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Nature Communications Dec 2023ATP-dependent chromatin remodeling SWI/SNF complexes exist in three subcomplexes: canonical BAF (cBAF), polybromo BAF (PBAF), and a newly described non-canonical BAF...
ATP-dependent chromatin remodeling SWI/SNF complexes exist in three subcomplexes: canonical BAF (cBAF), polybromo BAF (PBAF), and a newly described non-canonical BAF (ncBAF). While cBAF and PBAF regulate fates of multiple cell types, roles for ncBAF in hematopoietic stem cells (HSCs) have not been investigated. Motivated by recent discovery of disrupted expression of BRD9, an essential component of ncBAF, in multiple cancers, including clonal hematopoietic disorders, we evaluate here the role of BRD9 in normal and malignant HSCs. BRD9 loss enhances chromatin accessibility, promoting myeloid lineage skewing while impairing B cell development. BRD9 significantly colocalizes with CTCF, whose chromatin recruitment is augmented by BRD9 loss, leading to altered chromatin state and expression of myeloid-related genes within intact topologically associating domains. These data uncover ncBAF as critical for cell fate specification in HSCs via three-dimensional regulation of gene expression and illuminate roles for ncBAF in normal and malignant hematopoiesis.
Topics: Transcription Factors; Chromatin; Chromatin Assembly and Disassembly; Cell Differentiation; Hematopoietic Stem Cells
PubMed: 38102116
DOI: 10.1038/s41467-023-44081-6 -
Cells Apr 2023The Nucleosome Remodelling and Deacetylase (NuRD) complex represents one of the major chromatin remodelling complexes in mammalian cells, uniquely coupling the ability... (Review)
Review
The Nucleosome Remodelling and Deacetylase (NuRD) complex represents one of the major chromatin remodelling complexes in mammalian cells, uniquely coupling the ability to "open" the chromatin by inducing nucleosome sliding with histone deacetylase activity. At the core of the NuRD complex are a family of ATPases named CHDs that utilise the energy produced by the hydrolysis of the ATP to induce chromatin structural changes. Recent studies have highlighted the prominent role played by the NuRD in regulating gene expression during brain development and in maintaining neuronal circuitry in the adult cerebellum. Importantly, components of the NuRD complex have been found to carry mutations that profoundly affect neurological and cognitive development in humans. Here, we discuss recent literature concerning the molecular structure of NuRD complexes and how the subunit composition and numerous permutations greatly determine their functions in the nervous system. We will also discuss the role of the CHD family members in an array of neurodevelopmental disorders. Special emphasis will be given to the mechanisms that regulate the NuRD complex composition and assembly in the cortex and how subtle mutations may result in profound defects of brain development and the adult nervous system.
Topics: Animals; Humans; Mi-2 Nucleosome Remodeling and Deacetylase Complex; Nucleosomes; Chromatin; Chromatin Assembly and Disassembly; Mammals
PubMed: 37190088
DOI: 10.3390/cells12081179 -
Nucleic Acids Research Apr 2021DNA methylation is essential to development and cellular physiology in mammals. Faulty DNA methylation is frequently observed in human diseases like cancer and... (Review)
Review
DNA methylation is essential to development and cellular physiology in mammals. Faulty DNA methylation is frequently observed in human diseases like cancer and neurological disorders. Molecularly, this epigenetic mark is linked to other chromatin modifications and it regulates key genomic processes, including transcription and splicing. Each round of DNA replication generates two hemi-methylated copies of the genome. These must be converted back to symmetrically methylated DNA before the next S-phase, or the mark will fade away; therefore the maintenance of DNA methylation is essential. Mechanistically, the maintenance of this epigenetic modification takes place during and after DNA replication, and occurs within the very dynamic context of chromatin re-assembly. Here, we review recent discoveries and unresolved questions regarding the mechanisms, dynamics and fidelity of DNA methylation maintenance in mammals. We also discuss how it could be regulated in normal development and misregulated in disease.
