Arabidopsis SWR1-associated protein methyl-CpG-binding domain 9 is required for histone H2A.Z deposition

Magdalena E Potok; Yafei Wang; Linhao Xu; Zhenhui Zhong; Wanlu Liu; Suhua Feng; Bilguudei Naranbaatar; Shima Rayatpisheh; Zonghua Wang; James A Wohlschlegel; Israel Ausin; Steven E Jacobsen

doi:10.1038/s41467-019-11291-w

Arabidopsis SWR1-associated protein methyl-CpG-binding domain 9 is required for histone H2A.Z deposition

Nat Commun. 2019 Jul 26;10(1):3352. doi: 10.1038/s41467-019-11291-w.

Authors

Magdalena E Potok¹, Yafei Wang², Linhao Xu², Zhenhui Zhong^{1

2

3}, Wanlu Liu^{1

4}, Suhua Feng¹, Bilguudei Naranbaatar¹, Shima Rayatpisheh^{5

6}, Zonghua Wang^{3

7}, James A Wohlschlegel⁵, Israel Ausin⁸, Steven E Jacobsen^{9

10}

Affiliations

¹ Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
² Basic Forestry and Proteomics Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
³ State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
⁴ Zhejiang University-University of Edinburgh Institute, Zhejiang University School of Medicine, Hangzhou, 310058, China.
⁵ Department of Biological Chemistry, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
⁶ Genomic Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Dr., San Diego, CA, 92121, USA.
⁷ Institute of Oceanography, Minjiang University, Fuzhou, 350108, China.
⁸ Basic Forestry and Proteomics Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, China. israel.ausin@gmail.com.
⁹ Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, 90095, USA. jacobsen@ucla.edu.
¹⁰ Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA, 90095, USA. jacobsen@ucla.edu.

Abstract

Deposition of the histone variant H2A.Z by the SWI2/SNF2-Related 1 chromatin remodeling complex (SWR1-C) is important for gene regulation in eukaryotes, but the composition of the Arabidopsis SWR1-C has not been thoroughly characterized. Here, we aim to identify interacting partners of a conserved Arabidopsis SWR1 subunit ACTIN-RELATED PROTEIN 6 (ARP6). We isolate nine predicted components and identify additional interactors implicated in histone acetylation and chromatin biology. One of the interacting partners, methyl-CpG-binding domain 9 (MBD9), also strongly interacts with the Imitation SWItch (ISWI) chromatin remodeling complex. MBD9 is required for deposition of H2A.Z at a distinct subset of ARP6-dependent loci. MBD9 is preferentially bound to nucleosome-depleted regions at the 5' ends of genes containing high levels of activating histone marks. These data suggest that MBD9 is a SWR1-C interacting protein required for H2A.Z deposition at a subset of actively transcribing genes.

Publication types

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

MeSH terms

Arabidopsis / genetics
Arabidopsis / metabolism*
Arabidopsis Proteins / genetics
Arabidopsis Proteins / metabolism*
Chromatin Assembly and Disassembly
Gene Expression Regulation, Plant
Histone Acetyltransferases / genetics
Histone Acetyltransferases / metabolism*
Histones / genetics
Histones / metabolism*
Microfilament Proteins / genetics
Microfilament Proteins / metabolism*
Protein Binding

Substances

ARP6 protein, Arabidopsis
Arabidopsis Proteins
H2A.Z protein, Arabidopsis
Histones
Microfilament Proteins
AT3G01460 protein, Arabidopsis
Histone Acetyltransferases

Grants and funding

R35 GM130272/GM/NIGMS NIH HHS/United States