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Summary: Leaf senescence is an orderly process regulated by multiple internal factors and diverse environmental stresses including nutrient deficiency. Histone variants are involved in regulating plant growth and development. However, their functions and underlying regulatory mechanisms in leaf senescence remain largely unclear.Here, we found that H2B histone variant HTB4 functions as a negative regulator of leaf senescence. Loss of function of HTB4 led to early leaf senescence phenotypes that were rescued by functional complementation. RNA‐seq analysis revealed that several Ib subgroup basic helix–loop–helix (bHLH) transcription factors (TFs) involved in iron (Fe) homeostasis, including bHLH038, bHLH039, bHLH100, and bHLH101, were suppressed in the htb4 mutant, thereby compromising the expressions of FERRIC REDUCTION OXIDASE 2 (FRO2) and IRON‐REGULATED TRANSPORTER (IRT1), two important components of the Fe uptake machinery.Chromatin immunoprecipitation‐quantitative polymerase chain reaction analysis revealed that HTB4 could bind to the promoter regions of Ib bHLH TFs and enhance their expression by promoting the enrichment of the active mark H3K4me3 near their transcriptional start sites. Moreover, overexpression of Ib bHLH TFs or IRT1 suppressed the premature senescence phenotype of the htb4 mutant.Our work established a signaling pathway, HTB4‐bHLH TFs‐FRO2/IRT1‐Fe homeostasis, which regulates the onset and progression of leaf senescence. See also the Commentary on this article by Dubos, 240: 461–463. [ABSTRACT FROM AUTHOR]

Summary: Plants can sense temperature changes and adjust their development and morphology accordingly in a process called thermomorphogenesis. This phenotypic plasticity implies complex mechanisms regulating gene expression reprogramming in response to environmental alteration. Histone variants often associate with specific chromatin states; yet, how their deposition/eviction modulates transcriptional changes induced by environmental cues remains elusive.In Arabidopsis thaliana, temperature elevation‐induced transcriptional activation at thermo‐responsive genes entails the chromatin eviction of a histone variant H2A.Z by INO80, which is recruited to these loci via interacting with a key thermomorphogenesis regulator PIF4.Here, we show that both INO80 and the deposition chaperones of another histone variant H3.3 associate with ELF7, a critical component of the transcription elongator PAF1 complex. H3.3 promotes thermomorphogenesis and the high temperature‐enhanced RNA Pol II transcription at PIF4 targets, and it is broadly required for the H2A.Z removal‐induced gene activation. Reciprocally, INO80 and ELF7 regulate H3.3 deposition, and are necessary for the high temperature‐induced H3.3 enrichment at PIF4 targets.Our findings demonstrate close coordination between H2A.Z eviction and H3.3 deposition in gene activation induced by high temperature, and pinpoint the importance of histone variants dynamics in transcriptional regulation. [ABSTRACT FROM AUTHOR]

The relatively quiet mutational landscape of rhabdomyosarcoma (RMS) suggests that epigenetic deregulation could be central to oncogenesis and tumour aggressiveness. Histone variants have long been recognised as important epigenetic regulators of gene expression. However, the role of histone variants in RMS has not been studied hitherto. In this study, we show that histone variant H3.3 is overexpressed in alveolar RMS (ARMS), an aggressive subtype of RMS. Functionally, knockdown of H3F3A, which encodes for H3.3, significantly impairs the ability of ARMS cells to undertake migration and invasion and reduces Rho activation. In addition, a striking reduction in metastatic tumour burden and improved survival is apparent in vivo. Using RNA‐sequencing and ChIP‐sequencing analyses, we identified melanoma cell adhesion molecule (MCAM/CD146) as a direct downstream target of H3.3. Loss of H3.3 resulted in a reduction in the presence of active marks and an increase in the occupancy of H1 at the MCAM promoter. Cell migration and invasion were rescued in H3F3A‐depleted cells through MCAM overexpression. Moreover, we identified G9a, a lysine methyltransferase encoded by EHMT2, as an upstream regulator of H3F3A. Therefore, this study identifies a novel H3.3 dependent axis involved in ARMS metastasis. These findings establish the potential of MCAM as a therapeutic target for high‐risk ARMS patients. © 2022 The Pathological Society of Great Britain and Ireland. [ABSTRACT FROM AUTHOR]