Topics: Animals; Chromatin Assembly and Disassembly; DNA (Cytosine-5-)-Methyltransferase 1; DNA Methylation; DNA Replication; Epigenesis, Genetic; Humans; Mammals; Neoplasms; Nervous System Diseases; Ubiquitin-Protein Ligases
PubMed: 33300031
DOI: 10.1093/nar/gkaa1154 -
Nature Communications Dec 2021Numerous chromatin remodeling enzymes position nucleosomes in eukaryotic cells. Aside from these factors, transcription, DNA sequence, and statistical positioning of...
Numerous chromatin remodeling enzymes position nucleosomes in eukaryotic cells. Aside from these factors, transcription, DNA sequence, and statistical positioning of nucleosomes also shape the nucleosome landscape. The precise contributions of these processes remain unclear due to their functional redundancy in vivo. By incisive genome engineering, we radically decreased their redundancy in Saccharomyces cerevisiae. The transcriptional machinery strongly disrupts evenly spaced nucleosomes. Proper nucleosome density and DNA sequence are critical for their biogenesis. The INO80 remodeling complex helps space nucleosomes in vivo and positions the first nucleosome over genes in an H2A.Z-independent fashion. INO80 requires its Arp8 subunit but unexpectedly not the Nhp10 module for spacing. Cells with irregularly spaced nucleosomes suffer from genotoxic stress including DNA damage, recombination and transpositions. We derive a model of the biogenesis of the nucleosome landscape and suggest that it evolved not only to regulate but also to protect the genome.
Topics: Chromatin; Chromatin Assembly and Disassembly; DNA; DNA Damage; Engineering; Epigenomics; Eukaryotic Cells; High Mobility Group Proteins; Histones; Microfilament Proteins; Nucleosomes; Saccharomyces cerevisiae; Saccharomyces cerevisiae Proteins; Transcription Factors
PubMed: 34853297
DOI: 10.1038/s41467-021-27285-6 -
International Journal of Molecular... Aug 2022Robust, tightly regulated DNA repair is critical to maintaining genome stability and preventing cancer. Eukaryotic DNA is packaged into chromatin, which has a profound,... (Review)
Review
Robust, tightly regulated DNA repair is critical to maintaining genome stability and preventing cancer. Eukaryotic DNA is packaged into chromatin, which has a profound, yet incompletely understood, regulatory influence on DNA repair and genome stability. The chromatin remodeler HELLS (helicase, lymphoid specific) has emerged as an important epigenetic regulator of DNA repair, genome stability, and multiple cancer-associated pathways. HELLS belongs to a subfamily of the conserved SNF2 ATP-dependent chromatin-remodeling complexes, which use energy from ATP hydrolysis to alter nucleosome structure and packaging of chromatin during the processes of DNA replication, transcription, and repair. The mouse homologue, LSH (lymphoid-specific helicase), plays an important role in the maintenance of heterochromatin and genome-wide DNA methylation, and is crucial in embryonic development, gametogenesis, and maturation of the immune system. Human HELLS is abundantly expressed in highly proliferating cells of the lymphoid tissue, skin, germ cells, and embryonic stem cells. Mutations in HELLS cause the human immunodeficiency syndrome ICF (Immunodeficiency, Centromeric instability, Facial anomalies). HELLS has been implicated in many types of cancer, including retinoblastoma, colorectal cancer, hepatocellular carcinoma, and glioblastoma. Here, we review and summarize accumulating evidence highlighting important roles for HELLS in DNA repair, genome maintenance, and key pathways relevant to cancer development, progression, and treatment.
Topics: Adenosine Triphosphate; Animals; Chromatin; Chromatin Assembly and Disassembly; DNA Helicases; DNA Repair; Genomic Instability; Glioblastoma; Humans; Immunologic Deficiency Syndromes; Mice
PubMed: 36012581
DOI: 10.3390/ijms23169313 -
Journal of Virology Nov 2019We present the genome sequences of tailed phages Sasha, Sergei, and Solent. These phages, along with phages 9NA, FSL_SP-062, and FSL_SP-069 and the more distantly...
