Temporal dynamics of histone modification H3K9/14ac, H3K27ac, H3K4me3, H3K27me3, and H3K36me3 after wounding in Arabidopsis thaliana.
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ABSTRACT: After wounding in plants, a vast and rapid transcriptional reprogramming takes place. Interestingly, this reprogramming includes the reactivation of developmental regulators that in mature tissue normally are epigenetically repressed. We evaluated which histone modifications are associated with this rapid increase of these developmental regulators.
Project description:In a previous study, we found that wound-induced transcriptional expression is strongly correlated with an increase of the level of acetylation of the N-tails of histone 3. To investigate if the increase in histone acetylation is a prerequisite for the induction of wound-induced gene expression, we performed in another experiment the transcriptional profiling of wounded roots with and without treatment with γ-butyrolactone (MB3), a chemical inhibitor of GNAT-MYST family of histone acetyltransferase. In this experiment, to test whether the transcriptional changes we observed in presence of MB3 can be correlated with changes in the epigenetic landscape, we assessed by ChIP-sequencing the impact of MB3 on the enrichment levels of histone marks H3K4me3, H3K27me3, H3K27ac and H3K9/14ac, using H3 as a normalization reference.
Project description:Time course transcriptional profiling after wounding of 7 day old Arabidopsis roots, cut into 0.3 mm pieces. Samples were taken at 0 h, 1 h, 3 h, 6 h and 12 h after wounding.
Project description:In a previous study, we found that wound-induced transcriptional expression is strongly correlated with an increase of the level of acetylation of the N-tails of histone 3. To investigate if the increase in histone acetylation is a prerequisite for the induction of wound-induced gene expression, we performed transcriptional profiling of wounded roots with and without treatment with γ-butyrolactone (MB3), a chemical inhibitor of GNAT-MYST family of histone acetyltransferase .
Project description:Somatic cell reprogramming towards induced pluripotent stem cells (iPSCs) holds great promise in future regenerative medicine, however, the reprogramming process mediated by the traditional defined factors (OSNK) is slow and extremely inefficient. Here we show that a combination of modified reprogramming factors (OySyNyK), in which the transactivation domain of the Yes-associated protein is fused to OCT4, SOX2 and NANOG respectively, could be used to establish a highly efficient and rapid reprogramming system for iPSC generation. We show that the efficiency of OySyNyK-induced iPSCs was up to 100-fold higher than that of induction by traditional OSNK. Moreover we show that the reprogramming by OySyNyK is very rapid (initiated at 24 h versus 5 d by OSNK). Compared with OSNK, we found that OySyNyK factors significantly increased the expression of Tet1/2 at the early stage, which will interact with OSNK factors, and co-occupy pluripotency loci in the genome for somatic cell reprogramming. Our studies not only establish a rapid and highly efficient iPSC reprogramming system, but also uncover a novel mechanism by which OSNK factors coordinate with TET proteins to regulate 5hmC-mediated epigenetic control, thereby promoting somatic cell reprogramming. We examined DNA hydroxymethylation progression of reprogramming intermediates. To this end, we profiled the genome-wide 5hmC distribution in MEFs, the reprogramming intermediates at different stages induced by either the OSNK or OySyNyK methods, and iPSCs using the chemical capture approach
Project description:DELLA proteins act as hubs that relay environmental information to the multiple transcriptional circuits that control growth and development through physical interaction with transcription factors from different families. We have analyzed the presence of one DELLA protein at the Arabidopsis genome by chromatin immunoprecipitation coupled to large-scale sequencing and we find that it binds at the promoters of multiple genes. Enrichment analysis shows a strong preference for cis elements recognized by specific transcription factor families. In particular, we demonstrate that DELLA proteins are recruited by type-B ARABIDOPSIS RESPONSE REGULATORS (ARR) to the promoters of cytokinin-regulated genes, where they act as transcriptional co-activators. The biological relevance of this mechanism is underpinned by the necessity of simultaneous presence of DELLAs and ARRs to restrict root meristem growth and to promote photomorphogenesis. Provided are 3 biological replicates analysing RGA binding sites in Arabidopsis seedlings. ChIP-seq was performed on plants expressing RGA-GFP under the native RGA promoter and on non-transgenic control plants as reference
Project description:Analysis of chromatin state during differentiation of alveolar epithelial type 2 (AT2) cells into AT1 cells. Timepoints taken at Day 0 (AT2 cell), and Day 8 in culture (AT1-like cells). Examination of 2 different histone modifications in 2 cell types.
Project description:Ciona develops according to a stereotyped or invariant lineage. This allowed us to collect precisely defined replicates of all eight blastomeres of the right half of the embryo at the 16-cell stage of Ciona. We manually dissected each embryo, collecting and identifying each cell before library preparation and single-cell RNA-seq to give us a data set of 8 blastomeres x 4 embryos (32 cells). We sequenced these on MiSeq and HiSeq 2500. A fifth embryo was only sequenced on MiSeq and excluded from subsequent analysis.
Project description:Transcription factor-induced reprogramming of somatic cells to pluripotency is a very inefficient process, probably due to the existence of important epigenetic barriers that are imposed during differentiation and that contribute to preserve cell identity. In an effort to decipher the molecular nature of these barriers, we followed a genome-wide approach, in which we identified macro histone variants (macroH2A) as highly expressed in human somatic cells but downregulated after reprogramming to pluripotency, as well as strongly induced during differentiation. Knock down of macro histone variants in human keratinocytes increased the efficiency of reprogramming to pluripotency, while overexpression had opposite effects. Genome-wide occupancy profiles show that in human keratinocytes macroH2A.1 preferentially occupies genes that are expressed at low levels and are marked with H3K27me3, including pluripotency-related genes and bivalent developmental regulators, at which its presence prevents the regain of H3K4me2 during reprogramming, over imposing an additional layer of repression that preserves cell identity. Gemone wide occupancy of HA:macroH2A.1 in human keratinocytes
Project description:To date there are very few tools to reverse the induced dedifferentiation program in CRPC and to improve the response to the androgen deprivation therapy. Here we report that MAT2A is an important oncogenic cofactor of ERG/EZH2 transcriptional reprogramming impacting significantly the androgenic pathway. Using RNA sequencing coupled with ATAC, here we reveal an important link between ERG/MAT2A and EZH2 that impact on AR signaling pathway. This aberrant epigenetic program can be reversed by MAT2A inhibition which establish a near physiologic AR transcriptional program. Targeting MAT2A alone or in combination with EZH2 inhibitors reverse stemness in multiple models including prostatospheres from human PDX and GEM models of aggressive prostate cancer. Targeting MAT2A enhance the sensitivity to the androgenic blockade by Enzalutamide and to EZH2 inhibitors