Complete depletion of Arabidopsis linker histones impairs the correlations among chromatin compartmentalization, DNA methylation and gene expression

In eukaryotic cells, linker histone H1 anchors in and out ends of nucleosome DNA to promote chromatin to fold into the 30 nm fiber. However, if H1 plays a role in coordinating the three-dimensional (3D) chromatin architecture, DNA methylation, and transcriptional regulation is not clear. We engineered H1 knockout mutants in Arabidopsis thaliana which shows pleiotropic phenotypes. Using High-throughput Chromosome Conformation Capture (Hi-C), we found that H1 complete depletion dampens inter- and intra-chromosomal interactions, as well as intra- and inter-chromosomal arm interactions. MNase accessibility assays followed by sequencing (MNase-seq) showed that the nucleosome density decreases in centromeric regions and increases in chromosome arms. In contrast, DNA methylation level in CHG and CHH contexts increases in centromeric regions and decreases in chromosome arms as revealed by whole genome bisulfite sequencing (WGBS) in h1 mutant. Importantly, the functional link between DNA methylation and gene transcription is defected, and the extensive switches between chromatin compartment A and B are uncoupled from genome-wide DNA methylation and most of gene transcriptions upon H1 depletion. These results suggested that linker histone H1 works as linkers among chromatin compartmentalization, DNA methylation and transcription.

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The histone variant H2A.W and linker histone H1 co-regulate heterochromatin accessibility and DNA methylation

Nature Communications ◽

10.1038/s41467-021-22993-5 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Pierre Bourguet ◽

Colette L. Picard ◽

Ramesh Yelagandula ◽

Thierry Pélissier ◽

Zdravko J. Lorković ◽

...

Keyword(s):

Dna Methylation ◽

Histone H1 ◽

Epigenetic Modifications ◽

Flowering Plants ◽

Linker Histone ◽

Histone Variant ◽

Null Mutant ◽

Chromatin Compaction ◽

Linker Histone H1

AbstractIn flowering plants, heterochromatin is demarcated by the histone variant H2A.W, elevated levels of the linker histone H1, and specific epigenetic modifications, such as high levels of DNA methylation at both CG and non-CG sites. How H2A.W regulates heterochromatin organization and interacts with other heterochromatic features is unclear. Here, we create a h2a.w null mutant via CRISPR-Cas9, h2a.w-2, to analyze the in vivo function of H2A.W. We find that H2A.W antagonizes deposition of H1 at heterochromatin and that non-CG methylation and accessibility are moderately decreased in h2a.w-2 heterochromatin. Compared to H1 loss alone, combined loss of H1 and H2A.W greatly increases accessibility and facilitates non-CG DNA methylation in heterochromatin, suggesting co-regulation of heterochromatic features by H2A.W and H1. Our results suggest that H2A.W helps maintain optimal heterochromatin accessibility and DNA methylation by promoting chromatin compaction together with H1, while also inhibiting excessive H1 incorporation.

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Yeast HMO1: Linker Histone Reinvented

Microbiology and Molecular Biology Reviews ◽

10.1128/mmbr.00037-16 ◽

2016 ◽

Vol 81 (1) ◽

Cited By ~ 18

Author(s):

Arvind Panday ◽

Anne Grove

Keyword(s):

Ribosomal Proteins ◽

High Mobility ◽

Histone H1 ◽

Strand Break ◽

Linker Histone ◽

Content Type ◽

Linker Histone H1 ◽

Nucleosome Core ◽

Rich Domain ◽

Nucleosome Density

SUMMARY Eukaryotic genomes are packaged in chromatin. The higher-order organization of nucleosome core particles is controlled by the association of the intervening linker DNA with either the linker histone H1 or high mobility group box (HMGB) proteins. While H1 is thought to stabilize the nucleosome by preventing DNA unwrapping, the DNA bending imposed by HMGB may propagate to the nucleosome to destabilize chromatin. For metazoan H1, chromatin compaction requires its lysine-rich C-terminal domain, a domain that is buried between globular domains in the previously characterized yeast Saccharomyces cerevisiae linker histone Hho1p. Here, we discuss the functions of S. cerevisiae HMO1, an HMGB family protein unique in containing a terminal lysine-rich domain and in stabilizing genomic DNA. On ribosomal DNA (rDNA) and genes encoding ribosomal proteins, HMO1 appears to exert its role primarily by stabilizing nucleosome-free regions or “fragile” nucleosomes. During replication, HMO1 likewise appears to ensure low nucleosome density at DNA junctions associated with the DNA damage response or the need for topoisomerases to resolve catenanes. Notably, HMO1 shares with the mammalian linker histone H1 the ability to stabilize chromatin, as evidenced by the absence of HMO1 creating a more dynamic chromatin environment that is more sensitive to nuclease digestion and in which chromatin-remodeling events associated with DNA double-strand break repair occur faster; such chromatin stabilization requires the lysine-rich extension of HMO1. Thus, HMO1 appears to have evolved a unique linker histone-like function involving the ability to stabilize both conventional nucleosome arrays as well as DNA regions characterized by low nucleosome density or the presence of noncanonical nucleosomes.

