Similar Datasets
Project description:Chromatin integrates extracellular signals to regulate gene expression and, therefore, tightly controls development. Mutations in histone genes, including H3.3 and H4, were recently identified in children with developmental disorders characterized by intellectual disability and dysmorphic facial features1–7. However, the mechanistic and functional roles of these de novo, heterozygous germline mutations remain largely unknown. Here, we focus on the histone H4 lysine 91 to arginine (H4K91R) or glutamine (H4K91Q) mutations located within the highly conserved core histone fold domain. Our findings demonstrate that H4K91 mutants form aberrant nuclear puncta in mouse embryonic stem cells (mESCs), as well as in differentiated neural cells in vitro and in vivo. Genome-wide analyses revealed that H4K91 mutants accumulate ectopically at H3.3 and H3K9me3-enriched heterochromatin regions. Mechanistically, H4K91 mutants demonstrated enhanced binding to histone H3 variant H3.3, and ablation of H3.3 or the H3.3-specific chaperone DAXX diminished the formation of H4 mutant puncta and enrichment at heterochromatin regions. Additionally, H4 mutant expression increased chromatin accessibility in mammalian cells. Phenotypically, H4 mutant mice exhibit reduced brain size and altered cortical neuron layers, reminiscent of microcephaly phenotypes observed in patients. Consistent with the altered brain development in vivo, the expression of H4 mutants alter developmental gene expression and accelerate pro-neural differentiation in cell culture models. Together, these studies reveal multiple concurrent pathogenic mechanisms of H4 mutants found in developmental disorders and further our understanding of how histone mutants regulate cell fate during development.
2023-10-19 | GSE231566 | GEO
Project description:Chromatin integrates extracellular signals to regulate gene expression and, therefore, tightly controls development. Mutations in histone genes, including H3.3 and H4, were recently identified in children with developmental disorders characterized by intellectual disability and dysmorphic facial features1–7. However, the mechanistic and functional roles of these de novo, heterozygous germline mutations remain largely unknown. Here, we focus on the histone H4 lysine 91 to arginine (H4K91R) or glutamine (H4K91Q) mutations located within the highly conserved core histone fold domain. Our findings demonstrate that H4K91 mutants form aberrant nuclear puncta in mouse embryonic stem cells (mESCs), as well as in differentiated neural cells in vitro and in vivo. Genome-wide analyses revealed that H4K91 mutants accumulate ectopically at H3.3 and H3K9me3-enriched heterochromatin regions. Mechanistically, H4K91 mutants demonstrated enhanced binding to histone H3 variant H3.3, and ablation of H3.3 or the H3.3-specific chaperone DAXX diminished the formation of H4 mutant puncta and enrichment at heterochromatin regions. Additionally, H4 mutant expression increased chromatin accessibility in mammalian cells. Phenotypically, H4 mutant mice exhibit reduced brain size and altered cortical neuron layers, reminiscent of microcephaly phenotypes observed in patients. Consistent with the altered brain development in vivo, the expression of H4 mutants alter developmental gene expression and accelerate pro-neural differentiation in cell culture models. Together, these studies reveal multiple concurrent pathogenic mechanisms of H4 mutants found in developmental disorders and further our understanding of how histone mutants regulate cell fate during development.
2023-10-19 | GSE231558 | GEO
Project description:Altered chromatin occupancy of patient-associated H4 mutants misregulate neuronal differentiation
| PRJNA966973 | ENA
Project description:Altered chromatin occupancy of patient-associated H4 mutants misregulate neuronal differentiation [RNA-seq]
| PRJNA966984 | ENA
Project description:Altered chromatin occupancy of patient-associated H4 mutants misregulate neuronal differentiation [ChIP-seq]
| PRJNA967124 | ENA
Project description:Erythropoiesis is one of the best understood examples of cellular differentiation. Morphologically, erythroid differentiation proceeds in a nearly identical fashion between humans and mice, but recent evidence has shown that networks of gene expression governing this process are divergent between species. We undertook a systematic comparative analysis of six histone modifications and four transcriptional master regulators in primary proerythroblasts and erythroid cell lines to better understand the underlying basis of these transcriptional differences. Our analyses suggest that while chromatin structure across orthologous promoters is strongly conserved, subtle differences are associated with transcriptional divergence between species. Many transcription factor (TF) occupancy sites were poorly conserved across species (∼25% for GATA1, TAL1, and NFE2) but were more conserved between proerythroblasts and cell lines derived from the same species. We found that certain cis-regulatory modules co-occupied by GATA1, TAL1, and KLF1 are under strict evolutionary constraint and localize to genes necessary for erythroid cell identity. More generally, we show that conserved TF occupancy sites are indicative of active regulatory regions and strong gene expression that is sustained during maturation. Our results suggest that evolutionary turnover of TF binding sites associates with changes in the underlying chromatin structure, driving transcriptional divergence. We provide examples of how this framework can be applied to understand epigenomic variation in specific regulatory regions, such as the β-globin gene locus. Our findings have important implications for understanding epigenomic changes that mediate variation in cellular differentiation across species, while also providing a valuable resource for studies of hematopoiesis.
