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Inactivating mutations in chromatin modifiers, like the α-thalassemia/mental retardation, X-linked (ATRX)-death domain-associated protein (DAXX) chromatin remodeling/histone H3.3 deposition complex, drive the cancer-specific alternative lengthening of telomeres (ALT) pathway. Prior studies revealed that HIRA, another histone H3.3 chaperone, compensates for ATRX-DAXX loss at telomeres to sustain ALT cancer cell survival. How HIRA rescues telomeres from the consequences of ATRX-DAXX deficiency remains unclear. Here, using an assay for transposase-accessible chromatin using sequencing (ATAC-seq) and cleavage under targets and release using nuclease (CUT&RUN), we establish that HIRA-mediated deposition of new H3.3 maintains telomeric chromatin accessibility to prevent the detrimental accumulation of nucleosome-free single-stranded DNA (ssDNA) in ATRX-DAXX-deficient ALT cells. We show that the HIRA-UBN1/UBN2 complex deposits new H3.3 to prevent TERRA R-loop buildup and transcription-replication conflicts (TRCs) at telomeres. Furthermore, HIRA-mediated H3.3 incorporation into telomeric chromatin links productive ALT to the phosphorylation of serine 31, an H3.3-specific amino acid, by Chk1. Therefore, we identify a critical role for HIRA-mediated H3.3 deposition that ensures the survival of ATRX-DAXX-deficient ALT cancer cells. [Display omitted] • HIRA establishes greater telomeric chromatin accessibility after ATRX-DAXX loss • Deposition of new H3.3 by HIRA-UBN restricts telomeric ssDNA and TERRA R-loops • Unresolved TERRA R-loops block new H3.3 deposition by HIRA-UBN • CHK1 phosphorylation of H3.3 is critical to prevent ssDNA and TERRA R-loop buildup Lynskey et al. report links between HIRA-mediated histone H3.3 deposition and R-loop homeostasis at ALT telomeres. In most ALT cancer cells, after ATRX-DAXX is inactivated, HIRA regulates telomeric chromatin assembly. HIRA limits ssDNA accumulation and mitigates out-of-control R-loop formation and transcription-replication conflicts at telomeres, threatening cancer cell survival. [ABSTRACT FROM AUTHOR]

Kojic acid (KA) is a representative secondary metabolite of Aspergillus oryzae , but the underlying molecular mechanisms that regulate KA production are unknown. This study tried to find a genetic factor of KA production in A. oryzae , with a special focus on liquid cultures. We screened a gene predicted to encode HirA, a subunit of the histone chaperon, the HIR complex. A gene disruption strain of hirA showed decreased KA production in liquid culture, whereas it showed increased KA production in plate culture. We confirmed that a decrease/increase of KA production observed by hirA disruption was caused by altered expression of kojA and kojR. These observations suggested the regulatory role of histone chaperon in secondary metabolism in filamentous fungi. So far as we know, this report is the first showing that disruption of a gene resulted in the opposite effect on KA production in liquid and plate cultures in A. oryzae. [ABSTRACT FROM AUTHOR]

The highly repetitive and transcriptionally active ribosomal DNA (rDNA) genes are exceedingly susceptible to genotoxic stress. Induction of DNA double-strand breaks (DSBs) in rDNA repeats is associated with ataxia-telangiectasia-mutated (ATM)-dependent rDNA silencing and nucleolar reorganization where rDNA is segregated into nucleolar caps. However, the regulatory events underlying this response remain elusive. Here, we identify protein UFMylation as essential for rDNA-damage response in human cells. We further show the only ubiquitin-fold modifier 1 (UFM1)-E3 ligase UFL1 and its binding partner DDRGK1 localize to nucleolar caps upon rDNA damage and that UFL1 loss impairs ATM activation and rDNA transcriptional silencing, leading to reduced rDNA segregation. Moreover, analysis of nuclear and nucleolar UFMylation targets in response to DSB induction further identifies key DNA-repair factors including ATM, in addition to chromatin and actin network regulators. Taken together, our data provide evidence of an essential role for UFMylation in orchestrating rDNA DSB repair. [Display omitted] • The UFMylation pathway is important for cell survival in response to rDNA DSBs • UFL1 loss causes reduced ATM activation, rRNA transcriptional silencing, and nucleolar caps • The E3-like UFMylation proteins UFL1 and DDRGK1 associate with TCOF1 in nucleolar caps • Key DNA-repair factors and chromatin and actin network regulators are UFMylation targets Panichnantakul et al. identify protein UFMylation as essential for rDNA-damage response in human cells. They show that key DNA-repair factors and chromatin and actin network regulators are UFMylation targets in response to DSBs and that loss of UFM1-E3 ligase UFL1 impairs ATM activation and rDNA transcriptional silencing, leading to reduced rDNA segregation. [ABSTRACT FROM AUTHOR]

