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Eukaryotic chromatin is tightly packed into hierarchical structures, allowing appropriate gene transcription in response to environmental and developmental cues. Here, we provide a chromosome-scale de novo genome assembly of sesame with a total length of 292.3 Mb and scaffold N50 of 20.5 Mb, containing estimated 28,406 coding genes using PacBio long-reads combined with a genome-wide chromosome conformation capture (Hi-C) approach. Based on this high-quality reference genome, we detected changes of chromatin architectures between normally growth and dark treated sesame seedlings. Gene expression level was significantly higher in "A" compartment and TAD boundary regions than in "B" compartment and TAD interior regions, which is coincident with enrichment of H4K3me3 modification in these regions. Moreover, differentially expressed genes induced by dark treated were enriched in the changed TAD-related regions and genomic differential contact regions. Go enrichment analysis of differentially expressed genes showed that genes related to "Response to stress" and "Photosynthesis" functional categories were enriched which corresponds to dark treatment. These results suggested that chromatin organization is associated with gene transcription in response to dark treatment in sesame. Our results will facilitate understanding of regulatory mechanisms in response to environmental cues in plants.
This article was published in the following journal.
Name: Plant & cell physiology
Genetic information in the cell nucleus controls organismal development, responses to the environment and finally ensures own transmission to the next generations. To achieve so many different tasks, ...
Flooding due to extreme weather threatens crops and ecosystems. To understand variation in gene regulatory networks activated by submergence, we conducted a high-resolution analysis of chromatin acces...
Transcription factors (TFs) must access chromatin to bind to their response elements and regulate gene expression. A widely accepted model proposes that only a special subset of TFs, pioneer factors, ...
The cellular response to DNA breaks is influenced by chromatin compaction. To identify chromatin regulators involved in the DNA damage response, we screened for genes that affect recovery following DN...
The clonal proliferation of antigen-specific T cells during an immune response critically depends on the differential response to growth factors, such as IL-2. While activated T cells proliferate robu...
Dark chocolate is one of the richest sources of polyphenols though it has been hypothesised that the bioavailability and therefore probably the bioefficacy of epicatechin from milk chocola...
Flavanols, present in dark chocolate, were shown to induce Nitric Oxide synthesis. Since Nitric Oxide facilitates smooth muscle relaxation, it might ease the relaxation of the LES (lower e...
Scientific evidence shows that a major consume of flavonoids is associated with a minor risk of coronary disease and a modification of the gut microbiome profile. Dark chocolate has a maj...
The purpose of this graduate student study is to determine if ingestion of dark chocolate (70% cacao) will change brain frequencies between visualization at a state of rest and a state of ...
Shifts in accommodation at decreasing luminance levels are considered as principle cause for night myopia. Previous studies with laser optometers quantified the dark focus of accommodation...
An internationally recognized set of published rules used for evaluation of cancer treatment that define when tumors found in cancer patients improve, worsen, or remain stable during treatment. These criteria are based specifically on the response of the tumor(s) to treatment, and not on the overall health status of the patient resulting from treatment.
In the interphase nucleus, a condensed mass of chromatin representing an inactivated X chromosome. Each X CHROMOSOME, in excess of one, forms sex chromatin (Barr body) in the mammalian nucleus. (from King & Stansfield, A Dictionary of Genetics, 4th ed)
Adjustment of the eyes under conditions of low light. The sensitivity of the eye to light is increased during dark adaptation.
A Fanconi anemia complementation group protein that undergoes mono-ubiquitination by FANCL PROTEIN in response to DNA DAMAGE. Also, in response to IONIZING RADIATION it can undergo PHOSPHORYLATION by ataxia telangiectasia mutated protein. Modified FANCD2 interacts with BRCA2 PROTEIN in a stable complex with CHROMATIN, and it is involved in DNA REPAIR by homologous RECOMBINATION.
The mechanisms effecting establishment, maintenance, and modification of that specific physical conformation of CHROMATIN determining the transcriptional accessibility or inaccessibility of the DNA.
Bioinformatics is the application of computer software and hardware to the management of biological data to create useful information. Computers are used to gather, store, analyze and integrate biological and genetic information which can then be applied...
The process of gene expression is used by eukaryotes, prokaryotes, and viruses to generate the macromolecular machinery for life. Steps in the gene expression process may be modulated, including the transcription, RNA splicing, translation, and post-tran...