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In eukaryotic nuclei, DNA is wrapped around an octamer of core histones to form nucleosomes. H1 binds to the linker DNA of nucleosome to form the chromatosome, the next structural unit of chromatin. Structural features on individual chromatosomes contribute to chromatin structure, but not fully characterized. In addition to canonical nucleosomes composed of two copies each of histones H2A, H2B, H3, and H4 (H3 nucleosomes), centromeres chromatin contain nucleosomes in which H3 is replaced with its analog CENP-A, changing structural properties of CENP-A nucleosomes. Nothing is known about the interaction of H1 with CENP-A nucleosomes. Here we filled this gap and characterized the interaction of H1 histone with both types of nucleosomes. H1 does bind both types of the nucleosomes forming more compact chromosome particles with elevated affinity to H3 nucleosomes. H1 binding significantly increases the stability of chromatosomes preventing their spontaneous dissociation. In addition to binding to the entry-exit position of the DNA arms identified earlier, H1 is capable of bridging of distant DNA segments. H1 binding leads to the assembly of mononucleosomes in aggregates, stabilized by internucleosome interactions as well as bridging of the DNA arms of chromatosomes. Contribution of these finding to the chromatin structure and functions are discussed.
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Size-based expectation maximization for characterizing nucleosome positions and subtypes
Genome-wide nucleosome profiles are predominantly characterized using MNase-seq, which involves extensive MNase digestion and size selection to enrich for mononucleosome-sized fragments. Most available MNase-seq analysis packages assume that nucleosomes uniformly protect 147 bp DNA fragments. However, some nucleosomes with atypical histone or chemical compositions protect shorter lengths of DNA. The rigid assumptions imposed by current nucleosome analysis packages potentially prevent investigators from understanding the regulatory roles played by atypical nucleosomes. To enable the characterization of different nucleosome types from MNase-seq data, we introduce the size-based expectation maximization (SEM) nucleosome-calling package. SEM employs a hierarchical Gaussian mixture model to estimate nucleosome positions and subtypes. Nucleosome subtypes are automatically identified based on the distribution of protected DNA fragments. Benchmark analysis indicates that SEM is on par with existing packages in terms of standard nucleosome-calling accuracy metrics, while uniquely providing the ability to characterize nucleosome subtype identities. Applying SEM to a low-dose MNase-H2B-ChIP-seq data set from mouse embryonic stem cells, we identified three nucleosome types: short-fragment nucleosomes, canonical nucleosomes, and di-nucleosomes. Short-fragment nucleosomes can be divided further into two subtypes based on their chromatin accessibility. Short-fragment nucleosomes in accessible regions exhibit high MNase sensitivity and are enriched at transcription start sites (TSSs) and CTCF peaks, similar to previously reported “fragile nucleosomes.” These SEM-defined accessible short-fragment nucleosomes are found not just in promoters but also in distal regulatory regions. Additional analyses reveal their colocalization with the chromatin remodelers CHD6, CHD8, and EP400. In summary, SEM provides an effective platform for exploration of nonstandard nucleosome subtypes.
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- Award ID(s):
- 2045500
- PAR ID:
- 10574737
- Publisher / Repository:
- Cold Spring Harbor Laboratory Press
- Date Published:
- Journal Name:
- Genome Research
- Volume:
- 34
- Issue:
- 9
- ISSN:
- 1088-9051
- Page Range / eLocation ID:
- 1334 to 1343
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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- Free Publicly Accessible Full Text
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Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.1101/gr.279138.124
