Genome-wide maps of HMGD1 and H1-bound nucleosomes.
ABSTRACT: Chromatin architectural proteins interact with nucleosomes to modulate chromatin accessibility and higher-order chromatin structure. While these proteins are almost certainly important for gene regulation they have been studied far less than the core histone proteins. Here we describe the genomic distributions and functional roles of two chromatin architectural proteins: histone H1 and the high mobility group protein HMGD1, in Drosophila S2 cells. Using ChIP-seq, biochemical and gene specific approaches, we find that HMGD1 binds to highly accessible regulatory chromatin and active promoters. In contrast, H1 is primarily associated with heterochromatic regions marked with repressive histone marks. However, the ratio of HMGD1 to H1 is better correlated with chromatin accessibility, gene expression and nucleosome spacing variation than either protein alone suggesting a competitive mechanism between these proteins. Indeed, we show that HMGD1 and H1 compensate each other’s absence by binding reciprocally to chromatin resulting in changes to nucleosome repeat length and distinct gene expression patterns. Collectively our data suggest that dynamic and mutually exclusive binding of H1 and HMGD1 to nucleosomes and linker sequences may control the fluid chromatin structure that is required for transcriptional regulation. This study thus provides a framework to further study the interplay between chromatin architectural proteins and epigenetics in gene regulation. ChIP-seq of HMGD1 and Histone H1 bound nucleosomes as well as MNase-seq of total nucleosome in Drosophila S2 cells
Project description:Chromatin architectural protein NSBP1/HMGN5 belongs to the family of HMGN proteins which specifically interact with nucleosomes via Nucleosome Binding Domain, unfold chromatin and affect transcription. Mouse NSBP1 is a new and uncharacterized member of HMGN protein family. NSBP1 is a nuclear protein which is localized to euchromatin, binds to linker histone H1 and unfolds chromatin. We analyzed the effect of altered expression levels of mouse NSBP1 protein on global gene expression profile in AtT20 pituitary cells. We found that NSBP1 modulates the fidelity of cellular transcription in the nucleosome binding-dependent manner. Overall design: Stable clones overexpressing wild type mouse NSBP1 protein or mutated NSBP1SE protein which does not bind to nucleosomes were generated by retroviral infection of AtT20 cells. siRNA treatment was applied to down regulate NSBP1 in the cells. Total RNA was collected from biological triplicates and analyzed by Affymetrix expression arrays.
Project description:Chromatin architectural protein NSBP1/HMGN5 belongs to the family of HMGN proteins which specifically interact with nucleosomes via Nucleosome Binding Domain, unfold chromatin and affect transcription. Mouse NSBP1 is a new and uncharacterized member of HMGN protein family. NSBP1 is a nuclear protein which is localized to euchromatin, binds to linker histone H1 and unfolds chromatin. We analyzed the effect of altered expression levels of mouse NSBP1 protein on global gene expression profile in AtT20 pituitary cells. We found that NSBP1 modulates the fidelity of cellular transcription in the nucleosome binding-dependent manner. Experiment Overall Design: Stable clones overexpressing wild type mouse NSBP1 protein or mutated NSBP1SE protein which does not bind to nucleosomes were generated by retroviral infection of AtT20 cells. siRNA treatment was applied to down regulate NSBP1 in the cells. Total RNA was collected from biological triplicates and analyzed by Affymetrix expression arrays.
