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1.
Life Sci Alliance ; 7(8)2024 Aug.
Artículo en Inglés | MEDLINE | ID: mdl-38830772

RESUMEN

Nucleosome positioning is a key factor for transcriptional regulation. Nucleosomes regulate the dynamic accessibility of chromatin and interact with the transcription machinery at every stage. Influences to steer nucleosome positioning are diverse, and the according importance of the DNA sequence in contrast to active chromatin remodeling has been the subject of long discussion. In this study, we evaluate the functional role of DNA sequence for all major elements along the process of transcription. We developed a random forest classifier based on local DNA structure that assesses the sequence-intrinsic support for nucleosome positioning. On this basis, we created a simple data resource that we applied genome-wide to the human genome. In our comprehensive analysis, we found a special role of DNA in mediating the competition of nucleosomes with cis-regulatory elements, in enabling steady transcription, for positioning of stable nucleosomes in exons, and for repelling nucleosomes during transcription termination. In contrast, we relate these findings to concurrent processes that generate strongly positioned nucleosomes in vivo that are not mediated by sequence, such as energy-dependent remodeling of chromatin.


Asunto(s)
Ensamble y Desensamble de Cromatina , ADN , Regulación de la Expresión Génica , Nucleosomas , Transcripción Genética , Nucleosomas/metabolismo , Nucleosomas/genética , Humanos , Ensamble y Desensamble de Cromatina/genética , ADN/genética , ADN/metabolismo , Cromatina/metabolismo , Cromatina/genética , Genoma Humano , Secuencia de Bases
2.
J Cell Biol ; 223(8)2024 Aug 05.
Artículo en Inglés | MEDLINE | ID: mdl-38709169

RESUMEN

Histone H3 lysine36 dimethylation (H3K36me2) is generally distributed in the gene body and euchromatic intergenic regions. However, we found that H3K36me2 is enriched in pericentromeric heterochromatin in some mouse cell lines. We here revealed the mechanism of heterochromatin targeting of H3K36me2. Among several H3K36 methyltransferases, NSD2 was responsible for inducing heterochromatic H3K36me2. Depletion and overexpression analyses of NSD2-associating proteins revealed that NSD2 recruitment to heterochromatin was mediated through the imitation switch (ISWI) chromatin remodeling complexes, such as BAZ1B-SMARCA5 (WICH), which directly binds to AT-rich DNA via a BAZ1B domain-containing AT-hook-like motifs. The abundance and stoichiometry of NSD2, SMARCA5, and BAZ1B could determine the localization of H3K36me2 in different cell types. In mouse embryos, H3K36me2 heterochromatin localization was observed at the two- to four-cell stages, suggesting its physiological relevance.


Asunto(s)
Ensamble y Desensamble de Cromatina , Heterocromatina , N-Metiltransferasa de Histona-Lisina , Histonas , Proteínas Represoras , Animales , Humanos , Ratones , Adenosina Trifosfatasas , Proteínas que Contienen Bromodominio/genética , Proteínas que Contienen Bromodominio/metabolismo , Centrómero/metabolismo , Centrómero/genética , Proteínas Cromosómicas no Histona/metabolismo , Proteínas Cromosómicas no Histona/genética , Heterocromatina/metabolismo , Heterocromatina/genética , N-Metiltransferasa de Histona-Lisina/metabolismo , N-Metiltransferasa de Histona-Lisina/genética , Histonas/metabolismo , Histonas/genética , Metilación , Proteínas Represoras/metabolismo , Proteínas Represoras/genética , Factores de Transcripción/metabolismo , Factores de Transcripción/genética
3.
Biol Res ; 57(1): 22, 2024 May 04.
Artículo en Inglés | MEDLINE | ID: mdl-38704609

