Project description:We show that synthesising histones with different chemical modifications can induce a transcriptional response that alters the phenotype of those cells.
Project description:Chromatin organisation is disrupted genome wide during DNA replication. On newly synthesized DNA, nucleosomes are assembled from new naïve histones and old modified histones. It remains unknown whether the landscape of histone post-translational modifications (PTMs) is copied during DNA replication or the epigenomeis perturbed. Here we develop Chromatin Occupancy after Replication, ChOR-seq, a technology that combines chromatin immunopreciptation of histone marks and purification of newly replicated DNA by streptavidin pull-down followed by next generation sequencing. We use this technology to address propagation of epigenetic states across cell division and reveal that accurate recycling of modified parental histones ensures that positional information of histone marks is faithfully reproduced on daughter strands and inherited to daughter cells.
Project description:We applied RNA-Seq analysis to investigate the involvement of the DNA damage response kinase Rad53 and core histones in the transcriptional response to a carbon source switch from 2% glucose to 3% ethanol. Cells were cultured in synthetic complete medium with 2% glucose and switched to 3% ethanol. Samples were collleted in log phase in glucose, 1 hour after the switch (acute response) or 20 hours after the switch (adaptation). The data show that subtelomeric genes are repressed in sml1 rad53 mutants irrespective of the carbon source, in a histone-dependent manner. The data further show that Rad53 is not involved in the global carbon source switch response, but specifically in the expression of switch-inducible subtelomeric genes.
Project description:Chromatin organisation is disrupted genome wide during DNA replication. On newly synthesized DNA, nucleosomes are assembled from new naïve histones and old modified histones. It remains unknown whether the landscape of histone post-translational modifications (PTMs) is copied during DNA replication or the epigenomeis perturbed. Here we develop Chromatin Occupancy after Replication, ChOR-seq, a technology that combines chromatin immunopreciptation of histone marks and purification of newly replicated DNA by streptavidin pull-down followed by next generation sequencing. We use this technology to address propagation of epigenetic states across cell division and reveal that accurate recycling of modified parental histones ensures that positional information of histone marks is faithfully reproduced on daughter strands and inherited to daughter cells.
Project description:Chromatin organisation is disrupted genome wide during DNA replication. On newly synthesized DNA, nucleosomes are assembled from new naïve histones and old modified histones. It remains unknown whether the landscape of histone post-translational modifications (PTMs) is copied during DNA replication or the epigenomeis perturbed. Here we develop Chromatin Occupancy after Replication, ChOR-seq, a technology that combines chromatin immunopreciptation of histone marks and purification of newly replicated DNA by streptavidin pull down followed by next generation sequencing. We use this technology to address propagation of epigenetic states across cell division and reveal that accurate recycling of modified parental histones ensures that positional information of histone marks is faithfully reproduced on daughter strands and inherited to daughter cells.
Project description:In eukaryotic cells, DNA is tightly packed in the nucleus in chromatin which has histones as its main protein component. Histones are subject to a large number of distinct post-translational modifications, whose sequential or combinatorial action affects genome function. Here, we report the identification of acetylation at lysine 36 in histone H3 (H3K36ac) as a modification in Arabidopsis thaliana. H3K36ac was found to be an evolutionary conserved modification in seed plants. It is highly enriched in euchromatin and very low in heterochromatin. Genome-wide ChIP-seq experiments revealed that H3K36ac is generally found at the 5â?? end of genes. Independently of gene length, H3K36ac covers about 500 bp, about two to three nucleosomes, immediately downstream of the transcriptional start. H3K36ac overlaps with H3K4me3 and the H2A.Z histone variant. The histone acetyl transferase GCN5 and the histone deacetylase HDA19 are required for normal steady state levels of H3K36ac in plants. There is negative crosstalk between H3K36ac and H3K36me3, mediated by the histone methyl transferase SDG8 and GCN5. H3K36ac levels are associated with transcriptional activity but show no linear relation. Instead, H3K36ac is a binary indicator of transcription Characterization of the genome-wide distribution of H3K36ac using ChIP-seq. Analysis of the mechanistic crosstalk in the deposition of acetylation and methylation at H3K36 by ChIP-seq of H3K36ac and H3K36me3 in sdg8-2 and gcn5-1, respectively.