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Placing the HIRA histone chaperone complex in the chromatin landscape

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Homo sapiens

PROVIDER: GSE45025 | GEO | 2013/04/18

SECONDARY ACCESSION(S): PRJNA192849

REPOSITORIES: GEO

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Placing the HIRA histone chaperone complex in the chromatin landscape

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2013-04-18 | E-GEOD-45025 | biostudies-arrayexpress

Placing the HIRA histone chaperone complex in the chromatin landscape.

Project description:The HIRA chaperone complex, comprised of HIRA, UBN1, and CABIN1, collaborates with histone-binding protein ASF1a to incorporate histone variant H3.3 into chromatin in a DNA replication-independent manner. To better understand HIRA's function and mechanism, we integrated HIRA, UBN1, ASF1a, and histone H3.3 chromatin immunoprecipitation sequencing and gene expression analyses. Most HIRA-binding sites colocalize with UBN1, ASF1a, and H3.3 at active promoters and active and weak/poised enhancers. At promoters, binding of HIRA/UBN1/ASF1a correlates with the level of gene expression. HIRA is required for deposition of histone H3.3 at its binding sites. There are marked differences in nucleosome and coregulator composition at different classes of HIRA-bound regulatory sites. Underscoring this, we report physical interactions between the HIRA complex and transcription factors, a chromatin insulator and an ATP-dependent chromatin-remodeling complex. Our results map the distribution of the HIRA chaperone across the chromatin landscape and point to different interacting partners at functionally distinct regulatory sites.

| S-EPMC3974909 | biostudies-literature

The Mot1 ATPase and Spt16 Histone Chaperone Co-Regulate Transcription Through Preinitiation Complex Assembly and Nucleosome Organization

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2016-05-16 | E-GEOD-80235 | biostudies-arrayexpress

The histone acetylation module and histone chaperone in the Arabidopsis NuB4 complex have synergistic effect on chromatin accessibility

Project description:This SuperSeries is composed of the SubSeries listed below.

2024-10-25 | GSE259416 | GEO

Hira-dependent histone H3.3 deposition facilitates PRC2 recruitment at developmental loci in ES cells

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2013-09-30 | E-GEOD-42155 | biostudies-arrayexpress

Histone chaperone HIRA complex regulates retrotransposons in embryonic stem cells.

Project description:BackgroundHistone cell cycle regulator (HIRA) complex is an important histone chaperone that mediates the deposition of the H3.3 histone variant onto chromatin independently from DNA synthesis. However, it is still unknown whether it participates in the expression control of retrotransposons and cell fate determination.MethodsWe screened the role of HIRA complex members in repressing the expression of retrotransposons by shRNA depletion in embryonic stem cells (ESCs) followed by RT-qPCR. RNA-seq was used to study the expression profiles after depletion of individual HIRA member. RT-qPCR and western blot were used to determine overexpression of HIRA complex members. Chromatin immunoprecipitation (ChIP)-qPCR was used to find the binding of H3.3, HIRA members to chromatin. Co-immunoprecipitation was used to identify the interaction between Hira mutant and Ubn2. ChIP-qPCR was used to identify H3.3 deposition change and western blot of chromatin extract was used to validate the epigenetic change. Bioinformatics analysis was applied for the analysis of available ChIP-seq data.ResultsWe revealed that Hira, Ubn2, and Ubn1 were the main repressors of 2-cell marker retrotransposon MERVL among HIRA complex members. Surprisingly, Ubn2 and Hira targeted different groups of retrotransposons and retrotransposon-derived long noncoding RNAs (lncRNAs), despite that they partially shared target genes. Furthermore, Ubn2 prevented ESCs to gain a 2-cell like state or activate trophectodermal genes upon differentiation. Mechanistically, Ubn2 and Hira suppressed retrotransposons by regulating the deposition of histone H3.3. Decreased H3.3 deposition, that was associated with the loss of Ubn2 or Hira, caused the reduction of H3K9me2 and H3K9me3, which are known repressive marks of retrotransposons.ConclusionsOverall, our findings shed light on the distinct roles of HIRA complex members in controlling retrotransposons and cell fate conversion in ESCs.

| S-EPMC8973876 | biostudies-literature

Functional activity of the H3.3 histone chaperone complex HIRA requires trimerization of the HIRA subunit.

Project description:The HIRA histone chaperone complex deposits the histone variant H3.3 onto chromatin in a DNA synthesis-independent manner. It comprises three identified subunits, HIRA, UBN1 and CABIN1, however the functional oligomerization state of the complex has not been investigated. Here we use biochemical and crystallographic analysis to show that the HIRA subunit forms a stable homotrimer that binds two subunits of CABIN1 in vitro. A HIRA mutant that is defective in homotrimer formation interacts less efficiently with CABIN1, is not enriched at DNA damage sites upon UV irradiation and cannot rescue new H3.3 deposition in HIRA knockout cells. The structural homology with the homotrimeric replisome component Ctf4/AND-1 enables the drawing of parallels and discussion of the functional importance of the homotrimerization state of the HIRA subunit.

| S-EPMC6078998 | biostudies-literature

The histone chaperone CAF-1 safeguards somatic cell identity during transcription factor-induced reprogramming

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2015-12-10 | E-GEOD-66534 | biostudies-arrayexpress

Ubinuclein-1 confers histone H3.3-specific-binding by the HIRA histone chaperone complex.

Project description:Histone chaperones bind specific histones to mediate their storage, eviction or deposition from/or into chromatin. The HIRA histone chaperone complex, composed of HIRA, ubinuclein-1 (UBN1) and CABIN1, cooperates with the histone chaperone ASF1a to mediate H3.3-specific binding and chromatin deposition. Here we demonstrate that the conserved UBN1 Hpc2-related domain (HRD) is a novel H3.3-specific-binding domain. Biochemical and biophysical studies show the UBN1-HRD preferentially binds H3.3/H4 over H3.1/H4. X-ray crystallographic and mutational studies reveal that conserved residues within the UBN1-HRD and H3.3 G90 as key determinants of UBN1-H3.3-binding specificity. Comparison of the structure with the unrelated H3.3-specific chaperone DAXX reveals nearly identical points of contact between the chaperone and histone in the proximity of H3.3 G90, although the mechanism for H3.3 G90 recognition appears to be distinct. This study points to UBN1 as the determinant of H3.3-specific binding and deposition by the HIRA complex.

| S-EPMC4510971 | biostudies-literature

Regulation of Chromatin Accessibility by the Histone Chaperone CAF-1 Sustains Lineage Fidelity

Project description:This SuperSeries is composed of the SubSeries listed below.

2022-02-20 | GSE158229 | GEO