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

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

doi:10.1016/j.ymeth.2019.10.007

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

Journal Article · 23 October 2019 · Methods

DOI: https://doi.org/10.1016/j.ymeth.2019.10.007 · OSTI ID:1660761

^[1]; Malhan, Neha ^[2]; Ahkami, Amir H. ^[2]; Engbrecht, Kristin ^[2]; Myers, Gabriel ^[2]; Dahlberg, Jeffery ^[3]; Hollingsworth, Joy ^[3]; Sievert, Julie A. ^[3]; Hutmacher, Robert ^[4]; Madera, Mary ^[5]; Lemaux, Peggy G. ^[5]; Hixson, Kim K. ^[2]; Jansson, Christer ^[2]; Paša-Tolić, Ljiljana ^[2]

Pacific Northwest National Lab. (PNNL), Richland, WA (United States). Environmental Molecular Sciences Laboratory (EMSL); Pacific Northwest National Laboratory
Pacific Northwest National Lab. (PNNL), Richland, WA (United States). Environmental Molecular Sciences Laboratory (EMSL)
UC-ANR Kearney Agricultural Research & Extension Center, Parlier, CA (United States)
Univ. of California, Davis, CA (United States)
Univ. of California, Berkeley, CA (United States)

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.

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Research Organization:: Joint BioEnergy Institute (JBEI), Emeryville, CA (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); Pacific Northwest National Laboratory (PNNL), Richland, WA (United States). Environmental Molecular Sciences Laboratory (EMSL); University of California, Berkeley, CA (United States)

Sponsoring Organization:: USDA; USDOE; USDOE Office of Science (SC), Biological and Environmental Research (BER)

Grant/Contract Number:: AC02-05CH11231; AC05-76RL01830; SC0014081

OSTI ID:: 1660761

Report Number(s):: PNNL-SA--145507

Journal Information:: Methods, Journal Name: Methods Journal Issue: SI Vol. 184; ISSN 1046-2023

Publisher:: ElsevierCopyright Statement

Country of Publication:: United States

Language:: English

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59 BASIC BIOLOGICAL SCIENCES
Drought
Epigenetics
Histone clipping
Post-translational modifications
Sorghum
Top-down mass spectrometry

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

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