title: Histone H1 Limits DNA Methylation in Neurospora crassa.
abstract: Histone H1 variants, known as linker histones, are essential chromatin components in higher eukaryotes, yet compared to the core histones relatively little is known about their in vivo functions. The filamentous fungus Neurospora crassa encodes a single H1 protein that is not essential for viability. To investigate the role of N. crassa H1, we constructed a functional FLAG-tagged H1 fusion protein and performed genomic and molecular analyses. Cell fractionation experiments showed that H1-3XFLAG is a chromatin binding protein. Chromatin-immunoprecipitation combined with sequencing (ChIP-seq) revealed that H1-3XFLAG is globally enriched throughout the genome with a subtle preference for promoters of expressed genes. In mammals, the stoichiometry of H1 impacts nucleosome repeat length. To determine if H1 impacts nucleosome occupancy or nucleosome positioning in N. crassa, we performed micrococcal nuclease digestion in the wild-type and the [Formula: see text]hH1 strain followed by sequencing (MNase-seq). Deletion of hH1 did not significantly impact nucleosome positioning or nucleosome occupancy. Analysis of DNA methylation by whole-genome bisulfite sequencing (MethylC-seq) revealed a modest but global increase in DNA methylation in the [Formula: see text]hH1 mutant. Together, these data suggest that H1 acts as a nonspecific chromatin binding protein that can limit accessibility of the DNA methylation machinery in N. crassa.
authors.affiliation: Department of Microbiology, University of Georgia, Athens, Georgia 30602.
authors.forename: Michael
authors.initials: M
authors.lastname: Seymour
authors.affiliation: Institute of Bioinformatics, University of Georgia, Athens, Georgia 30602.
authors.forename: Lexiang
authors.initials: L
authors.lastname: Ji
authors.affiliation: Department of Plant Biology, University of Georgia, Athens, Georgia 30602.
authors.forename: Alex M
authors.initials: AM
authors.lastname: Santos
authors.affiliation: Department of Microbiology, University of Georgia, Athens, Georgia 30602.
authors.forename: Masayuki
authors.initials: M
authors.lastname: Kamei
authors.affiliation: Department of Microbiology, University of Georgia, Athens, Georgia 30602.
authors.forename: Takahiko
authors.initials: T
authors.lastname: Sasaki
authors.affiliation: Department of Microbiology, University of Georgia, Athens, Georgia 30602.
authors.forename: Evelina Y
authors.initials: EY
authors.lastname: Basenko
authors.affiliation: Department of Genetics, University of Georgia, Athens, Georgia 30602.
authors.forename: Robert J
authors.initials: RJ
authors.lastname: Schmitz
authors.affiliation: Department of Plant Biology, University of Georgia, Athens, Georgia 30602.
authors.forename: Xiaoyu
authors.initials: X
authors.lastname: Zhang
authors.affiliation: Department of Microbiology, University of Georgia, Athens, Georgia 30602 zlewis@uga.edu.
authors.forename: Zachary A
authors.identifier: 0000-0002-1735-8266
authors.initials: ZA
authors.lastname: Lewis
mesh_terms: D042002:Chromatin Assembly and Disassembly; D019175:DNA Methylation; D005656:Fungal Proteins / Q000235:genetics* / Q000378:metabolism; D015966:Gene Expression Regulation, Fungal; D016681:Genome, Fungal; D006657:Histones / Q000235:genetics*; D009492:Neurospora crassa / Q000235:genetics* / Q000378:metabolism; D009707:Nucleosomes / Q000737:chemistry / Q000378:metabolism; D009842:Oligopeptides / Q000235:genetics / Q000378:metabolism; D011401:Promoter Regions, Genetic; D011485:Protein Binding; D011993:Recombinant Fusion Proteins / Q000235:genetics / Q000378:metabolism
chemical_list: D005656:Fungal Proteins; D006657:Histones; D009707:Nucleosomes; D009842:Oligopeptides; D011993:Recombinant Fusion Proteins; C085706:FLAG peptide
keywords: DNA methylation; chromatin; histone H1; nucleosome positioning