Local compartment changes and regulatory landscape alterations in histone H1-depleted cells

Abstract

BackgroundLinker 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. Here we have used a combination of genome-wide approaches including DNA methylation, histone modification and DNase I 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.ResultsWe 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 associating 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.ConclusionsOur data show that cells require normal histone H1 levels to expose their proper regulatory landscape. Reducing the levels of histone H1 results in massive epigenetic changes and altered topological organization particularly at the most active chromosomal domains. Changes in TAD configuration coincide with epigenetic landscape changes but not with transcriptional output changes, supporting the emerging concept that transcriptional control and nuclear positioning of TADs are not causally related but independently controlled by the locally associated trans-acting factors.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-015-0857-0) contains supplementary material, which is available to authorized users.

Emerging roles of linker histones in regulating chromatin structure and function

“…4a). Genome-wide studies of the H1-depleted ES cells support the view that H1 promotes DNA methylation at many regulatory regions, particularly at enhancer regions 30 . The role of H1 in regulating DNA methylation may be important in many processes, including disease pathogenesis.…”

“…Although the structure of the nucleosome core particle at atomic resolution was solved more than a decade ago 29 , determination of the structures of the folded chromatin containing linker histones, and accordingly the structure of the chromatosome core particle, has been very challenging. Nevertheless, important progress has been made in resolving higher-order chromatin structures, including chromatosomes, the 30 nm chromatin fibre and topologically associating domains (TADs), and in elucidating the interactions involved, as well as the role of linker histones in establishing these higher-order structures 30 .…”

“…TADs are defined as continuous regions of chromatin (100 kb to 10 Mb of DNA) within which DNA–DNA interactions are much more frequent than in other chromatin regions. To investigate the role of linker histones in TAD structures, high-throughput chromatin conformation capture was applied to wild-type and linker-histone-depleted (triple knockout of H1.2, H1.3 and H1.4, resulting in an ~50% decrease in total levels of linker histones) mouse embryonic stem (ES) cells 22,30 . It was found that the location and size of TADs were largely unaltered between wild-type and linker-histone-depleted cells, but the frequency of their inter-domain interactions increased, suggesting that structural changes within TADs occurred when the H1-to-nucleosome stoichiometry was reduced.…”

SMARCA4 regulates gene expression and higher-order chromatin structure in proliferating mammary epithelial cells

“…Recent studies knocking down other fundamental chromatin organizers, CTCF (Zuin et al 2014), cohesin (Seitan et al 2013), and histone H1 (Geeven et al 2015) similarly showed little effect on overall genome organization as assayed by Hi-C. It is possible that the remaining SMARCA4 levels in the knockdown MCF-10A cells (Fig.…”

Transcriptome-wide characterization of the endogenous miR-34A-p53 tumor suppressor network

“…H1 histones are referred to as linker histones and bind to nucleosome constituents, stabilizing their interaction with DNA. Studies in H1-depleted mouse embryonic fibroblasts have shown that cells require homeostatic H1 levels to maintain their epigenetic landscape [18]. That exogenous miR-34A expression suppresses many of these replication-dependent transcripts in the presence of TP53 mutations, and to a greater extent than wild-type TP53 , suggests that miR- 34A may play an important role in sustaining epigenetic integrity when p53 function is compromised by mutation.…”