099 | GEO

EIN2 mediates histone H3K14 and non-canonical histone H3K23 acetylation in the nucleus in ethylene response [ChIP-seq]

Project description:We report that ethylene specifically elevated acetylation of histone H3 at K14 and the non-canonical acetylation of histone H3 at K23. We perform Chip-sequencing of H3K14Ac, H3K23Ac and H3K9Ac using chromatins isolated from 3-day old etiolated Col-0 seedlings treated with ethylene or air gas. Results show that ethylene specifically elevates H3K14Ac and non-canonical H3K23Ac in EIN3 targeted genes that are regulated at the transcriptional level by ethylene.

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Gain and loss of H4K16 acetylation during ES cell differentiation [Agilent arrays]

Project description:Genome wide gain and loss of H4K16ac upon differentiation correlated with changes in expression. Gene expression in undifferentiated ES cells, and cells after 3 days of differentiation in retinoic acid. 3 biological replicates with two technical replicates were performed for each sample.

2013-08-23 | E-GEOD-43101 | biostudies-arrayexpress

High-resolution mapping of H4K16 and H3K23 acetylation reveals conserved and unique distribution patterns and functions in Arabidopsis and rice

Project description:High-resolution mapping of H4K16 and H3K23 acetylation reveals conserved and unique distribution patterns and functions in Arabidopsis and rice

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PHF20 readers link methylation of histone H3K4 and p53 with H4K16 acetylation

Project description:PHF20 is a core component of the lysine acetyltransferase complex MOF-NSL that produces the major epigenetic mark, H4K16ac, and is necessary for transcriptional regulation and DNA repair, however the role of PHF20 in the complex remains elusive. Here, we report on functional crosstalk between epigenetic readers of PHF20. We show that the PHF20 PHD finger recognizes dimethylated lysine 4 of histone H3 (H3K4me2) and represents first example of a native PHD reader selective for this modification. Biochemical and structural analyses illuminate the molecular mechanism underlying this function and explain the preference of Tudor2, another reader in PHF20, for dimethylated p53. Binding of the PHD finger to H3K4me2 is required for histone acetylation, accumulation of PHF20 at target genes, and transcriptional activation. Together, our findings establish a novel PHF20-mediated link between MOF HAT, p53 and H3K4me2-dependent cellular events and suggest a model for rapid spreading of H4K16ac-encriched open chromatin.

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