Crystal Structure and Characterization of Novel Human Histone H3 Variants, H3.6, H3.7, and H3.8

Taguchi, Hiroyuki; Xie, Yan; Horikoshi, Naoki; Maehara, Kazuhira; Harada, Akihito; Nogami, Jumpei; Sato, Koichi; Arimura, Yasuhiro; Osakabe, Akihisa; Kujirai, Tomoya; Iwasaki, Takeshi; Semba, Yuichiro; Tachibana, Taro; Kimurâ, Hiroshi; Ohkawa, Yasuyuki; Kurumizaka, Hitoshi

doi:10.1021/acs.biochem.6b01098

Cited by 23 publications

(25 citation statements)

References 76 publications

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“…Other human variants, H3.6, H3.7 and H3.8, are tissue-specific (Taguchi et al, 2017). H3.6 forms nucleosomes that seem to have a deposition pattern similar to H3.3 nucleosomes, but are less stable because of an I62V change that reduces hydrophobic contact with H4.…”

Section: Glossarymentioning

confidence: 99%

Histone variants at a glance

Talbert

Henikoff

2021

Journal of Cell Science

137

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Eukaryotic nucleosomes organize chromatin by wrapping 147 bp of DNA around a histone core particle comprising two molecules each of histone H2A, H2B, H3 and H4. The DNA entering and exiting the particle may be bound by the linker histone H1. Whereas deposition of bulk histones is confined to S-phase, paralogs of the common histones, known as histone variants, are available to carry out functions throughout the cell cycle and accumulate in post-mitotic cells. Histone variants confer different structural properties on nucleosomes by wrapping more or less DNA or by altering nucleosome stability. They carry out specialized functions in DNA repair, chromosome segregation and regulation of transcription initiation, or perform tissue-specific roles. In this Cell Science at a Glance article and the accompanying poster, we briefly examine new insights into histone origins and discuss variants from each of the histone families, focusing on how structural differences may alter their functions.

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Section: Glossarymentioning

confidence: 99%

Histone variants at a glance

Talbert

Henikoff

2021

Journal of Cell Science

137

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“…Histone H2A has a relatively high number of variants, while histones H2B and H4 have undergone little evolutionary divergence–likely reflecting their positions within the nucleosome and their roles in stabilization of the nucleosome core particle ( Henikoff and Smith, 2015 ). There are, however, a large number of histone H3 variants in humans, namely H3.1, H3.2, H3.3, H3t/H3.4, H3.5, H3.Y, H3.X, CENP-A, the more recently proposed H3.3-like H3.6 and H3.8, as well as the H3.1-like H3.7 ( Franklin and Zweidler, 1977 ; Earnshaw and Rothfield, 1985 ; Albig et al, 1996 ; Wiedemann et al, 2010 ; Schenk et al, 2011 ; Taguchi et al, 2017 ). Of these, the replication-coupled H3.1, and replication-independent H3.3 variants are arguably some of the better-studied histone proteins and hence the focus herein.…”

Section: Histone Variants and Post-translational Modificationsmentioning

confidence: 99%

Interactions With Histone H3 & Tools to Study Them

Scott

Campos

2020

Front. Cell Dev. Biol.

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Histones are an integral part of chromatin and thereby influence its structure, dynamics, and functions. The effects of histone variants, posttranslational modifications, and binding proteins is therefore of great interest. From the moment that they are deposited on chromatin, nucleosomal histones undergo dynamic changes in function of the cell cycle, and as DNA is transcribed and replicated. In the process, histones are not only modified and bound by various proteins, but also shuffled, evicted, or replaced. Technologies and tools to study such dynamic events continue to evolve and better our understanding of chromatin and of histone proteins proper. Here, we provide an overview of H3.1 and H3.3 histone dynamics throughout the cell cycle, while highlighting some of the tools used to study their protein-protein interactions. We specifically discuss how histones are chaperoned, modified, and bound by various proteins at different stages of the cell cycle. Established and select emerging technologies that furthered (or have a high potential of furthering) our understanding of the dynamic histone-protein interactions are emphasized. This includes experimental tools to investigate spatiotemporal changes on chromatin, the role of histone chaperones, histone posttranslational modifications, and histone-binding effector proteins.

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“…This means that the absence of a PS suffix does not indicate a functional gene, and that there is no positional information in the gene symbols of most pseudogenes. Recently, some pseudogenes have also been shown to be functional histone variants [74].…”

Section: Histone Genesmentioning

confidence: 99%

The human canonical core histone catalogue

Pinto

Flaus

2019

Preprint

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Core histone proteins H2A, H2B, H3, and H4 are encoded by a large family of genes distributed across the human genome. Canonical core histones contribute the majority of proteins to bulk chromatin packaging, and are encoded in 4 clusters by 65 coding genes comprising 17 for H2A, 18 for H2B, 15 for H3, and 15 for H4, along with at least 17 total pseudogenes. The canonical core histone genes display coding variation that gives rise to 11 H2A, 15 H2B, 4 H3, and 2 H4 unique protein isoforms. Although histone proteins are highly conserved overall, these isoforms represent a surprising and seldom recognised variation with amino acid identity as low as 77 % between canonical histone proteins of the same type. The gene sequence and protein isoform diversity also exceeds commonly used subtype designations such as H2A.1 and H3.1, and exists in parallel with the well-known specialisation of variant histone proteins. RNA sequencing of histone transcripts shows evidence for differential expression of histone genes but the functional significance of this variation has not yet been investigated. To assist understanding of the implications of histone gene and protein diversity we have catalogued the entire human canonical core histone gene and protein complement. In order to organise this information in a robust, accessible, and accurate form, we applied software build automation tools to dynamically generate the canonical core histone repertoire based on current genome annotations and then to organise the information into a manuscript format. Automatically generated values are shown with a light grey background. Alongside recognition of the encoded protein diversity, this has led to multiple corrections to human histone annotations, reflecting the flux of the human genome as it is updated and enriched in reference databases. This dynamic manuscript approach is inspired by the aims of reproducible research and can be readily adapted to other gene families.

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Crystal Structure and Characterization of Novel Human Histone H3 Variants, H3.6, H3.7, and H3.8

Cited by 23 publications

References 76 publications

Histone variants at a glance

Histone variants at a glance

Interactions With Histone H3 & Tools to Study Them

The human canonical core histone catalogue

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