RESUMEN

BACKGROUND: Chromatin dynamics is deeply involved in processes that require access to DNA, such as transcriptional regulation. Among the factors involved in chromatin dynamics at gene regulatory regions are general regulatory factors (GRFs). These factors contribute to establishment and maintenance of nucleosome-depleted regions (NDRs). These regions are populated by nucleosomes through histone deposition and nucleosome sliding, the latter catalyzed by a number of ATP-dependent chromatin remodeling complexes, including ISW1a. It has been observed that GRFs can act as barriers against nucleosome sliding towards NDRs. However, the relative ability of the different GRFs to hinder sliding activity is currently unknown. RESULTS: Considering this, we performed a comparative analysis for the main GRFs, with focus in their ability to modulate nucleosome sliding mediated by ISW1a. Among the GRFs tested in nucleosome remodeling assays, Rap1 was the only factor displaying the ability to hinder the activity of ISW1a. This effect requires location of the Rap1 cognate sequence on linker that becomes entry DNA in the nucleosome remodeling process. In addition, Rap1 was able to hinder nucleosome assembly in octamer transfer assays. Concurrently, Rap1 displayed the highest affinity for and longest dwell time from its target sequence, compared to the other GRFs tested. Consistently, through bioinformatics analyses of publicly available genome-wide data, we found that nucleosome occupancy and histone deposition in vivo are inversely correlated with the affinity of Rap1 for its target sequences in the genome. CONCLUSIONS: Our findings point to DNA binding affinity, residence time and location at particular translational positions relative to the nucleosome core as the key features of GRFs underlying their roles played in nucleosome sliding and assembly.


Asunto(s)
Ensamble y Desensamble de Cromatina , Proteínas de Unión al ADN , Nucleosomas , Nucleosomas/metabolismo , Nucleosomas/genética , Ensamble y Desensamble de Cromatina/fisiología , Adenosina Trifosfatasas/metabolismo , Adenosina Trifosfatasas/genética , Proteínas de Saccharomyces cerevisiae/metabolismo , Proteínas de Saccharomyces cerevisiae/genética , Factores de Transcripción/metabolismo , Factores de Transcripción/genética , Saccharomyces cerevisiae/genética , Saccharomyces cerevisiae/metabolismo , Histonas/metabolismo
4.
Nat Commun ; 15(1): 4095, 2024 May 15.
Artículo en Inglés | MEDLINE | ID: mdl-38750021

RESUMEN

Polymerized ß-actin may provide a structural basis for chromatin accessibility and actin transport into the nucleus can guide mesenchymal stem cell (MSC) differentiation. Using MSC, we show that using CK666 to inhibit Arp2/3 directed secondary actin branching results in decreased nuclear actin structure, and significantly alters chromatin access measured with ATACseq at 24 h. The ATAC-seq results due to CK666 are distinct from those caused by cytochalasin D (CytoD), which enhances nuclear actin structure. In addition, nuclear visualization shows Arp2/3 inhibition decreases pericentric H3K9me3 marks. CytoD, alternatively, induces redistribution of H3K27me3 marks centrally. Such alterations in chromatin landscape are consistent with differential gene expression associated with distinctive differentiation patterns. Further, knockdown of the non-enzymatic monomeric actin binding protein, Arp4, leads to extensive chromatin unpacking, but only a modest increase in transcription, indicating an active role for actin-Arp4 in transcription. These data indicate that dynamic actin remodeling can regulate chromatin interactions.


Asunto(s)
Complejo 2-3 Proteico Relacionado con la Actina , Actinas , Núcleo Celular , Cromatina , Células Madre Mesenquimatosas , Actinas/metabolismo , Cromatina/metabolismo , Núcleo Celular/metabolismo , Complejo 2-3 Proteico Relacionado con la Actina/metabolismo , Complejo 2-3 Proteico Relacionado con la Actina/genética , Células Madre Mesenquimatosas/metabolismo , Células Madre Mesenquimatosas/citología , Animales , Diferenciación Celular , Citocalasina D/farmacología , Histonas/metabolismo , Humanos , Proteínas de Microfilamentos/metabolismo , Proteínas de Microfilamentos/genética , Ratones , Ensamble y Desensamble de Cromatina
5.
Epigenetics Chromatin ; 17(1): 18, 2024 May 23.
Artículo en Inglés | MEDLINE | ID: mdl-38783373

