Fission Yeast Homologs of Human Histone H3 Lysine 4 Demethylase Regulate a Common Set of Genes with Diverse Functions

Abstract

Schizosaccharomyces pombe contains two proteins, SWIRM1 and SWIRM2, with close homology to human histone H3 lysine 4 demethylase. Both proteins contain the amino oxidase catalytic domain and a recently described DNA interaction SWIRM domain. Here we describe the biochemical isolation and the functional characterization of SWIRM1 and SWIRM2. Our results indicate that while SWIRM2 is an essential gene, cells lacking SWIRM1 are viable. We found that SWIRM1 and SWIRM2 are stably associated in a multiprotein complex, but intriguingly, unlike their human counterpart, S. pombe SWIRM complex contains neither a histone deacetylase nor any detectable demethylase activity. Genome-wide chromatin immunoprecipitation unexpectedly showed the absence of both SWIRM proteins from heterochromatic domains. Instead, consistent with biochemical analyses, SWIRM1 and SWIRM2 co-localize to a common set of target gene promoters whose functions are implicated in diverse processes including mitochondrial metabolism and transcriptional regulation. Importantly, we show that SWIRM1 is not only required for optimum transcription of its target genes but also display a global role in regulation of antisense transcription.Histones, the building blocks of chromatin in eukaryotic cells, are subject to several posttranslational modifications including methylation, acetylation, phosphorylation, and ubiquitylation (1). These histone modifications play a central role in modulating chromatin structure and function (2, 3). Of particular interest in recent years, histone methylation is known to impact several cellular processes such as chromatin organization, genomic imprinting, and transcriptional regulation (4 -6). This modification occurs on five lysine (K) residues of histone H3 and one lysine residue of histone H4 that can be methylated in three different modes, i.e. mono-, di-, or trimethylation. Generally, methylated H3K4, H3K36, and H3K79 residues are thought to be activation marks, whereas methylated H3K9, H3K27, and H4K20 residues represent repressive marks (4, 7). Arginine residues can also be methylated to generally lead to transcriptional activation (5).Although other histone modifications such as acetylation, phosphorylation, and ubiquitylation have been known to be reversible, histone methylation was considered irreversible. However, recent discoveries of several histone demethylases that can reverse methylated lysine and arginine residues have altered our views of histone demethylation (8 -13). PAD4/ PADI4 was the first reported histone arginine demethylase that demethyliminates monomethylarginine to produce citrulline (8, 9). BHC110/LSD1 has been identified as the first histone lysine demethylase that removes mono-or dimethyl-H3K4 by oxidation-based demethylation (13). More recently, a new family of histone demethylases was discovered to contain a JmjC domain capable of removing methyl groups on lysine residues by hydroxylation-based demethylation (10 -12).We and others (14 -20) have purified BHC110 as a component of several multiprotein ...

Genome-Wide Studies of Histone Demethylation Catalysed by the Fission Yeast Homologues of Mammalian LSD1

“…The results of the MS analysis are presented in Table S1 in the Supplementary Information and are summarized in Figure 1. In brief, our data confirm the results of Nicolas et al, (2006) [14] and show that the Swm1 complex contains Swm2 and two new PHD domain containing proteins ( S. pombe DB CDS: SPCC4G3.07 and SPAC30D11.08c), hereafter referred to as Swp1 ( Sw m associated P HD1) and Swp2 ( Sw m associated P HD2). Surprisingly, the purified Swm2 complex contained only Swm1 and Swp1, but not Swp2, suggesting that the Swm proteins may exist in more than one complex.…”

Erasing the methyl mark: histone demethylases at the center of cellular differentiation and disease

“…These studies have corroborated the notion that LSD1 can act as a H3K9 demethylase associated with heterochromatin boundaries and euchromatic promoters (Nicolas et al 2006;Lan et al 2007c) or as a H3K4 demethylase (Rudolph et al 2007). Thus, in S. pombe the LSD1 ortholog SWIRM1/2 (also referred to as spLsd1/2) has been demonstrated to demethylate H3K9 and depletion of SWIRM1/2 induces heterochromatin spreading beyond normal heterochromatin regions (Lan et al 2007c).…”

“…Studies performed in Schizosacchaomyces pombe and Drosophilia melanogaster have implicated LSD1 orthologs in the organization of higher-order structure of chromatin (Nicolas et al 2006;Lan et al 2007c;Rudolph et al 2007). These studies have corroborated the notion that LSD1 can act as a H3K9 demethylase associated with heterochromatin boundaries and euchromatic promoters (Nicolas et al 2006;Lan et al 2007c) or as a H3K4 demethylase (Rudolph et al 2007).…”

Genome-Wide Dynamics of SAPHIRE, an Essential Complex for Gene Activation and Chromatin Boundaries

“…Extensive biochemical testing of both native and recombinant SAPHIRE complexes has not revealed appreciable activity. This is consistent with the work of others on these S. pombe orthologs, showing no observed activity in vitro (31). Therefore, we focused on the biological and genomic impact of removing the conserved catalytic residue of these enzymes, as described below.…”

“…Our in vivo work also provides several lines of evidence that SAPHIRE promotes gene activation. While we were preparing this paper for submission, others purified a complex of largely the same composition, localized the complex to promoters, and demonstrated that transcription is reduced at three selected targets in saf110⌬ mutants (31). However, our work is unique in its (i) evidence for nucleosome binding, (ii) examination of knockouts of all four complex members, (iii) preparation and analysis of catalytically impaired mutants, (iv) observation of occupancy of the complex at heterochromatin regions, (v) genome-wide analysis of the impact of both saf110⌬ and catalytic mutants on transcription, (vi) observation of changes in histone methylation that occur in catalytic mutant strains at occupied genes, (vii) observation of dynamic relocalization of SAPHIRE during gene activation, and (viii) demonstration of a large shift in the euchromatin-heterochromatin boundary at chromosome 1 in catalytic mutants, suggesting a novel role in boundary formation.…”