KdmB, a Jumonji Histone H3 Demethylase, Regulates Genome-Wide H3K4 Trimethylation and Is Required for Normal Induction of Secondary Metabolism in Aspergillus nidulans.

Agnieszka Gacek-Matthews,Takahiko Sasaki,Harald Berger,Kathrin Wittstein,Clemens Gruber,Zachary A Lewis,Joseph Strauss,Eva H Stukenbrock

doi:10.1371/journal.pgen.1006222

Abstract

Histone posttranslational modifications (HPTMs) are involved in chromatin-based regulation of fungal secondary metabolite biosynthesis (SMB) in which the corresponding genes—usually physically linked in co-regulated clusters—are silenced under optimal physiological conditions (nutrient-rich) but are activated when nutrients are limiting. The exact molecular mechanisms by which HPTMs influence silencing and activation, however, are still to be better understood. Here we show by a combined approach of quantitative mass spectrometry (LC-MS/MS), genome-wide chromatin immunoprecipitation (ChIP-seq) and transcriptional network analysis (RNA-seq) that the core regions of silent A. nidulans SM clusters generally carry low levels of all tested chromatin modifications and that heterochromatic marks flank most of these SM clusters. During secondary metabolism, histone marks typically associated with transcriptional activity such as H3 trimethylated at lysine-4 (H3K4me3) are established in some, but not all gene clusters even upon full activation. KdmB, a Jarid1-family histone H3 lysine demethylase predicted to comprise a BRIGHT domain, a zinc-finger and two PHD domains in addition to the catalytic Jumonji domain, targets and demethylates H3K4me3 in vivo and mediates transcriptional downregulation. Deletion of kdmB leads to increased transcription of about ~1750 genes across nutrient-rich (primary metabolism) and nutrient-limiting (secondary metabolism) conditions. Unexpectedly, an equally high number of genes exhibited reduced expression in the kdmB deletion strain and notably, this group was significantly enriched for genes with known or predicted functions in secondary metabolite biosynthesis. Taken together, this study extends our general knowledge about multi-domain KDM5 histone demethylases and provides new details on the chromatin-level regulation of fungal secondary metabolite production.

Highlights

Chromatin is the natural substrate for all eukaryotic nuclear processes such as transcription, replication, recombination or DNA repair
In this work we monitored by proteomic analysis and Chromatin immunoprecipitation (ChIP)-seq the genome-wide distribution of several key modifications on histone H3 in the model fungus Aspergillus nidulans cultivated either under optimal physiological conditions or less favourable conditions which are known to promote the production of secondary metabolites (SM)
When we correlated the chromatin status to transcriptional activities in actively growing cells we found that the silenced SM gene clusters are flanked by heterochromatic domains presumably contributing to silencing but that the bodies of the clusters only carry background levels of any of the investigated marks

Summary

Introduction

Chromatin is the natural substrate for all eukaryotic nuclear processes such as transcription, replication, recombination or DNA repair. Chromatin structure is necessarily dynamic and the underlying mechanisms involve remodeling of nucleosomes as well as depositing and removing posttranslational modifications on N-terminal and central residues of histones proteins (HPTMs) present in the nucleosome octamer [1,2,3,4]. Similar to animals in N. crassa Heterochromatin Protein 1 (HP1), docks on di- or trimethylated lysine-9 on histone H3 (H3K9me2/3) to promote heterochromatin formation [13, 14] and in addition is important to maintain H3K27me, another repressive mark, at facultative heterochromatin [15, 16].

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