RESUMEN

The three-dimensional organization of the genome plays a central role in the regulation of cellular functions, particularly in the human brain. This review explores the intricacies of chromatin organization, highlighting the distinct structural patterns observed between neuronal and non-neuronal brain cells. We integrate findings from recent studies to elucidate the characteristics of various levels of chromatin organization, from differential compartmentalization and topologically associating domains (TADs) to chromatin loop formation. By defining the unique chromatin landscapes of neuronal and non-neuronal brain cells, these distinct structures contribute to the regulation of gene expression specific to each cell type. In particular, we discuss potential functional implications of unique neuronal chromatin organization characteristics, such as weaker compartmentalization, neuron-specific TAD boundaries enriched with active histone marks, and an increased number of chromatin loops. Additionally, we explore the role of Polycomb group (PcG) proteins in shaping cell-type-specific chromatin patterns. This review further emphasizes the impact of variations in chromatin architecture between neuronal and non-neuronal cells on brain development and the onset of neurological disorders. It highlights the need for further research to elucidate the details of chromatin organization in the human brain in order to unravel the complexities of brain function and the genetic mechanisms underlying neurological disorders. This research will help bridge a significant gap in our comprehension of the interplay between chromatin structure and cell functions.


Asunto(s)
Encéfalo , Cromatina , Neuronas , Humanos , Neuronas/metabolismo , Neuronas/citología , Cromatina/metabolismo , Animales , Encéfalo/metabolismo , Proteínas del Grupo Polycomb/metabolismo , Proteínas del Grupo Polycomb/genética , Ensamble y Desensamble de Cromatina
6.
Nat Commun ; 15(1): 4376, 2024 May 23.
Artículo en Inglés | MEDLINE | ID: mdl-38782890

RESUMEN

Topologically associating domains (TADs), megabase-scale features of chromatin spatial architecture, are organized in a domain-within-domain TAD hierarchy. Within TADs, the inner and smaller subTADs not only manifest cell-to-cell variability, but also precisely regulate transcription and differentiation. Although over 20 TAD callers are able to detect TAD, their usability in biomedicine is confined by a disagreement of outputs and a limit in understanding TAD hierarchy. We compare 13 computational tools across various conditions and develop a metric to evaluate the similarity of TAD hierarchy. Although outputs of TAD hierarchy at each level vary among callers, data resolutions, sequencing depths, and matrices normalization, they are more consistent when they have a higher similarity of larger TADs. We present comprehensive benchmarking of TAD hierarchy callers and operational guidance to researchers of life science researchers. Moreover, by simulating the mixing of different types of cells, we confirm that TAD hierarchy is generated not simply from stacking Hi-C heatmaps of heterogeneous cells. Finally, we propose an air conditioner model to decipher the role of TAD hierarchy in transcription.


Asunto(s)
Benchmarking , Cromatina , Cromatina/química , Humanos , Biología Computacional/métodos , Programas Informáticos , Ensamble y Desensamble de Cromatina
7.
Genome Biol ; 25(1): 122, 2024 May 13.
Artículo en Inglés | MEDLINE | ID: mdl-38741214

RESUMEN

BACKGROUND: Pluripotent states of embryonic stem cells (ESCs) with distinct transcriptional profiles affect ESC differentiative capacity and therapeutic potential. Although single-cell RNA sequencing has revealed additional subpopulations and specific features of naive and primed human pluripotent stem cells (hPSCs), the underlying mechanisms that regulate their specific transcription and that control their pluripotent states remain elusive. RESULTS: By single-cell analysis of high-resolution, three-dimensional (3D) genomic structure, we herein demonstrate that remodeling of genomic structure is highly associated with the pluripotent states of human ESCs (hESCs). The naive pluripotent state is featured with specialized 3D genomic structures and clear chromatin compartmentalization that is distinct from the primed state. The naive pluripotent state is achieved by remodeling the active euchromatin compartment and reducing chromatin interactions at the nuclear center. This unique genomic organization is linked to enhanced chromatin accessibility on enhancers and elevated expression levels of naive pluripotent genes localized to this region. In contradistinction, the primed state exhibits intermingled genomic organization. Moreover, active euchromatin and primed pluripotent genes are distributed at the nuclear periphery, while repressive heterochromatin is densely concentrated at the nuclear center, reducing chromatin accessibility and the transcription of naive genes. CONCLUSIONS: Our data provide insights into the chromatin structure of ESCs in their naive and primed states, and we identify specific patterns of modifications in transcription and chromatin structure that might explain the genes that are differentially expressed between naive and primed hESCs. Thus, the inversion or relocation of heterochromatin to euchromatin via compartmentalization is related to the regulation of chromatin accessibility, thereby defining pluripotent states and cellular identity.


