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Mass Spectrometry Analysis of Histone Modifications in Sorghum during Drought Acclimation

ABSTRACT: This bottom-up analysis is the supplementary data file to the top-down analysis deposited with identifier PXD014660. The peptide data are used to support assignments of modifications detected in top-down. Details are described in the associated manuscript.

INSTRUMENT(S): Q Exactive HF

ORGANISM(S): Sorghum Bicolor

TISSUE(S): Leaf

SUBMITTER: Matthew Monroe

LAB HEAD: Ljiljana Pasa-Tolic

PROVIDER: PXD015508 | Pride | 2019-10-30

REPOSITORIES: Pride

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Dataset's files

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			Action	DRS
	EPICONyr1_Sorghum_histoneBU_15Nov18_Merry_18-09-02.raw	Raw
	EPICONyr1_Sorghum_histoneBU_15Nov18_Merry_18-09-02.raw_20181207trypsin.byparms	Raw
	EPICONyr1_Sorghum_histoneBU_15Nov18_Merry_18-09-02.raw_20181207trypsin.byrslt	Raw
	EPICONyr1_Sorghum_histoneBU_15Nov18_Merry_18-09-02.raw_20181207trypsin.xlsx	Xlsx
	UniProt_sorghum_focus.fasta	Fasta

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Publications

Top-down mass spectrometry of histone modifications in sorghum reveals potential epigenetic markers for drought acclimation.

Zhou Mowei M Malhan Neha N Ahkami Amir H AH Engbrecht Kristin K Myers Gabriel G Dahlberg Jeffery J Hollingsworth Joy J Sievert Julie A JA Hutmacher Robert R Madera Mary M Lemaux Peggy G PG Hixson Kim K KK Jansson Christer C Paša-Tolić Ljiljana L

Methods (San Diego, Calif.) 20191023

Sorghum [Sorghum bicolor (L.) Moench] is an important cereal crop noted for its ability to survive water-limiting conditions. Herein, we present an analytical workflow to explore the changes in histone modifications through plant developmental stages and two drought stresses in two sorghum genotypes that differ in their response to drought. Top-down mass spectrometry (MS) is an ideal method to profile histone modifications and distinguish closely related histone proteoforms. We analyzed leaves o ...[more]

PMID: 31655121

Similar Datasets

Top-Down Mass Spectrometry Analysis of Histone Modifications in Sorghum during Drought Acclimation

Project description:This study explores the changes in histone modifications of sorghum bicolor through developmental stages and in response to drought stress in two sorghum genotypes. We analyzed the leaves of 48 plants using top-down mass spectrometry and identified 26 unique histone proteins and 677 unique histone proteoforms. We detected trimethylation on nearly all H2B N-termini where acetylation is commonly expected. In addition, an unexpected modification on H2A histones was assigned to N-pyruvic acid 2-iminylation based on its unique neutral loss of CO2.

2019-10-30 | PXD014660 | Pride

Epigenetic Control of Drought Acclimation in Sorghum (EPICON): Leaf and Root Proteomics

Project description:Two cultivars of Sorghum biocolor were examined from a study performed at the Kearney Research Station in California; 1) a pre-flowering drought tolerant, post-flowering drought susceptible cultivar RTx430 and 2) a pre-flowering drought susceptible, post-flowering drought-tolerant cultivar BTx642. Samples are from leaves and roots collected at 2, 3, 4, 6, 8, 9, 10, 11, 13, 15, 17 weeks post soil emergence and under a perturbation of either well-watered (control), pre-flowering drought, or post-flowering drought. A liquid-based bottom up proteomics analysis was performed using an iTRAQ labeling multiplexing approach to determine relative abundances. After the peptides were digested with trypsin and iTRAQ labeled, they were fractionated into 12 fractions offline using a C-18 column under high-pH solvent conditions Each fraction was further separated on a low pH C-18 column with direct infusion into a ThermoScientific Q-Exactive mass spectrometer. See the supplementary files for iTRAQ reporter ions details.

2018-06-21 | MSV000082487 | MassIVE

Epigenetic Control of Drought Acclimation in Sorghum (EPICON)

Project description:Two cultivars of sorghum were examined from a study performed at the Kearney Research Station in California; 1) a pre-flowering drought tolerant, post-flowering drought susceptible cultivar RTx430 and 2) a pre-flowering drought susceptible, post-flowering drought-tolerant cultivar BTx642. These data are the methanol/water metabolite fraction obtained from a Folsh extraction from Sorghum bicolor leaves and roots. The metabolites were derivatized and analyzed via GC-MS at PNNL. Analyses represent the metabolite profile collected at 2, 3, 4, 6, 8, 9, 10, 11, 13, 15, 17 weeks post soil emergence and under a perturbation of either well-watered (control), pre-flowering drought, or post-flowering drought.