Project description:Chromatin accessibility plays a fundamental role in gene regulation. One mechanism to regulate accessibility is nucleosome placement, which is often measured by quantifying protection of DNA from enzymatic digestion. We introduce a metric that uses micrococcal nuclease (MNase) digestion in a novel manner to measure chromatin accessibility by combining information from several digests of increasing depths. This metric, MACC, quantifies the inherent heterogeneity of nucleosome accessibility in which some nucleosomes are seen preferentially at high MNase and some at low MNase. MACC interrogates each genomic locus, measuring both location of nucleosomes and accessibility to MNase in the same assay. MACC can be performed either with or without a histone immunoprecipitation step, and thereby compares behavior of nucleosomes to that of non-histone proteins. We find that enhancers, promoters and other regulatory regions have changes in accessibility that do not correlate with changes in nucleosome occupancy. Moreover, we show that high nucleosome occupancy does not necessarily preclude high accessibility, revealing novel principles of chromatin regulation. Overall design: MNase-seq profiles for different concentrations obtained for fly, mouse and human samples
Project description:The nucleosome plays a central role in genome regulation. Traditional methods for mapping nucleosomes depend on the resistance of the nucleosome core to micrococcal nuclease (MNase). However, the lengths of the protected DNA fragments are heterogeneous, limiting the accuracy of nucleosome position information. To resolve this problem, we removed residual linker DNA by simultaneous digestion of yeast chromatin with MNase and exonuclease III (ExoIII). Paired-end sequencing of mono-nucleosomes revealed not only core particles (145-147 bp), but also intermediate particles in which ~8 bp project from one side (154 bp) or both sides (161 bp) of the nucleosome core. We term these particles "pseudo-chromatosomes" because they are present in yeast lacking linker histone. They are also observed after MNase-ExoIII digestion of chromatin reconstituted using recombinant core histones. We propose that the pseudo-chromatosome provides a DNA framework to facilitate H1 binding. Comparison of budding yeast nucleosome sequences obtained using micrococcal nuclease (MNase-seq) and MNase + exonuclease III (ExoIII) (MNase-ExoIII-seq): wild type cells and hho1-null cells. Nucleosome sequences from native chromatin and H1-depleted chromatin from mouse liver. Nucleosome sequences from a plasmid reconstituted into nucleosomes using recombinant yeast histones or native chicken erythrocyte histones.
Project description:Knowing the exact positions of nucleosomes not only advances our understanding of their role in gene regulation, but also the mechanisms that underlie between-species variation in chromatin structure. We have generated a chemical map of nucleosomes in vivo in Schizosaccharomyces pombe at base pair resolution. This new map reveals that S.pombe genome shares a similar periodic linker length distribution with Saccharomyces cerevisiae, but with major distinctions in nucleosomal/linker DNA sequence features. In S.pombe, A/T rich sequences are enriched in the nucleosome core region, particularly +/-20 bp of dyad, while they are disfavored in S.cerevisiae nucleosomes. The poly (dA-dT) tracts only slightly affect the nucleosome occupancy in S.pombe; and they possess preferential rotational positions within the nucleosome core with significant enrichment in the 10-30 bp region from the dyad for longer tracts. S.pombe does not have well-defined nucleosome free region immediately upstream of most transcription start sites (TSS), instead the -1 nucleosome is positioned with regular distance to the +1 nucleosome, and its occupancy is negatively correlated with gene expression. The nucleosomes around TSS show more pronounced bidirectional phasing when the intergenic distance is relatively short, and the downstream nucleosome positioning is strongly correlated with DNA sequence features. We discovered that heterochromatin regions tend to have sparse nucleosome positioning, mixed with both well-positioned and fuzzy nucleosomes. The S.pombe map suggests that some of nucleosome positioning codes, formerly thought to be intrinsic, may largely depend on species-specific extrinsic factors including linker histone, chromatin remodelers and other DNA-binding proteins. 2 samples were analyzed with high throughput paired-end parallel sequencing. Both samples were created using the same chemical mapping protocol
Project description:Mammalian embryonic stem (ES) cells and sperm exhibit unusual chromatin packaging that plays important roles in cellular function. Here, we extend a recently developed technique, based on deep paired-end sequencing of lightly digested chromatin, to assess footprints of nucleosomes and other DNA-binding proteins genome-wide in murine ES cells and sperm. In ES cells, we recover well-characterized features of chromatin such as promoter nucleosome depletion, and further identify widespread footprints of sequence-specific DNA-binding proteins such as CTCF, which we validate in knockdown studies. We document global differences in nuclease accessibility between ES cells and sperm, finding that the majority of histone retention in sperm preferentially occurs in large gene-poor genomic regions, with only a small subset of nucleosomes being retained over promoters of developmental regulators. Finally, we describe evidence that CTCF remains associated with the genome in mature sperm, where it could play a role in organizing the sperm genome. We use Micrococcal Nuclease (MNase) to map chromatin structure in mouse ES cells and sperm. Specifically, we generate paired-end deep-sequencing libraries that are able to distinguish DNA digestion products by size, thus allowing us to simultaneously map nucleosomes as well as other DNA-binding proteins such as transcription factors.
