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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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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

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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.

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Epigenetic Control of Drought Acclimation in Sorghum (EPICON)

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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

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

Project description: Not available

| S-EPMC7037816 | biostudies-literature

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Rat liver. Control vs. Chemical treated, 28 days

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Integrative genomic and epigenetic analysis in cholangiocarcinoma [batch2]

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2017-07-03 | GSE89748 | GEO

Integrative genomic and epigenetic analysis in cholangiocarcinoma [batch1]

Project description:Analysis of gene expression in cholangiocarcinoma patients. Please download the supplementary file GSE89747_CCA_batch01_illumina_Gene_expression_noNorm_noBKGD.txt.gz (link below) to obtain gene expression matrix with sample IDs used in the publication.

2017-07-03 | GSE89747 | GEO

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