Distinct Features of the Histone Core Structure in Nucleosomes Containing the Histone H2A.B Variant

Sugiyama, Masaaki; Arimura, Yasuhiro; Shirayama, Kazuyoshi; Fujita, Ryosuke; Oba, Yojiro; Sato, Nobuhiro; Inoue, Rintaro; Oda, Takashi; Sato, Mamoru; Heenan, Richard K.; Kurumizaka, Hitoshi

doi:10.1016/j.bpj.2014.04.007

Cited by 26 publications

(33 citation statements)

References 39 publications

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“…Not surprisingly, H2A.B-containing mononucleosomes are unstable [7,8], which is also consistent with numerous studies showing the unwrapping of nucleosomal DNA from the octamer surface at the DNA entry and exit points [8–10]. This unwrapping of DNA also appears to cause a major reorganization of the histone tails within the nucleosome [11], and allows octamer formation on DNA fragments smaller than the typical 145 base pairs in vitro that are associated with a canonical nucleosome [12]. Third, the N-terminal tails of H2A.B histones distinctively lack lysine residues, but instead are enriched for arginines.…”

Section: Introductionsupporting

confidence: 75%

A new link between transcriptional initiation and pre-mRNA splicing: The RNA binding histone variant H2A.B

et al. 2017

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The replacement of histone H2A with its variant forms is critical for regulating all aspects of genome organisation and function. The histone variant H2A.B appeared late in evolution and is most highly expressed in the testis followed by the brain in mammals. This raises the question of what new function(s) H2A.B might impart to chromatin in these important tissues. We have immunoprecipitated the mouse orthologue of H2A.B, H2A.B.3 (H2A.Lap1), from testis chromatin and found this variant to be associated with RNA processing factors and RNA Polymerase (Pol) II. Most interestingly, many of these interactions with H2A.B.3 (Sf3b155, Spt6, DDX39A and RNA Pol II) were inhibited by the presence of endogenous RNA. This histone variant can bind to RNA directly in vitro and in vivo, and associates with mRNA at intron—exon boundaries. This suggests that the ability of H2A.B to bind to RNA negatively regulates its capacity to bind to these factors (Sf3b155, Spt6, DDX39A and RNA Pol II). Unexpectedly, H2A.B.3 forms highly decompacted nuclear subdomains of active chromatin that co-localizes with splicing speckles in male germ cells. H2A.B.3 ChIP-Seq experiments revealed a unique chromatin organization at active genes being not only enriched at the transcription start site (TSS), but also at the beginning of the gene body (but being excluded from the +1 nucleosome) compared to the end of the gene. We also uncover a general histone variant replacement process whereby H2A.B.3 replaces H2A.Z at intron-exon boundaries in the testis and the brain, which positively correlates with expression and exon inclusion. Taken together, we propose that a special mechanism of splicing may occur in the testis and brain whereby H2A.B.3 recruits RNA processing factors from splicing speckles to active genes following its replacement of H2A.Z.

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Section: Introductionsupporting

confidence: 75%

A new link between transcriptional initiation and pre-mRNA splicing: The RNA binding histone variant H2A.B

et al. 2017

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“…Nucleosome unwinding experiments using optical tweezers recently revealed the existence of multiple unwound states suggesting the symmetrical split of the octamer through H3-H3 interface under tension at specific conditions [18]. At the same time, equilibrium FRET experiments suggest an open intermediate state of the nucleosome, where the interface between (H3–H4) 2 tetramer and H2A–H2B dimer may be reversibly opened under physiological conditions [19].…”

Section: H2a-h2b Dimer As a Semi-independent Unit In Nucleosome Dynamicsmentioning

confidence: 99%

“…For example, the conformation of H2A.B-variant nucleosome was recently characterized by small angle neutron scattering, which revealed that the DNA ends were detached from the histone core surface and flexibly expanded toward the solvent. At the same time, the histone tails seem to be more compact in this variant compared to tails in canonical nucleosomes [18]. H2A.B-containing nucleosomes are destabilized relative to canonical nucleosomes in a way similar to that seen in hyperacetylated histones [32], and associate with only 118 to 130 bp of DNA [43,44] (Figure 3d).…”

Section: Structure and Stability Of H2a And H2b Variant Nucleosomesmentioning

confidence: 99%

Nucleosome adaptability conferred by sequence and structural variations in histone H2A–H2B dimers

Shaytan

Landsman

Panchenko

2015

Current Opinion in Structural Biology

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Nucleosome variability is essential for their functions in compacting the chromatin structure and regulation of transcription, replication and cell reprogramming. The DNA molecule in nucleosomes is wrapped around an octamer composed of four types of core histones (H3, H4, H2A, H2B). Nucleosomes represent dynamic entities and may change their conformation, stability and binding properties by employing different sets of histone variants or by becoming post-translationally modified. There are many variants of histones H2A and H2B. Specific H2A and H2B variants may preferentially associate with each other resulting in different combinations of variants and leading to the increased combinatorial complexity of nucleosomes. In addition, the H2A-H2B dimer can be recognized and substituted by chaperones/remodelers as a distinct unit, can assemble independently and is stable during nucleosome unwinding. In this review we discuss how sequence and structural variations in H2A-H2B dimers may provide necessary complexity and confer the nucleosome functional variability.

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“…Recent X-ray scattering analysis has also supported a more open H2A.B nucleosomal structure, whereby the H2A.B octasome is more extended as compared to the H2A octasome [80•]. In addition, small-angle neutron scattering analysis comparing the H2A.B nucleosome structure with canonical H2A revealed that while the DNA is more loosely attached in the H2A.B nucleosome, the histone tails are more tightly associated with the histone core within the nucleosome [81]. Altogether, these data showed that H2A.B incorporation results in a distinct nucleosome structure whereby the interactions with DNA segments are weaker and, thus, result in a less stable nucleosome.…”

Section: H2ab Localization and Impact On Chromatin Structurementioning

confidence: 98%

Chemical “Diversity” of Chromatin Through Histone Variants and Histone Modifications

2015

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The eukaryotic genome is highly complex and compartmentalized into distinct physical and functional domains. Although the majority of genomic DNA is wrapped around histone proteins in the same manner to form repeating units of nucleosomes, the use of distinct histone variants and the myriad of posttranslational modifications (PTMs) on different histones and amino acid residues create great diversity among these nucleosomes. In this review, we summarize some of the most recent findings in the histone variant and PTM fields and update the readers on our current understanding of various histone-related pathways. Furthermore, we discuss how homotypic or heterotypic deposition of histone variants as well as symmetric or asymmetric histone PTMs within the nucleosome context can further expand the diversity and functionality of chromatin. Altogether, this review highlights the complexity of chromatin composition and organization and their regulatory functions within the eukaryotic genome.

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Distinct Features of the Histone Core Structure in Nucleosomes Containing the Histone H2A.B Variant

Cited by 26 publications

References 39 publications

A new link between transcriptional initiation and pre-mRNA splicing: The RNA binding histone variant H2A.B

A new link between transcriptional initiation and pre-mRNA splicing: The RNA binding histone variant H2A.B

Nucleosome adaptability conferred by sequence and structural variations in histone H2A–H2B dimers

Chemical “Diversity” of Chromatin Through Histone Variants and Histone Modifications

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