H3K23me1 is an evolutionarily conserved histone modification associated with CG DNA methylation in Arabidopsis.
Amino-terminal tails of histones are targets for diverse post-translational modifications whose combinatorial action may constitute a code that will be read and interpreted by cellular proteins to define particular transcriptional states. Here, we describe monomethylation of histone H3 lysine 23 (H3K23me1) as a histone modification not previously described in plants. H3K23me1 is an evolutionarily conserved mark in diverse species of flowering plants. Chromatin immunoprecipitation followed by high-throughput sequencing in Arabidopsis thaliana showed that H3K23me1 was highly enriched in pericentromeric regions and depleted from chromosome arms. In transposable elements it co-localized with CG, CHG and CHH DNA methylation as well as with the heterochromatic histone mark H3K9me2. Transposable elements are often rich in H3K23me1 but different families vary in their enrichment: LTR-Gypsy elements are most enriched and RC/Helitron elements are least enriched. The histone methyltransferase KRYPTONITE and normal DNA methylation were required for normal levels of H3K23me1 on transposable elements. Immunostaining experiments confirmed the pericentromeric localization and also showed mild enrichment in less condensed regions. Accordingly, gene bodies of protein-coding genes had intermediate H3K23me1 levels, which coexisted with CG DNA methylation. Enrichment of H3K23me1 along gene bodies did not correlate with transcription levels. Together, this work establishes H3K23me1 as a so far undescribed component of the plant histone code.
Department of Plant Biology and Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, PO-Box 7080, Uppsala, SE-75007, Sweden.
Minerva S
http://orcid.org/0000-0002-1982-3475
MS
Trejo-Arellano
Department of Plant Biology and Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, PO-Box 7080, Uppsala, SE-75007, Sweden.|Department of Biology and Zurich-Basel Plant Science Center, ETH Zurich, Zurich, CH-8092, Switzerland.
Walid
W
Mahrez
Department of Plant Biology and Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, PO-Box 7080, Uppsala, SE-75007, Sweden.
Miyuki
M
Nakamura
Department of Plant Biology and Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, PO-Box 7080, Uppsala, SE-75007, Sweden.
Jordi
J
Moreno-Romero
Functional Genomics Center Zurich, University of Zurich/ETH Zurich, Zurich, CH-8057, Switzerland.
Paolo
P
Nanni
Department of Plant Biology and Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, PO-Box 7080, Uppsala, SE-75007, Sweden.
Claudia
C
Köhler
Department of Plant Biology and Linnean Center for Plant Biology, Swedish University of Agricultural Sciences, PO-Box 7080, Uppsala, SE-75007, Sweden.
Lars
L
Hennig
D017360:Arabidopsis / Q000235:genetics* / Q000378:metabolism*; D029681:Arabidopsis Proteins / Q000235:genetics / Q000378:metabolism*; D019175:DNA Methylation / Q000235:genetics* / Q000502:physiology; D044127:Epigenesis, Genetic / Q000235:genetics; D018506:Gene Expression Regulation, Plant / Q000235:genetics / Q000502:physiology; D006570:Heterochromatin / Q000235:genetics; D006657:Histones / Q000235:genetics / Q000378:metabolism*; D011499:Protein Processing, Post-Translational / Q000235:genetics / Q000502:physiology
D029681:Arabidopsis Proteins; D006570:Heterochromatin; D006657:Histones

Arabidopsis thaliana
; ChIP-seq; DNA methylation; epigenetics; gene body methylation; heterochromatin; histone post-translational modifications; mass spectrometry