In the last 15 years, increasing evidence linking epigenetics to various aspects of cancer biology has prompted the investigation of histone post‐translational modifications (PTMs) and histone variants in the context of clinical samples. The studies performed so far demonstrated the potential of this type of investigations for the discovery of both potential epigenetic biomarkers for patient stratification and novel epigenetic mechanisms potentially targetable for cancer therapy. Although traditionally the analysis of histones in clinical samples was performed through antibody‐based methods, mass spectrometry (MS) has emerged as a more powerful tool for the unbiased, comprehensive, and quantitative investigation of histone PTMs and variants. MS has been extensively used for the analysis of epigenetic marks in cell lines and animal tissue and, thanks to recent technological advances, is now ready to be applied also to clinical samples. In this review, we will provide an overview on the quantitative MS‐based analysis of histones, their PTMs and their variants in cancer clinical samples, highlighting current achievements and future perspectives for this novel field of research. Among the different MS‐based approaches currently available for histone PTM profiling, we will focus on the 'bottom‐up' strategy, namely the analysis of short proteolytic peptides, as it has been already successfully employed for the analysis of clinical samples. [ABSTRACT FROM AUTHOR]

Chromatin integrity is essential for cellular homeostasis. Polycomb group proteins modulate chromatin states and transcriptionally repress developmental genes to maintain cell identity. They also repress repetitive sequences such as major satellites and constitute an alternative state of pericentromeric constitutive heterochromatin at paternal chromosomes (pat‐PCH) in mouse pre‐implantation embryos. Remarkably, pat‐PCH contains the histone H3.3 variant, which is absent from canonical PCH at maternal chromosomes, which is marked by histone H3 lysine 9 trimethylation (H3K9me3), HP1, and ATRX proteins. Here, we show that SUMO2‐modified CBX2‐containing Polycomb Repressive Complex 1 (PRC1) recruits the H3.3‐specific chaperone DAXX to pat‐PCH, enabling H3.3 incorporation at these loci. Deficiency of Daxx or PRC1 components Ring1 and Rnf2 abrogates H3.3 incorporation, induces chromatin decompaction and breakage at PCH of exclusively paternal chromosomes, and causes their mis‐segregation. Complementation assays show that DAXX‐mediated H3.3 deposition is required for chromosome stability in early embryos. DAXX also regulates repression of PRC1 target genes during oogenesis and early embryogenesis. The study identifies a novel critical role for Polycomb in ensuring heterochromatin integrity and chromosome stability in mouse early development. Synopsis: Formation of pericentromeric heterochromatin (PCH) in early mouse embryos involves selective incorporation of the histone variant H3.3. Polycomb repressive complex 1 (PRC1) facilitates this by recruitment of H3.3 chaperone/remodeler DAXX‐ATRX in a SUMOylation‐dependent manner. Histone chaperone DAXX controls H3.3 deposition into pericentromeric heterochromatin exclusively at paternal chromosomes of early mouse embryos.Canonical PRC1, but not PRC2, is required for recruitment of DAXX and H3.3 deposition at paternal PCH.SUMOylation of the PRC1 component CBX2 mediates interaction between CBX2 and DAXX.DAXX contributes to PRC1‐dependent gene repression in oocytes. [ABSTRACT FROM AUTHOR]

In postmitotic neurons, nucleosomal turnover was long considered to be a static process that is inconsequential to transcription. However, our recent studies in human and rodent brain indicate that replication-independent (RI) nucleosomal turnover, which requires the histone variant H3.3, is dynamic throughout life and is necessary for activity-dependent gene expression, synaptic connectivity, and cognition. H3.3 turnover also facilitates cellular lineage specification and plays a role in suppressing the expression of heterochromatic repetitive elements, including mutagenic transposable sequences, in mouse embryonic stem cells. In this essay, we review mechanisms and functions for RI nucleosomal turnover in brain and present the hypothesis that defects in histone dynamics may represent a common mechanism underlying neurological aging and disease. [ABSTRACT FROM AUTHOR]

Histone H3.3 turnover displays distinct dynamics at various genomic elements such as promoters, enhancers, gene bodies, and heterochromatic regions, suggesting that it is differentially regulated according to chromatin context. Incorporation of variant histones into chromatin provides a mechanism to modulate chromatin states in addition to histone modifications. The replication-independent deposition and replacement of histone variant H3.3, i.e. H3.3 turnover, is mainly associated with transcriptional activity. H3.3 or H3.3-like histone turnover has been studied in various organisms from yeast to mammals. Here, we review the recent progress on this topic. The diversified turnover profiles of H3.3, and their corresponding underlying mechanisms, may reflect distinct requirements for chromatin accessibility in different biological events. [ABSTRACT FROM AUTHOR]