Dual recognition of H3K4me3 and H3K27me3 by a plant histone reader SHL

Shuiming Qian; Xinchen Lv; Ray N Scheid; Li Lu; Zhenlin Yang; Wei Chen; Rui Liu; Melissa D Boersma; John M Denu; Xuehua Zhong; Jiamu Du

doi:10.1038/s41467-018-04836-y

Dual recognition of H3K4me3 and H3K27me3 by a plant histone reader SHL

Nat Commun. 2018 Jun 21;9(1):2425. doi: 10.1038/s41467-018-04836-y.

Authors

Shuiming Qian^{1

2}, Xinchen Lv^{3

4}, Ray N Scheid^{1

2}, Li Lu^{1

2}, Zhenlin Yang^{3

4}, Wei Chen³, Rui Liu³, Melissa D Boersma², John M Denu^{2

5

6}, Xuehua Zhong^{7

8}, Jiamu Du⁹

Affiliations

¹ Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, 53706, USA.
² Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, 53706, USA.
³ National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 201602, China.
⁴ University of Chinese Academy of Sciences, Beijing, 100049, China.
⁵ Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA.
⁶ Morgridge Institute for Research, Madison, WI, 53706, USA.
⁷ Laboratory of Genetics, University of Wisconsin-Madison, Madison, WI, 53706, USA. xuehua.zhong@wisc.edu.
⁸ Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, 53706, USA. xuehua.zhong@wisc.edu.
⁹ National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Center for Plant Stress Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 201602, China. jmdu@sibs.ac.cn.

Abstract

The ability of a cell to dynamically switch its chromatin between different functional states constitutes a key mechanism regulating gene expression. Histone mark "readers" display distinct binding specificity to different histone modifications and play critical roles in regulating chromatin states. Here, we show a plant-specific histone reader SHORT LIFE (SHL) capable of recognizing both H3K27me3 and H3K4me3 via its bromo-adjacent homology (BAH) and plant homeodomain (PHD) domains, respectively. Detailed biochemical and structural studies suggest a binding mechanism that is mutually exclusive for either H3K4me3 or H3K27me3. Furthermore, we show a genome-wide co-localization of SHL with H3K27me3 and H3K4me3, and that BAH-H3K27me3 and PHD-H3K4me3 interactions are important for SHL-mediated floral repression. Together, our study establishes BAH-PHD cassette as a dual histone methyl-lysine binding module that is distinct from others in recognizing both active and repressive histone marks.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Arabidopsis / genetics*
Arabidopsis / metabolism
Arabidopsis Proteins / metabolism*
Chromatin / metabolism*
Gene Expression Regulation, Plant*
Histone Code
Histones / metabolism*
Homeodomain Proteins / genetics
Homeodomain Proteins / metabolism
Homeodomain Proteins / physiology
Methylation
Models, Genetic

Substances

Arabidopsis Proteins
Chromatin
Histones
Homeodomain Proteins

Abstract

Publication types

MeSH terms

Substances

Grants and funding