| S-EPMC4270484 | biostudies-literature
Project description:Activating anaplastic lymphoma kinase (ALK) receptor tyrosine kinase (RTK) mutations occur in pediatric neuroblastoma and are associated with poor prognosis. To study ALK-activating mutations in a genetically controllable system, we employed CRIPSR/Cas9, incorporating orthologs of the human oncogenic mutations ALKF1174L and ALKY1278S in the Drosophila Alk locus. AlkF1251L and AlkY1355S mutant Drosophila exhibited enhanced Alk signaling phenotypes, but unexpectedly depended on the Jelly belly (Jeb) ligand for activation. Both AlkF1251L and AlkY1355S mutant larval brains displayed hyperplasia, represented by increased numbers of Alk-positive neurons. Despite this hyperplasic phenotype, no brain tumors were observed in mutant animals. We showed that hyperplasia in Alk mutants was not caused by significantly increased rates of proliferation, but rather by decreased levels of apoptosis in the larval brain. Using single-cell RNA sequencing, we identified perturbations during temporal fate specification in AlkY1355S mutant mushroom body lineages. These findings shed light on the role of Alk in neurodevelopmental processes and highlight the potential of Alk-activating mutations to perturb specification and promote survival in neuronal lineages. This article has an associated First Person interview with the first author of the paper.
| S-EPMC9403751 | biostudies-literature
Project description:Mitochondria are multifunctional, dynamic organelles important for stress response, cell longevity, ageing and death. Although the mitochondrion has its genome, nuclear-encoded proteins are essential in regulating mitochondria biogenesis, morphology, dynamics and function. Moreover, chromatin structure and epigenetic mechanisms govern the accessibility to DNA and control gene transcription, indirectly influencing nucleo-mitochondrial communications. Thus, they exert crucial functions in maintaining proper chromatin structure, cell morphology, gene expression, stress resistance and ageing. Here, we present our studies on the mtDNA copy number in Saccharomyces cerevisiae chromatin mutants and investigate the mitochondrial membrane potential throughout their lifespan. The mutants are arp4 (with a point mutation in the ARP4 gene, coding for actin-related protein 4-Arp4p), hho1Δ (lacking the HHO1 gene, coding for the linker histone H1), and the double mutant arp4 hho1Δ cells with the two mutations. Our findings showed that the three chromatin mutants acquired strain-specific changes in the mtDNA copy number. Furthermore, we detected the disrupted mitochondrial membrane potential in their chronological lifespan. In addition, the expression of nuclear genes responsible for regulating mitochondria biogenesis and turnover was changed. The most pronounced were the alterations found in the double mutant arp4 hho1Δ strain, which appeared as the only petite colony-forming mutant, unable to grow on respiratory substrates and with partial depletion of the mitochondrial genome. The results suggest that in the studied chromatin mutants, hho1Δ, arp4 and arp4 hho1Δ, the nucleus-mitochondria communication was disrupted, leading to impaired mitochondrial function and premature ageing phenotype in these mutants, especially in the double mutant.
| S-EPMC10058930 | biostudies-literature
Project description:Transcription factors are DNA-binding proteins that have key roles in gene regulation1,2. Genome-wide occupancy maps of transcriptional regulators are important for understanding gene regulation and its effects on diverse biological processes3-6. However, only a minority of the more than 1,600 transcription factors encoded in the human genome has been assayed. Here we present, as part of the ENCODE (Encyclopedia of DNA Elements) project, data and analyses from chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) experiments using the human HepG2 cell line for 208 chromatin-associated proteins (CAPs). These comprise 171 transcription factors and 37 transcriptional cofactors and chromatin regulator proteins, and represent nearly one-quarter of CAPs expressed in HepG2 cells. The binding profiles of these CAPs form major groups associated predominantly with promoters or enhancers, or with both. We confirm and expand the current catalogue of DNA sequence motifs for transcription factors, and describe motifs that correspond to other transcription factors that are co-enriched with the primary ChIP target. For example, FOX family motifs are enriched in ChIP-seq peaks of 37 other CAPs. We show that motif content and occupancy patterns can distinguish between promoters and enhancers. This catalogue reveals high-occupancy target regions at which many CAPs associate, although each contains motifs for only a minority of the numerous associated transcription factors. These analyses provide a more complete overview of the gene regulatory networks that define this cell type, and demonstrate the usefulness of the large-scale production efforts of the ENCODE Consortium.
| S-EPMC7398277 | biostudies-literature
Project description:The acetylation of the NH2-terminal tail of histone H4 by type B histone acetyltransferases (HATs) is involved in the process of chromatin assembly. Histone H4 associated with a nuclear type B HAT complex contains modifications in its globular core domain as well. In particular, acetylation was found at lysine 91. A mutation that alters this residue, which lies in the interface between histone H3/H4 tetramers and H2A/H2B dimers, confers phenotypes consistent with defects in chromatin assembly such as sensitivity to DNA damaging agents and derepression and alteration of silent chromatin structure. In addition, this mutation destabilizes the histone octamer, leading to defects in chromatin structure. These results indicate an important role for histone modifications outside the NH2-tail domains in the processes of chromatin assembly, DNA repair, and transcriptional silencing.
| S-EPMC2855496 | biostudies-literature