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

Abstract

Sorghum [Sorghum bicolor (L.) Moench] is an important cereal crop noted for its ability to survive water-limiting conditions. In this paper, 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 of 48 plants and identified 26 unique histone proteins and 677 unique histone proteoforms (124 full-length and 553 truncated 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. Interestingly, some of the truncated histones, in particular H4 and H3.2, showed significant changes that correlated with the growth and water conditions. Furthermore, the histone proteoforms could serve as targets in search of chromatin modifiers and ultimately have important ramifications in future attempts of studying plant epigenetic reprogramming under stress.

Authors:
ORCiD logo [1];  [1];  [1];  [1];  [1];  [2];  [2];  [2];  [3];  [4];  [4];  [1];  [1];  [1]
+ Show Author Affiliations
  1. Pacific Northwest National Lab. (PNNL), Richland, WA (United States). Environmental Molecular Sciences Laboratory (EMSL)
  2. UC-ANR Kearney Agricultural Research & Extension Center, Parlier, CA (United States)
  3. Univ. of California, Davis, CA (United States)
  4. Univ. of California, Berkeley, CA (United States)
Publication Date:
Research Org.:
Pacific Northwest National Laboratory (PNNL), Richland, WA (United States). Environmental Molecular Sciences Laboratory (EMSL); University of California, Berkeley, CA (United States); Joint BioEnergy Institute (JBEI), Emeryville, CA (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER); USDA
OSTI Identifier:
1660761
Alternate Identifier(s):
OSTI ID: 1773357; OSTI ID: 1809705
Report Number(s):
PNNL-SA-145507
Journal ID: ISSN 1046-2023
Grant/Contract Number:  
SC0014081; AC02-05CH11231; AC05-76RL01830
Resource Type:
Accepted Manuscript
Journal Name:
Methods
Additional Journal Information:
Journal Volume: 184; Journal Issue: SI; Journal ID: ISSN 1046-2023
Publisher:
Elsevier
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Drought; Epigenetics; Histone clipping; Post-translational modifications; Sorghum; Top-down mass spectrometry

Citation Formats

Zhou, Mowei, Malhan, Neha, Ahkami, Amir H., Engbrecht, Kristin, Myers, Gabriel, Dahlberg, Jeffery, Hollingsworth, Joy, Sievert, Julie A., Hutmacher, Robert, Madera, Mary, Lemaux, Peggy G., Hixson, Kim K., Jansson, Christer, and Paša-Tolić, Ljiljana. Top-down mass spectrometry of histone modifications in sorghum reveals potential epigenetic markers for drought acclimation. United States: N. p., 2019. Web. doi:10.1016/j.ymeth.2019.10.007.
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Zhou, Mowei, Malhan, Neha, Ahkami, Amir H., Engbrecht, Kristin, Myers, Gabriel, Dahlberg, Jeffery, Hollingsworth, Joy, Sievert, Julie A., Hutmacher, Robert, Madera, Mary, Lemaux, Peggy G., Hixson, Kim K., Jansson, Christer, & Paša-Tolić, Ljiljana. Top-down mass spectrometry of histone modifications in sorghum reveals potential epigenetic markers for drought acclimation. United States. https://doi.org/10.1016/j.ymeth.2019.10.007
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Zhou, Mowei, Malhan, Neha, Ahkami, Amir H., Engbrecht, Kristin, Myers, Gabriel, Dahlberg, Jeffery, Hollingsworth, Joy, Sievert, Julie A., Hutmacher, Robert, Madera, Mary, Lemaux, Peggy G., Hixson, Kim K., Jansson, Christer, and Paša-Tolić, Ljiljana. Wed . "Top-down mass spectrometry of histone modifications in sorghum reveals potential epigenetic markers for drought acclimation". United States. https://doi.org/10.1016/j.ymeth.2019.10.007. https://www.osti.gov/servlets/purl/1660761.
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@article{osti_1660761,
title = {Top-down mass spectrometry of histone modifications in sorghum reveals potential epigenetic markers for drought acclimation},
author = {Zhou, Mowei and Malhan, Neha and Ahkami, Amir H. and Engbrecht, Kristin and Myers, Gabriel and Dahlberg, Jeffery and Hollingsworth, Joy and Sievert, Julie A. and Hutmacher, Robert and Madera, Mary and Lemaux, Peggy G. and Hixson, Kim K. and Jansson, Christer and Paša-Tolić, Ljiljana},
abstractNote = {Sorghum [Sorghum bicolor (L.) Moench] is an important cereal crop noted for its ability to survive water-limiting conditions. In this paper, 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 of 48 plants and identified 26 unique histone proteins and 677 unique histone proteoforms (124 full-length and 553 truncated 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. Interestingly, some of the truncated histones, in particular H4 and H3.2, showed significant changes that correlated with the growth and water conditions. Furthermore, the histone proteoforms could serve as targets in search of chromatin modifiers and ultimately have important ramifications in future attempts of studying plant epigenetic reprogramming under stress.},
doi = {10.1016/j.ymeth.2019.10.007},
journal = {Methods},
number = SI,
volume = 184,
place = {United States},
year = {Wed Oct 23 00:00:00 EDT 2019},
month = {Wed Oct 23 00:00:00 EDT 2019}
}
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Journal Article:
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Publisher's Version of Record
https://doi.org/10.1016/j.ymeth.2019.10.007
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Figures / Tables:

Fig. 1 Fig. 1: (a) Experimental design for studying the response of two sorghum genotypes to different watering conditions. Top panel shows the watering conditions and sample collection time points for histone analysis. The table shows the number of biological replicates (i.e. different plants) used. Some biological replicates were pooled to providemore » sufficient material for the analysis. (b) A representative LC-MS feature map of intact histones extracted from sorghum leaves. The 2D display plots the LC retention time vs. the mass for all detected proteoforms. The log abundance is coded by the color as shown by the scale in the top right corner. The major histone peaks are labeled by the dashed green boxes. The features outside the boxes are primarily truncated histones and ribosomal proteins. Zoom-in views of (c) H4, (d) H3, (e) H2B/16 kDa H2A, and (f) 14 kDa H2A feature maps in the same format as used for (b). Only major histone species are annotated with their PTMs. A complete list of identified histone proteoforms is presented in Table S1. In (e), all 16 kDa H2A species are denoted in green. In (f), the major 14 kDa H2A species (UniProt: C5XAT9) are denoted in green. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)« less
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