We present the genome sequences of tailed phages Sasha, Sergei, and Solent. These phages, along with phages 9NA, FSL_SP-062, and FSL_SP-069 and the more distantly related phage PmiS-Isfahan, have similarly sized genomes of between 52 and 57 kbp in length that are largely syntenic. Their genomes also show substantial genome mosaicism relative to one another, which is common within tailed phage clusters. Their gene content ranges from 80 to 99 predicted genes, of which 40 are common to all seven and form the core genome, which includes all identifiable virion assembly and DNA replication genes. The total number of gene types (pangenome) in the seven phages is 176, and 59 of these are unique to individual phages. Their core genomes are much more closely related to one another than to the genome of any other known phage, and they comprise a well-defined cluster within the family To begin to characterize this group of phages in more experimental detail, we identified the genes that encode the major virion proteins and examined the DNA packaging of the prototypic member, phage 9NA. We show that it uses a site-directed headful packaging mechanism that results in virion chromosomes that are circularly permuted and about 13% terminally redundant. We also show that its packaging series initiates with double-stranded DNA cleavages that are scattered across a 170-bp region and that its headful measuring device has a precision of ±1.8%. The 9NA-like phages are clearly highly related to each other but are not closely related to any other known phage type. This work describes the genomes of three new 9NA-like phages and the results of experimental analysis of the proteome of the 9NA virion and DNA packaging into the 9NA phage head. There is increasing interest in the biology of phages because of their potential for use as antibacterial agents and for their ecological roles in bacterial communities. 9NA-like phages that infect two bacterial genera have been identified to date, and related phages infecting additional Gram-negative bacterial hosts are likely to be found in the future. This work provides a foundation for the study of these phages, which will facilitate their study and potential use.
Topics: DNA Packaging; DNA Replication; DNA, Viral; Genome; Genome, Viral; Genomics; Phylogeny; Salmonella; Salmonella Phages; Siphoviridae; Viral Proteins; Virion
PubMed: 31462565
DOI: 10.1128/JVI.00848-19 -
Viruses Apr 2022The phage-inducible chromosomal islands (PICIs) of Gram-negative bacteria are analogous to defective prophages that have lost the ability to propagate without the aid of...
The phage-inducible chromosomal islands (PICIs) of Gram-negative bacteria are analogous to defective prophages that have lost the ability to propagate without the aid of a helper phage. PICIs have acquired genes that alter the genetic repertoire of the bacterial host, including supplying virulence factors. Recent work by the Penadés laboratory elucidates how a helper phage infection or prophage induction induces the island to excise from the bacterial chromosome, replicate, and become packaged into functional virions. PICIs lack a complete set of morphogenetic genes needed to construct mature virus particles. Rather, PICIs hijack virion assembly functions from an induced prophage acting as a helper phage. The hijacking strategy includes preventing the helper phage from packaging its own DNA while enabling PICI DNA packaging. In the case of recently described Gram-negative PICIs, the PICI changes the specificity of DNA packaging. This is achieved by an island-encoded protein (Rpp) that binds to the phage protein (TerS), which normally selects phage DNA for packaging from a DNA pool that includes the helper phage and host DNAs. The Rpp-TerS interaction prevents phage DNA packaging while sponsoring PICI DNA packaging. Our communication reviews published data about the hijacking mechanism and its implications for phage DNA packaging. We propose that the Rpp-TerS complex binds to a site in the island DNA that is positioned analogous to that of the phage DNA but has a completely different sequence. The critical role of TerS in the Rpp-TerS complex is to escort TerL to the PICI , ensuring appropriate DNA cutting and packaging.
Topics: Bacteriophage lambda; Bacteriophages; DNA Packaging; DNA, Viral; Endodeoxyribonucleases; Genomic Islands
PubMed: 35458547
DOI: 10.3390/v14040818 -
Nature Communications Mar 2024Artificial biomolecular condensates are emerging as a versatile approach to organize molecular targets and reactions without the need for lipid membranes. Here we ask...