Project description:Eukaryotic DNA is wrapped around histone octamers to form nucleosomes, which are separated by linker DNA bound by histone H1. In many species, the DNA exhibits methylation of CG dinucleotides, which is epigenetically inherited via a semiconservative mechanism. How methyltransferases access DNA within nucleosomes remains mysterious. Here we show that methylation of nucleosomes requires DDM1/Lsh nucleosome remodelers in Arabidopsis thaliana and mouse. We also show that removal of histone H1, which partially restores methylation in ddm1 mutants, does so primarily in the linker DNA between nucleosomes. In h1ddm1 compound mutants, substantial portions of the genome exhibit dramatically periodic methylation that approaches wild-type levels in linker DNA but is virtually absent in nucleosomes. We also present evidence that de novo methylation supplements semiconservative maintenance of CG methylation across generations. Overall, our results demonstrate that nucleosomes and H1 are barriers to DNA methylation, which are overcome by DDM1/Lsh nucleosome remodelers. Overall design: Bisulfite sequencing to determine single-base DNA methylation: 4 different genotypes from F4 generation, without replicates; MNase sequencing to identify nucleosome positions genomewide: single generation in leaf tissue for 4 different genotypes, 2 or 3 biological replicates; RNA-seq to define expression deciles in wild-type: single generation in leaf tissue for WT, 2 replicates.
Project description: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-FLAG 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 stochiometery 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 wildtype and the ∆hH1 strain followed by sequencing (MNase-Seq). Deletion of hH1 did not significantly impact nucleosome positioning or nucleosome occupancy. Analysis of DNA methylation using methylC-sequencing (mC-Seq) revealed a modest but global increase in DNA methylation in the ∆hH1 mutant. Together, these data suggest that H1 acts as a non-specific chromatin binding protein that can limit accessibility of the DNA methylation machinery in N. crassa. Overall design: Investigations used either wildtype, an H1 mutant strain, or an engineered strain containing a FLAG-tagged H1. In all cases, at least 2 biological replicate experiments were performed.
Project description:Linker histone H1 is a core chromatin component that binds to nucleosome core particles and the linker DNA between nucleosomes. It has been implicated in chromatin compaction and gene regulation and is anticipated to play a role in higher-order genome structure. We find that depletion of histone H1 changes the epigenetic signature of thousands of potential regulatory sites across the genome. Many of them show cooperative loss or gain of multiple chromatin marks. Epigenetic alterations cluster to gene-dense topologically associated domains (TADs) that already showed a high density of corresponding chromatin features. Genome organization at the three-dimensional level is largely intact, but we find changes in the structural segmentation of chromosomes specifically for the epigenetically most modified TADs. Overall design: We have used a combination of genome-wide approaches including DNA methylation, histone modification and DNaseI hypersensitivity profiling as well as Hi-C to investigate the impact of reduced cellular levels of histone H1 in embryonic stem cells on chromatin folding and function.
Project description:Nucleosome positioning dictates the DNA accessibility for regulatory proteins, and thus is critical for gene expression and regulation. It has been well documented that only a subset of nucleosomes are reproducibly positioned (phased) in eukaryotic genomes. The most prominent example of phased nucleosomes is the context of genes, where phased nucleosomes flank the transcriptional starts sites (TSSs). It is unclear, however, what factors influence nucleosome phasing in regions that are not close to genes. We performed a combinational mapping of nucleosome positioning and DNase I hypersensitive sites (DHSs) across the rice genome. We discovered that DHSs located in a variety of contexts, both genic and intergenic, were flanked by strongly phased nucleosome arrays. Our results support the barrier model for nucleosome organization as a general feature of eukaryote genomes, including plant genomes, and not limited to TSSs. Specifically, regions bound with regulatory proteins, including intergenic regions, can serve as barriers that organize phased nucleosome arrays on both sides. Our results also suggest that rice DHSs often span a single, phased nucleosome, similar to the H2A.Z-containing nucleosomes observed in DHSs in the human genome. We propose that genome-wide nucleosome positioning in the eukaryotic genomes is orchestrated by genomic regions associated with regulatory proteins. Rice chromatin was digested by micrococcal nuclease (MNase) into mono-nucleosome size. Mono-nucleosomal DNA was isolated and sequenced (MNase-seq) using Illumina sequencing platforms. We obtained a total of 38 million (M) single-end reads from our first MNase-seq experiment and mapped ~26 M to unique positions in the rice genome. We also conducted pair-end sequencing of an independent MNase-seq library, obtained 274 M paired-end reads, and mapped ~231 M read pairs to unique positions in the rice genome.We applied a strategy of combinational mapping of nucleosome positioning and DHSs (GSE26610) to examine whether nucleosome positioning is associated with all cis-regulatory elements in the rice genome. All datasets used in the analysis were developed using rice leaf tissue in the same developmental stage