Characterization of the plant homeodomain (PHD) reader family for their histone tail interactions

Kanishk Jain,Cari Sagum,Madison M Parker,Brian D Strahl,Mark T Bedford,Matthew R Marunde,Jonathan M Burg,Keli L Rodriguez,Caroline S Fraser,Krzysztof Krajewski,Nathan Hall,Michael-Christopher Keogh,Anup Vaidya,Irina K Popova

doi:10.1186/s13072-020-0328-z

Abstract

BackgroundPlant homeodomain (PHD) fingers are central “readers” of histone post-translational modifications (PTMs) with > 100 PHD finger-containing proteins encoded by the human genome. Many of the PHDs studied to date bind to unmodified or methylated states of histone H3 lysine 4 (H3K4). Additionally, many of these domains, and the proteins they are contained in, have crucial roles in the regulation of gene expression and cancer development. Despite this, the majority of PHD fingers have gone uncharacterized; thus, our understanding of how these domains contribute to chromatin biology remains incomplete.ResultsWe expressed and screened 123 of the annotated human PHD fingers for their histone binding preferences using reader domain microarrays. A subset (31) of these domains showed strong preference for the H3 N-terminal tail either unmodified or methylated at H3K4. These H3 readers were further characterized by histone peptide microarrays and/or AlphaScreen to comprehensively define their H3 preferences and PTM cross-talk.ConclusionsThe high-throughput approaches utilized in this study establish a compendium of binding information for the PHD reader family with regard to how they engage histone PTMs and uncover several novel reader domain–histone PTM interactions (i.e., PHRF1 and TRIM66). This study highlights the usefulness of high-throughput analyses of histone reader proteins as a means of understanding how chromatin engagement occurs biochemically.

Highlights

Plant homeodomain (PHD) fingers are central “readers” of histone post-translational modifications (PTMs) with > 100 PHD finger-containing proteins encoded by the human genome
Distinct classes of reader domains bind to specific types of PTMs; for example, bromodomains recognize lysine acetylation [4], chromodomains recognize methyl-lysine [5], and the PHD fingers characterized to date generally recognize unmodified or methylated lysine residues [6]
Analysis of the PHD finger proteome via protein domain microarrays To define the histone binding preferences of the PHD finger proteome, we expressed and purified 123 annotated human PHD-containing domains as GST-tagged recombinant fusions from E. coli

Summary

Introduction

Plant homeodomain (PHD) fingers are central “readers” of histone post-translational modifications (PTMs) with > 100 PHD finger-containing proteins encoded by the human genome. Many of the PHDs studied to date bind to unmodified or methylated states of histone H3 lysine 4 (H3K4) Many of these domains, and the proteins they are contained in, have crucial roles in the regulation of gene expression and cancer development. Histone proteins are fundamental to genome organization and packaging, and are chemically modified by a wide range of “writer” or “eraser” enzymes that, respectively, install or remove histone post-translational modifications (PTMs) [1, 2]. These PTMs play a central role in. A number of these PHD fingers occur in tandem (e.g., MLL1-4 [7] and PZP-containing proteins [18, 19]) or next to additional reader domain types (e.g., bromodomains and chromodomains) [20,21,22], suggesting combinatorial interaction capabilities

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