2017-10-23 | MSV000081639 | MassIVE

Drought-responsive small RNAs in Sorghum bicolor (L.) Moench

Project description:The present study is expected to reveal regulatory network of small RNAs under drought in Sorghum (Sorghum bicolor (L.) Moench). Sorghum genotype drought tolerant (DT) and drought susceptible (DS) were grown at 28-32 degrees C day/night temperature with 12/12 h light/dark period in the phytotron glass house. The fully opened uppermost leaves from control and drought stressed seedlings were sampled and stored at -80 degrees C, and used for generation of a small RNA library. Total RNA was isolated from the leaves using the TRIzol reagent (Invitrogen, USA). Small RNA sequencing libraries were prepared using Illumina Truseq small RNA Library preparation kit following manufacturer's protocol and these libraries were sequenced on GAIIx platform (Illumina Inc., USA). Small RNA reads contaminated with poor-quality and adaptor sequences were trimmed by using the UEA sRNA workbench 2.4- Plant version sequence file pre-processing (http://srna-tools.cmp.uea.ac.uk/). Then, all unique reads were submitted to the UEA sRNA toolkit-Plant version miRCat pipeline (http://srna-tools.cmp.uea.ac.uk/) to predict novel miRNAs from high-throughput small RNA sequencing data.

2014-04-15 | E-MTAB-1630 | biostudies-arrayexpress

GNPS - Epigenetic Control of Drought Acclimation in Sorghum (EPICON)

2017-10-23 | MSV000081639 | GNPS

Rat liver: Control vs. Chemical treated, 14 days

Project description:The final goal of this study is to develop a short term and highly accurate prediction method of carcinogenicity based on gene expression profiles of rats subjected to carcinogen exposure. We conducted 3 day-, 14 day- and 28 day-repeated dose experiments in male F344 rats with 47 carcinogens and 26 non-carcinogens, and the gene expression profiles in liver were investigated by custom glass microarrays. Supplementary file "73 Compounds for training" indicates 47 carcinogens and 26 non-carcinogens. Supplementary file "15 Compounds for test" lists the other compounds which are for test.

2009-06-23 | GSE16743 | GEO

Rat liver. Control vs. Chemical treated, 3 days

Project description:The final goal of this study is to develop a short term and highly accurate prediction method of carcinogenicity based on gene expression profile of rats administrated by carcinogens. We conducted 3 days-, 14 days- and 28 days-repeated dose experiments in male F344 rats with 47 carcinogens and 26 non-carcinogens, and the gene expression profiles in liver were investigated by custom glass microarrays. Supplementary file "73 Compounds for training" indicates 47 carcinogens and 26 non-carcinogens. Supplementary file "15 Compounds for test" lists the other compounds which are for test.

2009-06-22 | GSE16340 | GEO

Rat liver. Control vs. Chemical treated, 28 days

2009-06-21 | GSE16394 | GEO

Transcriptome Analysis of Drought-Resistant and Drought-Sensitive Sorghum (Sorghum bicolor) Genotypes in Response to PEG-Induced Drought Stress.

Project description:Drought is a major limiting factor of crop yields. In response to drought, plants reprogram their gene expression, which ultimately regulates a multitude of biochemical and physiological processes. The timing of this reprogramming and the nature of the drought-regulated genes in different genotypes are thought to confer differential tolerance to drought stress. Sorghum is a highly drought-tolerant crop and has been increasingly used as a model cereal to identify genes that confer tolerance. Also, there is considerable natural variation in resistance to drought in different sorghum genotypes. Here, we evaluated drought resistance in four genotypes to polyethylene glycol (PEG)-induced drought stress at the seedling stage and performed transcriptome analysis in seedlings of sorghum genotypes that are either drought-resistant or drought-sensitive to identify drought-regulated changes in gene expression that are unique to drought-resistant genotypes of sorghum. Our analysis revealed that about 180 genes are differentially regulated in response to drought stress only in drought-resistant genotypes and most of these (over 70%) are up-regulated in response to drought. Among these, about 70 genes are novel with no known function and the remaining are transcription factors, signaling and stress-related proteins implicated in drought tolerance in other crops. This study revealed a set of drought-regulated genes, including many genes encoding uncharacterized proteins that are associated with drought tolerance at the seedling stage.

| S-EPMC7037816 | biostudies-literature

Integrative genomic and epigenetic analysis in cholangiocarcinoma [batch2]

Project description:Analysis of gene expression in cholangiocarcinoma patients. Please download the supplementary file GSE89748_CCA_batch02_illumina_Gene_expression_noNorm_noBKGD.txt.gz (link below) to obtain gene expression matrix with sample IDs used in the publication.

2017-07-03 | GSE89748 | GEO