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Inference of genomic spatial organization from a whole genome bisulfite sequencing sample

10.1101/384578 ◽

2018 ◽

Cited By ~ 1

Author(s):

Emanuele Raineri ◽

François Serra ◽

Renée Beekman ◽

Beatriz García Torre ◽

Roser Vilarrasa-Blasi ◽

...

Keyword(s):

Dna Methylation ◽

Bisulfite Sequencing ◽

Three Dimensional ◽

Dna Structure ◽

Whole Genome ◽

Simple Method ◽

Intact Cells ◽

Chromosome Conformation ◽

Whole Genome Bisulfite Sequencing ◽

Genome Bisulfite Sequencing

AbstractCommon approaches to characterize the structure of the DNA in the nucleus, such as the different Chromosome Conformation Capture methods, have not currently been widely applied to different tissue types due to several practical difficulties including the requirement for intact cells to start the sample preparation. In contrast, techniques based on sodium bisulfite conversion of DNA to assay DNA methylation, have been widely applied to many different tissue types in a variety of organisms. Recent work has shown the possibility of inferring some aspects of the three dimensional DNA structure from DNA methylation data, raising the possibility of three dimensional DNA structure prediction using the large collection of already generated DNA methylation datasets. We propose a simple method to predict the values of the first eigenvector of the Hi-C matrix of a sample (and hence the positions of the A and B compartments) using only the GC content of the sequence and a single whole genome bisulfite sequencing (WGBS) experiment which yields information on the methylation levels and their variability along the genome. We train and test our model on 10 samples for which we have data from both bisulfite sequencing and chromosome conformation experiments and our most relevant finding is that the variability of DNA methylation along the sequence is often a better predictor than methylation itself. We then run a prediction on 206 DNA methylation profiles produced by the Blueprint project and use ChIP-Seq and RNA-Seq data to confirm that the forecasted eigenvector delineates correctly the physical chromatin compartments observed with the Hi-C experiment.

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MethHaplo: combining allele-specific DNA methylation and SNPs for haplotype region identification

BMC Bioinformatics ◽

10.1186/s12859-020-03798-7 ◽

2020 ◽

Vol 21 (1) ◽

Author(s):

Qiangwei Zhou ◽

Ze Wang ◽

Jing Li ◽

Wing-Kin Sung ◽

Guoliang Li

Keyword(s):

Dna Methylation ◽

Epigenetic Modification ◽

Critical Role ◽

Three Dimensional ◽

Hybrid Vigor ◽

Nucleotide Polymorphisms ◽

Chromosome Conformation ◽

Genome Bisulfite Sequencing ◽

Allele Specific ◽

Eukaryotic Organisms

Abstract Background DNA methylation is an important epigenetic modification that plays a critical role in most eukaryotic organisms. Parental alleles in haploid genomes may exhibit different methylation patterns, which can lead to different phenotypes and even different therapeutic and drug responses to diseases. However, to our knowledge, no software is available for the identification of DNA methylation haplotype regions with combined allele-specific DNA methylation, single nucleotide polymorphisms (SNPs) and high-throughput chromosome conformation capture (Hi-C) data. Results In this paper, we developed a new method, MethHaplo, that identify DNA methylation haplotype regions with allele-specific DNA methylation and SNPs from whole-genome bisulfite sequencing (WGBS) data. Our results showed that methylation haplotype regions were ten times longer than haplotypes with SNPs only. When we integrate WGBS and Hi-C data, MethHaplo could call even longer haplotypes. Conclusions This study illustrates the usefulness of methylation haplotypes. By constructing methylation haplotypes for various cell lines, we provide a clearer picture of the effect of DNA methylation on gene expression, histone modification and three-dimensional chromosome structure at the haplotype level. Our method could benefit the study of parental inheritance-related disease and hybrid vigor in agriculture.

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Simultaneous profiling of DNA methylation and chromatin architecture in mixed populations and in single cells

10.1101/470963 ◽

2018 ◽

Cited By ~ 1

Author(s):

Guoqiang Li ◽

Yaping Liu ◽

Yanxiao Zhang ◽

Rongxin Fang ◽

Manolis Kellis ◽

...