Asunto(s)
Células Madre Pluripotentes , Análisis de la Célula Individual , Humanos , Células Madre Pluripotentes/metabolismo , Células Madre Pluripotentes/citología , Genoma Humano , Eucromatina/genética , Eucromatina/metabolismo , Cromatina/metabolismo , Células Madre Embrionarias Humanas/metabolismo , Células Madre Embrionarias Humanas/citología , Heterocromatina/metabolismo , Células Madre Embrionarias/metabolismo , Ensamble y Desensamble de Cromatina
8.
Elife ; 132024 May 29.
Artículo en Inglés | MEDLINE | ID: mdl-38809771

RESUMEN

The yeast SWR1C chromatin remodeling enzyme catalyzes the ATP-dependent exchange of nucleosomal histone H2A for the histone variant H2A.Z, a key variant involved in a multitude of nuclear functions. How the 14-subunit SWR1C engages the nucleosomal substrate remains largely unknown. Studies on the ISWI, CHD1, and SWI/SNF families of chromatin remodeling enzymes have demonstrated key roles for the nucleosomal acidic patch for remodeling activity, however a role for this nucleosomal epitope in nucleosome editing by SWR1C has not been tested. Here, we employ a variety of biochemical assays to demonstrate an essential role for the acidic patch in the H2A.Z exchange reaction. Utilizing asymmetrically assembled nucleosomes, we demonstrate that the acidic patches on each face of the nucleosome are required for SWR1C-mediated dimer exchange, suggesting SWR1C engages the nucleosome in a 'pincer-like' conformation, engaging both patches simultaneously. Loss of a single acidic patch results in loss of high affinity nucleosome binding and nucleosomal stimulation of ATPase activity. We identify a conserved arginine-rich motif within the Swc5 subunit that binds the acidic patch and is key for dimer exchange activity. In addition, our cryoEM structure of a Swc5-nucleosome complex suggests that promoter proximal, histone H2B ubiquitylation may regulate H2A.Z deposition. Together these findings provide new insights into how SWR1C engages its nucleosomal substrate to promote efficient H2A.Z deposition.


Asunto(s)
Adenosina Trifosfatasas , Histonas , Nucleosomas , Proteínas de Saccharomyces cerevisiae , Saccharomyces cerevisiae , Histonas/metabolismo , Histonas/química , Nucleosomas/metabolismo , Saccharomyces cerevisiae/genética , Saccharomyces cerevisiae/metabolismo , Proteínas de Saccharomyces cerevisiae/metabolismo , Proteínas de Saccharomyces cerevisiae/genética , Proteínas de Saccharomyces cerevisiae/química , Adenosina Trifosfatasas/metabolismo , Adenosina Trifosfatasas/química , Adenosina Trifosfatasas/genética , Ensamble y Desensamble de Cromatina , Unión Proteica , Multimerización de Proteína
9.
Nat Commun ; 15(1): 4139, 2024 May 16.
Artículo en Inglés | MEDLINE | ID: mdl-38755155

RESUMEN

The natural history of multiple myeloma is characterized by its localization to the bone marrow and its interaction with bone marrow stromal cells. The bone marrow stromal cells provide growth and survival signals, thereby promoting the development of drug resistance. Here, we show that the interaction between bone marrow stromal cells and myeloma cells (using human cell lines) induces chromatin remodeling of cis-regulatory elements and is associated with changes in the expression of genes involved in the cell migration and cytokine signaling. The expression of genes involved in these stromal interactions are observed in extramedullary disease in patients with myeloma and provides the rationale for survival of myeloma cells outside of the bone marrow microenvironment. Expression of these stromal interaction genes is also observed in a subset of patients with newly diagnosed myeloma and are akin to the transcriptional program of extramedullary disease. The presence of such adverse stromal interactions in newly diagnosed myeloma is associated with accelerated disease dissemination, predicts the early development of therapeutic resistance, and is of independent prognostic significance. These stromal cell induced transcriptomic and epigenomic changes both predict long-term outcomes and identify therapeutic targets in the tumor microenvironment for the development of novel therapeutic approaches.


