The histone H3 variant H3.3 regulates gene body DNA methylation in Arabidopsis thaliana

Yoshiaki Tarutani,Xin Nie,Hidenori Takeuchi,Tetsuji Kakutani,Ramesh Yelagandula,Heike Wollmann,Frédéric Berger,Sarah Holec,Bhagyshree Jamge,Danhua Jiang,Li Jing,Steven E Jacobsen,Hume Stroud

doi:10.1186/s13059-017-1221-3

Abstract

BackgroundGene bodies of vertebrates and flowering plants are occupied by the histone variant H3.3 and DNA methylation. The origin and significance of these profiles remain largely unknown. DNA methylation and H3.3 enrichment profiles over gene bodies are correlated and both have a similar dependence on gene transcription levels. This suggests a mechanistic link between H3.3 and gene body methylation.ResultsWe engineered an H3.3 knockdown in Arabidopsis thaliana and observed transcription reduction that predominantly affects genes responsive to environmental cues. When H3.3 levels are reduced, gene bodies show a loss of DNA methylation correlated with transcription levels. To study the origin of changes in DNA methylation profiles when H3.3 levels are reduced, we examined genome-wide distributions of several histone H3 marks, H2A.Z, and linker histone H1. We report that in the absence of H3.3, H1 distribution increases in gene bodies in a transcription-dependent manner.ConclusionsWe propose that H3.3 prevents recruitment of H1, inhibiting H1’s promotion of chromatin folding that restricts access to DNA methyltransferases responsible for gene body methylation. Thus, gene body methylation is likely shaped by H3.3 dynamics in conjunction with transcriptional activity.

Highlights

Gene bodies of vertebrates and flowering plants are occupied by the histone variant H3.3 and DNA methylation
H3.3 impacts plant development In Arabidopsis H3.3 is encoded by three HISTONE 3 RELATED (HTR) genes, HTR4 (At4g40030), HTR5 (At4g40040), and HTR8 (At5g10980), which are highly expressed throughout development [14, 32]
In contrast to double homozygous htr4/htr4;htr8/htr8 plants that looked similar to wild type (WT; Additional file 2: Figure S2b), htr4/ htr4;htr8/htr8 plants that carried either amiR-HTR5-I or amiR-HTR5-II showed serration of leaf margins, reduced growth, and partial sterility (Fig. 1a; Additional file 1: Table S2; Additional file 2: Figure S2b, c)

Summary

Introduction

Gene bodies of vertebrates and flowering plants are occupied by the histone variant H3.3 and DNA methylation. Genome-wide analysis of chromatin immunoprecipitation (ChIP) in several model organisms, including plants, showed that H3.3 is predominantly enriched near transcription end sites (TES) of genes and positively associated with transcription [18,19,20,21], suggesting a direct mechanistic link between H3.3 enrichment and transcription. This distinctive pattern of H3.3 over genes overlaps with the enrichment of RNA polymerase II (RNAPII) [19, 21]. The functional relationship between H3.3 enrichment and transcriptional activity remains unresolved

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