Artificial biomolecular condensates are emerging as a versatile approach to organize molecular targets and reactions without the need for lipid membranes. Here we ask whether the temporal response of artificial condensates can be controlled via designed chemical reactions. We address this general question by considering a model problem in which a phase separating component participates in reactions that dynamically activate or deactivate its ability to self-attract. Through a theoretical model we illustrate the transient and equilibrium effects of reactions, linking condensate response and reaction parameters. We experimentally realize our model problem using star-shaped DNA motifs known as nanostars to generate condensates, and we take advantage of strand invasion and displacement reactions to kinetically control the capacity of nanostars to interact. We demonstrate reversible dissolution and growth of DNA condensates in the presence of specific DNA inputs, and we characterize the role of toehold domains, nanostar size, and nanostar valency. Our results will support the development of artificial biomolecular condensates that can adapt to environmental changes with prescribed temporal dynamics.
Topics: DNA Packaging; Biomolecular Condensates; DNA Replication; Gene Conversion; Nucleotide Motifs
PubMed: 38429336
DOI: 10.1038/s41467-024-46266-z -
Biochimica Et Biophysica Acta.... Dec 2022The critical role of dysregulated epigenetic pathways in cancer genesis, development, and therapy has typically been established as a result of scientific and technical... (Review)
Review
The critical role of dysregulated epigenetic pathways in cancer genesis, development, and therapy has typically been established as a result of scientific and technical innovations in next generation sequencing. RNA interference, histone modification, DNA methylation and chromatin remodelling are epigenetic processes that control gene expression without causing mutations in the DNA. Although epigenetic abnormalities are thought to be a symptom of cell tumorigenesis and malignant events that impact tumor growth and drug resistance, physicians believe that related processes might be a key therapeutic target for cancer treatment and prevention due to the reversible nature of these processes. A plethora of novel strategies for addressing epigenetics in cancer therapy for immuno-oncological complications are currently available - ranging from basic treatment to epigenetic editing. - and they will be the subject of this comprehensive review. In this review, we cover most of the advancements made in the field of targeting epigenetics with special emphasis on microbiology, plasma science, biophysics, pharmacology, molecular biology, phytochemistry, and nanoscience.
Topics: Chromatin Assembly and Disassembly; DNA Methylation; Epigenesis, Genetic; Epigenomics; Humans; Neoplasms
PubMed: 36126898
DOI: 10.1016/j.bbadis.2022.166552 -
Structure (London, England : 1993) Apr 2022Bacteriophage lambda is an excellent model system for studying capsid assembly of double-stranded DNA (dsDNA) bacteriophages, some dsDNA archaeal viruses, and...
Bacteriophage lambda is an excellent model system for studying capsid assembly of double-stranded DNA (dsDNA) bacteriophages, some dsDNA archaeal viruses, and herpesviruses. HK97 fold coat proteins initially assemble into a precursor capsid (procapsid) and subsequent genome packaging triggers morphological expansion of the shell. An auxiliary protein is required to stabilize the expanded capsid structure. To investigate the capsid maturation mechanism, we determined the cryo-electron microscopy structures of the bacteriophage lambda procapsid and mature capsid at 3.88 Å and 3.76 Å resolution, respectively. Besides primarily rigid body movements of common features of the major capsid protein gpE, large-scale structural rearrangements of other domains occur simultaneously. Assembly of intercapsomers within the procapsid is facilitated by layer-stacking effects at 3-fold vertices. Upon conformational expansion of the capsid shell, the missing top layer is fulfilled by cementing the gpD protein against the internal pressure of DNA packaging. Our structures illuminate the assembly mechanisms of dsDNA viruses.
Topics: Bacteriophage lambda; Capsid; Capsid Proteins; Cryoelectron Microscopy; DNA Packaging; Virus Assembly
PubMed: 35026161
DOI: 10.1016/j.str.2021.12.009