Keyword(s):

Dna Methylation ◽

Single Cells ◽

Three Dimensional ◽

Embryonic Stem ◽

Specific Gene ◽

Mixed Cell ◽

Chromosome Conformation ◽

Chromatin Architecture ◽

Genome Bisulfite Sequencing ◽

Genomic Regions

AbstractDynamic DNA methylation and three-dimensional chromatin architecture compose a major portion of a cell’s epigenome and play an essential role in tissue specific gene expression programs. Currently, DNA methylation and chromatin organization are generally profiled in separate assays. Here, we report Methyl-HiC, a method combining in situ Hi-C and whole genome bisulfite sequencing (WGBS) to simultaneously capture chromosome conformation and DNA methylome in a single assay. Methyl-HiC analysis of mouse embryonic stem cells reveals coordinated DNA methylation between distant yet spatially proximal genomic regions. Extension of Methyl-HiC to single cells further enables delineation of the heterogeneity of both chromosomal conformation and DNA methylation in a mixed cell population, and uncovers increased dynamics of chromatin contacts and decreased stochasticity in DNA methylation in genomic regions that replicate early during cell cycle.

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Linker Histone H1 per se Can Induce Three-Dimensional Folding of Chromatin Fiber†

Biochemistry ◽

10.1021/bi050623v ◽

2005 ◽

Vol 44 (39) ◽

pp. 12978-12989 ◽

Cited By ~ 61

Author(s):

Kohji Hizume ◽

Shige H. Yoshimura ◽

Kunio Takeyasu

Keyword(s):

Three Dimensional ◽

Histone H1 ◽

Linker Histone ◽

Chromatin Fiber ◽

Linker Histone H1 ◽

Per Se

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Faculty Opinions recommendation of Phosphorylation of the linker histone H1 by CDK regulates its binding to HP1alpha.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1033234.375772 ◽

2006 ◽

Author(s):

William Earnshaw

Keyword(s):

Histone H1 ◽

Linker Histone ◽

Linker Histone H1

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Site-specific ubiquitylation acts as a regulator of linker histone H1

Nature Communications ◽

10.1038/s41467-021-23636-5 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

Eva Höllmüller ◽

Simon Geigges ◽

Marie L. Niedermeier ◽

Kai-Michael Kammer ◽

Simon M. Kienle ◽

...

Keyword(s):

Posttranslational Modifications ◽

Histone H1 ◽

Linker Histone ◽

Active Chromatin ◽

Site Specific ◽

Linker Histone H1 ◽

Fundamental Process ◽

Core Histones ◽

Wide Scale

AbstractDecoding the role of histone posttranslational modifications (PTMs) is key to understand the fundamental process of epigenetic regulation. This is well studied for PTMs of core histones but not for linker histone H1 in general and its ubiquitylation in particular due to a lack of proper tools. Here, we report on the chemical synthesis of site-specifically mono-ubiquitylated H1.2 and identify its ubiquitin-dependent interactome on a proteome-wide scale. We show that site-specific ubiquitylation of H1 at position K64 modulates interactions with deubiquitylating enzymes and the deacetylase SIRT1. Moreover, it affects H1-dependent chromatosome assembly and phase separation resulting in a more open chromatosome conformation generally associated with a transcriptionally active chromatin state. In summary, we propose that site-specific ubiquitylation plays a general regulatory role for linker histone H1.

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Label-Free Mass Spectrometry-Based Quantification of Linker Histone H1 Variants in Clinical Samples

International Journal of Molecular Sciences ◽

10.3390/ijms21197330 ◽

2020 ◽

Vol 21 (19) ◽

pp. 7330

Author(s):

Roberta Noberini ◽

Cristina Morales Torres ◽

Evelyn Oliva Savoia ◽

Stefania Brandini ◽

Maria Giovanna Jodice ◽

...

Keyword(s):

Mass Spectrometry ◽

Histone H1 ◽

Histone Variants ◽

Linker Histone ◽

Clinical Samples ◽

Label Free ◽

Complex Samples ◽

Linker Histone H1 ◽

Ideal Tool ◽

Free Quantification

Epigenetic aberrations have been recognized as important contributors to cancer onset and development, and increasing evidence suggests that linker histone H1 variants may serve as biomarkers useful for patient stratification, as well as play an important role as drivers in cancer. Although traditionally histone H1 levels have been studied using antibody-based methods and RNA expression, these approaches suffer from limitations. Mass spectrometry (MS)-based proteomics represents the ideal tool to accurately quantify relative changes in protein abundance within complex samples. In this study, we used a label-free quantification approach to simultaneously analyze all somatic histone H1 variants in clinical samples and verified its applicability to laser micro-dissected tissue areas containing as low as 1000 cells. We then applied it to breast cancer patient samples, identifying differences in linker histone variants patters in primary triple-negative breast tumors with and without relapse after chemotherapy. This study highlights how label-free quantitation by MS is a valuable option to accurately quantitate histone H1 levels in different types of clinical samples, including very low-abundance patient tissues.

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