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Plant and Cell Physiology Advance Access originally published online on September 8, 2008
Plant and Cell Physiology 2008 49(10):1580-1588; doi:10.1093/pcp/pcn133
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© The Author 2008. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved. For permissions, please email: journals.permissions@oxfordjournals.org

Alterations of Lysine Modifications on the Histone H3 N-Tail under Drought Stress Conditions in Arabidopsis thaliana

Jong-Myong Kim1, Taiko Kim To1, Junko Ishida1, Taeko Morosawa1, Makiko Kawashima1, Akihiro Matsui1, Tetsuro Toyoda2, Hiroshi Kimura3, Kazuo Shinozaki4 and Motoaki Seki1,5,*

1 Plant Genomic Network Research Team, Plant Functional Genomics Research Group, RIKEN Plant Science Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045 Japan
2 Bioinformatics and Systems Engineering Division, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa, 230-0045 Japan
3 Graduate School of Frontier Biological Science, Osaka University, 1-3 Yamadaoka, Suita, Osaka, 565-0871 Japan
4 Gene Discovery Research Team, Gene Discovery Research Group, RIKEN Plant Science Center, 3-1-1 Koyadai, Tsukuba, Ibaraki, 305-0074 Japan
5 Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka-cho, Totsuka-ku, Yokohama, Kanagawa, 244-0813 Japan

*Corresponding author: E-mail, mseki{at}psc.riken.jp; Fax, +81-45-503-9586.


  Abstract

Post-translational modification of histone N-tails affects eukaryotic gene activity. In Arabidopsis, the histone modification level correlates with gene activation and repression in vernalization and flowering processes, but there is little information on changes in histone modification status and nucleosome structure under abiotic stresses. We determined the temporal and spatial changes in nucleosome occupancy and levels of H3K4me3, H3K9ac, H3K14ac, H3K23ac and H3K27ac in the histone H3 N-tail on the regions of four Arabidopsis drought stress-inducible genes, RD29A, RD29B, RD20 and RAP2.4, under drought stress conditions by chromatin immunoprecipitation analysis. We found two types of regulatory mechanisms of nucleosome occupancy function in the drought stress response. For RD29A and RD29B genes, nucleosome occupancy of promoter regions is low compared with that of coding regions, and no notable nucleosome loss occurs under drought stress. In contrast, nucleosome density is gradually decreased in response to drought stress on RD20 and RAP2.4 genes. Enrichments of H3K4me3 and H3K9ac correlate with gene activation in response to drought stress in all four genes. Interestingly, establishment of H3K4me3 occurs after accumulation of RNAPII on the coding regions of RD29A and RAP2.4. Enrichment of H3K23ac and H3K27ac occurs in response to drought stress on the coding regions of RD29B, RD20 and RAP2.4, but not on the coding region of RD29A. Our results indicate that histone modifications on the H3 N-tail are altered with gene activation on the coding regions of drought stress-responsive genes under drought stress conditions and that several patterns of nucleosome changes function in the drought stress response.

Keywords: Chromatin - Drought - Histone modification - Transcriptional regulation

Abbreviations: ABRE, ABA-responsive element; ChIP, chromatin immunoprecipitation; DRE, dehydration-responsive element; H3K4me, methylation of histone H3 Lys4; H3K4me3, tri-methylation of histone H3 Lys4; H3K9ac, acetylation of histone H3 Lys9; H3K9me, methylation of histone H3 Lys9; H3K14ac, acetylation of histone H3 Lys14; H3K23ac, acetylation of histone H3 Lys23; H3K27ac, acetylation of histone H3 Lys27; H3K27me, methylation of histone H3 Lys27; H3K36me, methylation of histone H3 Lys36; RAP2, related to AP2; RD, responsive to dehydration; RNAPII, RNA polymerase II; RT–PCR, reverse transcription–PCR; UTR, untranslated region

(Received August 5, 2008; Accepted August 28, 2008)
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