Abstract: Due to its extensive length, DNA is packaged into a protective chromatin structure known as the nucleosome. In order to carry out various cellular functions, nucleosomes must be disassembled, allowing access to the underlying DNA, and subsequently reassembled on completion of these processes. The assembly and disassembly of nucleosomes is dependent on the function of histone modifiers, chromatin remodelers and histone chaperones. In this review, we discuss the roles of an evolutionarily conserved histone chaperone known as the HIR/HIRA complex. In S. cerevisiae, the HIR complex is made up of the proteins Hir1, Hir2, Hir3 and Hpc2, which collectively act in transcriptional regulation, elongation, gene silencing, cellular senescence and even aging. This review presents an overview of the role of the HIR complex, in yeast as well as other organisms, in each of these processes, in order to give a better understanding of how nucleosome assembly is imperative for cellular homeostasis and genomic integrity. This article is part of a Special Issue entitled: Histone chaperones and Chromatin assembly. [Copyright &y& Elsevier]

Abstract: Chromatin, a complex of DNA and associated proteins, governs diverse processes including gene transcription, DNA replication and DNA repair. The fundamental unit of chromatin is the nucleosome, consisting of 147bp of DNA wound about 1.6 turns around a histone octamer of one (H3–H4)2 tetramer and two H2A–H2B dimers. In order to form nucleosomes, (H3–H4)2 tetramers are deposited first, followed by the rapid deposition of H2A–H2B. It is believed that the assembly of (H3–H4)2 tetramers into nucleosomes is the rate-limiting step of nucleosome assembly. Moreover, assembly of H3–H4 into nucleosomes following DNA replication, DNA repair and gene transcription is likely to be a key step in the inheritance of epigenetic information and maintenance of genome integrity. In this review, we discuss how nucleosome assembly of H3–H4 is regulated by concerted actions of histone chaperones and modifications on newly synthesized H3 and H4. This article is part of a Special Issue entitled: Histone chaperones and Chromatin assembly. [Copyright &y& Elsevier]

Abstract: Cellular senescence is an important tumor suppression process, and a possible contributor to tissue aging. Senescence is accompanied by extensive changes in chromatin structure. In particular, many senescent cells accumulate specialized domains of facultative heterochromatin, called Senescence-Associated Heterochromatin Foci (SAHF), which are thought to repress expression of proliferation-promoting genes, thereby contributing to senescence-associated proliferation arrest. This article reviews our current understanding of the structure, assembly and function of these SAHF at a cellular level. The possible contribution of SAHF to tumor suppression and tissue aging is also critically discussed. [Copyright &y& Elsevier]

Abstract: In mammalian fertilization, the paternal genome is delivered to the secondary oocyte by sperm with protamine compacted DNA, while the maternal genome is arrested in meiotic metaphase II. Thus, at the beginning of fertilization, the two gametic chromatin sets are strikingly different. We elaborate on this contrast by reporting asymmetry for histone H3 type in the pre-S-phase zygote when male chromatin is virtually devoid of histone H3.1/3.2. Localization of the histone H3.3/H4 assembly factor Hira with the paternal chromatin indicates the presence of histone H3.3. In conjunction with this, we performed a systematic immunofluorescence analysis of histone N-tail methylations at position H3K4, H3K9, H3K27 and H4K20 up to the young pronucleus stage and show that asymmetries reported earlier are systematic for virtually all di- and tri-methylations but not for mono-methylation of H3K4 and H4K20, the only marks studied present in the early male pronucleus. For H4K20 the expanding male chromatin is rapidly mono-methylated. This coincides with the formation of maternally derived nucleosomes, a process which is observed as early as sperm chromatin decondensation occurs. Absence of tri-methylated H3K9, tri-methylated H4K20 and presence of loosely anchored HP1-β combined with the homogenous presence of mono-methylated H4K20 suggests the absence of a division of the paternal chromatin in eu- and heterochromatin. In summary the male, in contrast to female G1 chromatin, is uniform and contains predominantly histone H3.3 as histone H3 variant. [Copyright &y& Elsevier]

