Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Whole-genome methylome sequencing (EM-seq) of Arabidopsis thaliana Col-0, nuclear-envelope mutants crwn1–4, crwn1 crwn4 and kaku4 at 12 and 150 days after sowing under short-day conditions

ABSTRACT: Enzymatic methyl-seq (EM-seq) was used to profile whole-genome cytosine methylation in Arabidopsis thaliana wild type and nuclear-envelope mutants that display premature aging phenotypes. All lines are in the Col-0 background and include wild-type Col-0, single mutants in crwn1, crwn2, crwn3, crwn4 and kaku4, the crwn1 crwn4 double mutant, and a second-generation kaku4 line (kaku4-G2). For late-age samples, rosette tissue was harvested from soil-grown plants under short-day conditions (8 h light / 16 h dark) at 150 days after sowing, when nuclear-envelope mutants show strong rosette senescence, meristem failure and reduced lifespan. For young reference samples, whole seedlings of Col-0 (wildtype) and kaku4-G2 were collected at 12 days after sowing. For each genotype and age, pooled material from multiple plants was used to obtain sufficient genomic DNA. Genomic DNA was extracted from each pooled sample and converted using the NEBNext Enzymatic Methyl-seq (EM-seq) protocol, followed by Illumina library preparation and paired-end high-throughput sequencing. This dataset is used to (i) quantify genome-wide CG, CHG and CHH methylation in wild type and nuclear-envelope mutants, (ii) compare age-dependent methylation drift between 12-day seedlings and 150-day short-day rosettes, and (iii) identify chromatin-state- and transposable-element-specific methylation changes associated with nuclear-envelope dysfunction and premature aging in Arabidopsis.

INSTRUMENT(S): Illumina NovaSeq 6000, Liquid-nitrogen mortar and pestle, benchtop microcentrifuge, vortex mixer, Covaris sonicator, PCR thermocycler, magnetic rack for SPRI bead clean-up, Controlled-environment growth chamber (short-day; 8 h light / 16 h dark), Dissecting tools, liquid nitrogen, −80 °C freezer

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Oscar Juez

PROVIDER: E-MTAB-16263 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Chloroplast is a major plant cell organelle that fulfills essential metabolic and biosynthetic functions. Located at the interface between the chloroplast and other cell compartments, the chloroplast envelope system is a strategic barrier controlling exchanges of ions, metabolites and proteins, thus regulating essential metabolic functions (synthesis of hormones precursors, amino acids, pigments, sugars, vitamins, lipids, nucleotides…) of the plant cell. However, chloroplast envelope membranes remain the hidden part of the chloroplast proteome and many envelope proteins remain to be characterized (known but uncharacterized envelope proteins) or identified (orphan known envelope-associated functions carried by unidentified proteins) Indeed, the envelope contains only 1% of the chloroplast proteins (i.e. 0.25% of the whole cell proteome). When comparing the composition crude leaf extract and purified envelope vesicles, a high theoretical enrichment factor (EF) of specific envelope proteins is thus expected. This is especially true for minor envelope proteins (e.g. representing 1/100 or 1/1000 of the envelope protein content). Sensitivity of MS technique has been greatly improved during the last decade. Today, thanks to the continuous improvement of MS techniques, we are able to detect more components in a complex sample, to generate quantitative data and to statistically validate above-cited enrichment factor. Here, we have taken advantage of present-days better MS sensitivity towards a better definition (differentiate genuine envelope proteins from contaminants) of the chloroplast envelope proteome. This MS- and statistical-based analysis relied on an enrichment factor calculated for each protein identified in purified envelope fractions when compared to the value obtained for the same protein in crude cell extracts. Using this approach, a total of 1376 proteins was detected in purified envelope fractions, of which, more than 500 could be assigned an envelope localization combining MS-based statistical analyses and manual annotation using data from the literature or prediction tools. Interestingly, many of such proteins being unknown or unexpected envelope components, these data constitute a new resource of significant value to the broader plant science community aiming to define principles and molecular mechanisms controlling fundamental aspects of plastid biogenesis and functions.

Dataset Information

Whole-genome methylome sequencing (EM-seq) of Arabidopsis thaliana Col-0, nuclear-envelope mutants crwn1–4, crwn1 crwn4 and kaku4 at 12 and 150 days after sowing under short-day conditions

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