Project description:We investigated the chromatin modifications H3K4me3 and H3K27me3 in the A. thaliana shoot phloem companion cells using INTACT reporter lines. Samples were collected in two biological replications.
Project description:Histone modifications play an integral role in plant development, but have been poorly studied in woody plants. Investigating chromatin organization in wood-forming tissue and its role in regulating gene expression allows us to understand the mechanisms underlying cellular differentiation during xylogenesis (wood formation) and identify novel functional regions in plant genomes. However, woody tissue poses unique challenges for using high-throughput chromatin immunoprecipitation (ChIP) techniques for studying genome-wide histone modifications in vivo. We investigated the role of the modified histone H3K4me3 (trimethylated lysine 4 of histone H3) in gene expression during the early stages of wood formation using ChIP-seq in Eucalyptus grandis, a woody biomass model. Plant chromatin fixation and isolation protocols were optimized for developing xylem tissue collected from field-grown E. grandis trees. A “nano-ChIP-seq” procedure was employed for ChIP DNA amplification. Over 9 million H3K4me3 ChIP-seq and 18 million control paired-end reads were mapped to the E. grandis reference genome for peak-calling using Model-based Analysis of ChIP-Seq. The 12,177 significant H3K4me3 peaks identified covered ~1.5% of the genome and overlapped some 9,623 protein-coding genes and 38 noncoding RNAs. H3K4me3 library coverage, peaking ~600 - 700 bp downstream of the transcription start site, was highly correlated with gene expression levels measured with RNA-seq. Overall, H3K4me3-enriched genes tended to be less tissue-specific than unenriched genes and were overrepresented for general cellular metabolism and development gene ontology terms. Relative expression of H3K4me3-enriched genes in developing secondary xylem was higher than unenriched genes, however, and highly expressed secondary cell wall-related genes were enriched for H3K4me3 as validated using ChIP-qPCR. In this first genome-wide analysis of a modified histone in a woody tissue, we developed optimized a ChIP-seq procedure suitable for field-collected samples. In developing E. grandis xylem, H3K4me3 enrichment is an indicator of active transcription, consistent with its known role in sustaining pre-initiation complex formation in yeast. The H3K4me3 ChIP-seq data from this study paves the way to understanding the chromatin landscape and epigenomic architecture of xylogenesis in plants, and complements RNA-seq evidence of gene expression for the future improvement of the E. grandis genome annotation. Examination of H3K4me3 in developing secondary xylem tissue from two clonal individuals of E. grandis growing in the field
Project description:The study set out to assess the genome-wide distribution of the chromatin modifications H3K4me3 and H3K27me3 in mature thymic epithelial cells. ChIP and input DNA was prepared from biological replicated FACS sorted mature mTEC samples and sequenced.
Project description:Mammalian Rif1 defines the architecture of replication-timing domains interactions through the three-dimensional organization of the nuclear volume. Deletion of RIf1 in mammalian cells causes an initial alteration of three-dimensional chromatin organization which impacts first on replication timing and genome stability, but has long-term indirect repercussions also on gene expression
Project description:Ribosome profiling of MDA-MB-231 cells treated with Silvestrol to monitor transcriptome wide, eIF4A-dependent changes in translation efficiency Translation efficiency (TE) of mRNAs dervied from ribosome footprints was monitored in the presence or absence of 25 nM Silvestrol, an inhibitor of eukaryotic translation initiation factor 4A (eIF4A). Transcripts with reduced TE in the presence of Silvestrol were compare to transcripts with reduced TE in the presence of INK128, a catalytic mTOR inhbitor.
Project description:. In this study, we have investigated the capacities of last-generation Ultra-High Resolution Q-Tof systems to deal with high complexity intact protein samples, have developed the tools to process the intact protein data in an existing label-free quantification pipeline, and have evaluated the approach on a cohort of patients suffering from neurodegenerative disease in a proof-of concept study. Several proteoforms have been pointed out for their capacity to distinguish Alzheimer disease patients from patients suffering from other neurodegenerative disease and have been characterized.
Project description:We investigated the transcriptomes and differential gene expression at the Arabidopsis shoot meristem during flowering using INTACT reporter lines. Samples were collected in four biological replications.