7Be radioactive ion beam (RIB) has been produced by an in-flight separation technique using the recoil mass spectrometer Heavy Ion Reaction Analyzer (HIRA) at NSC. To carry out nuclear reaction studies using the low-intensity RIB, a compact geometry detector system has been installed at the HIRA focal plane. The new detector setup consists of a Multi-Wire Proportional Counter (MWPC) followed by a DE-E detector telescope. The MWPC is used for obtaining the RIB profile and normalization. Fast timing signal of the MWPC is also used for the time-of-flight measurements for correction of energy spread of the RIBs in event mode. The detector telescope consists of a gas ionization chamber which gives energy loss (DE), followed by a two-dimensional position-sensitive silicon detector which gives residual energy and position. The telescope provides particle identification, energy and reaction angle information. The measured position resolution of the MWPC is about 0.9 mm (FWHM). The detector setup has also been used in stable beam experiments as well where the MWPC provides mass spectrum of the recoils at the RMS focal plane according to their position. [Copyright &y& Elsevier]

HIRA is a histone chaperone that deposits the histone variant H3.3 in transcriptionally active genes. In DiGeorge syndromes, a DNA stretch encompassing HIRA is deleted. The syndromes manifest varied abnormalities, including immunodeficiency and thrombocytopenia. HIRA is essential in mice, as total knockout (KO) results in early embryonic death. However, the role of HIRA in hematopoiesis is poorly understood. We investigate hematopoietic cell-specific Hira deletion in mice and show that it dramatically reduces bone marrow hematopoietic stem cells (HSCs), resulting in anemia, thrombocytopenia, and lymphocytopenia. In contrast, fetal hematopoiesis is normal in Hira-KO mice, although fetal HSCs lack the reconstitution capacity. Transcriptome analysis reveals that HIRA is required for expression of many transcription factors and signaling molecules critical for HSCs. ATAC-seq analysis demonstrates that HIRA establishes HSC-specific DNA accessibility, including the SPIB/PU.1 sites. Together, HIRA provides a chromatin environment essential for HSCs, thereby steering their development and survival. • HIRA confers chromatin accessibility that defines the HSC transcriptome • Long-term HSCs in adult Hira KO incur increased DNA damage and apoptosis • Hira KO has some similarity to DiGeorge syndromes, which lack the HIRA locus • Fetal hematopoiesis is spared in Hira-KO mice Chen et al. show that the histone H3.3 chaperone HIRA directs development and survival of adult hematopoietic stem cells (HSCs). Hira deletion impairs development of all lineages of hematopoiesis. [ABSTRACT FROM AUTHOR]

Metastasis is the leading cause of cancer mortality. Chromatin remodeling provides the foundation for the cellular reprogramming necessary to drive metastasis. However, little is known about the nature of this remodeling and its regulation. Here, we show that metastasis-inducing pathways regulate histone chaperones to reduce canonical histone incorporation into chromatin, triggering deposition of H3.3 variant at the promoters of poor-prognosis genes and metastasis-inducing transcription factors. This specific incorporation of H3.3 into chromatin is both necessary and sufficient for the induction of aggressive traits that allow for metastasis formation. Together, our data clearly show incorporation of histone variant H3.3 into chromatin as a major regulator of cell fate during tumorigenesis, and histone chaperones as valuable therapeutic targets for invasive carcinomas. • Metastasis inducers lead to a decline in CAF-1 suppressing canonical H3 incorporation • EMT and metastatic colonization occur as a function of CAF-1 levels • Histone H3.3 variant is essential for tumor progression and aggressive phenotypes • HIRA-mediated H3.3 gap filling induces a pro-metastatic transcriptional reprogramming Gomes et al. reveal metastatic stimuli reduce histone H3.1/H3.2 deposition on chromatin by suppressing the CAF-1 complex in breast and NSCLC cancer cells, leading to increased incorporation of non-canonical histone H3.3, which in turn induces chromatin remodeling and expression of metastatic genes. [ABSTRACT FROM AUTHOR]