Asunto(s)
Ensamble y Desensamble de Cromatina , Regulación Neoplásica de la Expresión Génica , Células Madre Mesenquimatosas , Mieloma Múltiple , Microambiente Tumoral , Mieloma Múltiple/genética , Mieloma Múltiple/patología , Mieloma Múltiple/metabolismo , Humanos , Microambiente Tumoral/genética , Línea Celular Tumoral , Células Madre Mesenquimatosas/metabolismo , Células Madre Mesenquimatosas/patología , Transcripción Genética , Células de la Médula Ósea/metabolismo , Movimiento Celular/genética , Células del Estroma/metabolismo , Células del Estroma/patología , Femenino , Masculino
10.
Biomed Pharmacother ; 175: 116747, 2024 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-38744217

RESUMEN

Schizophrenia, influenced by genetic and environmental factors, may involve epigenetic alterations, notably histone modifications, in its pathogenesis. This review summarizes various histone modifications including acetylation, methylation, phosphorylation, ubiquitination, serotonylation, lactylation, palmitoylation, and dopaminylation, and their implications in schizophrenia. Current research predominantly focuses on histone acetylation and methylation, though other modifications also play significant roles. These modifications are crucial in regulating transcription through chromatin remodeling, which is vital for understanding schizophrenia's development. For instance, histone acetylation enhances transcriptional efficiency by loosening chromatin, while increased histone methyltransferase activity on H3K9 and altered histone phosphorylation, which reduces DNA affinity and destabilizes chromatin structure, are significant markers of schizophrenia.


Asunto(s)
Histonas , Esquizofrenia , Esquizofrenia/metabolismo , Esquizofrenia/genética , Humanos , Histonas/metabolismo , Animales , Epigénesis Genética , Procesamiento Proteico-Postraduccional , Acetilación , Metilación , Fosforilación , Ensamble y Desensamble de Cromatina
11.
Cell Rep ; 43(5): 114227, 2024 May 28.
Artículo en Inglés | MEDLINE | ID: mdl-38735044

RESUMEN

CUX1 is a homeodomain-containing transcription factor that is essential for the development and differentiation of multiple tissues. CUX1 is recurrently mutated or deleted in cancer, particularly in myeloid malignancies. However, the mechanism by which CUX1 regulates gene expression and differentiation remains poorly understood, creating a barrier to understanding the tumor-suppressive functions of CUX1. Here, we demonstrate that CUX1 directs the BAF chromatin remodeling complex to DNA to increase chromatin accessibility in hematopoietic cells. CUX1 preferentially regulates lineage-specific enhancers, and CUX1 target genes are predictive of cell fate in vivo. These data indicate that CUX1 regulates hematopoietic lineage commitment and homeostasis via pioneer factor activity, and CUX1 deficiency disrupts these processes in stem and progenitor cells, facilitating transformation.


Asunto(s)
Cromatina , Células Madre Hematopoyéticas , Proteínas de Homeodominio , Proteínas Represoras , Humanos , Proteínas de Homeodominio/metabolismo , Proteínas de Homeodominio/genética , Células Madre Hematopoyéticas/metabolismo , Células Madre Hematopoyéticas/citología , Cromatina/metabolismo , Proteínas Represoras/metabolismo , Proteínas Represoras/genética , Factores de Transcripción/metabolismo , Factores de Transcripción/genética , Animales , Ratones , Proteínas Nucleares/metabolismo , Proteínas Nucleares/genética , Linaje de la Célula , Ensamble y Desensamble de Cromatina , Diferenciación Celular , Proteínas de Unión al ADN/metabolismo , Proteínas de Unión al ADN/genética , Elementos de Facilitación Genéticos/genética
12.
Genes (Basel) ; 15(5)2024 Apr 27.
Artículo en Inglés | MEDLINE | ID: mdl-38790189

RESUMEN

BACKGROUND: Cervical cancer is among the highest-ranking types of cancer worldwide, with human papillomavirus (HPV) as the agent driving the malignant process. One aspect of the infection's evolution is given by epigenetic modifications, mainly DNA methylation and chromatin alteration. These processes are guided by several chromatin remodeling complexes, including NuRD. The purpose of this study was to evaluate the genome-wide binding patterns of the NuRD complex components (MBD2 and MBD3) in the presence of active HPV16 E6 and E7 oncogenes and to determine the potential of identified genes through an experimental model to differentiate between cervical precursor lesions, with the aim of establishing their utility as biomarkers. METHODS: The experimental model was built using the CaSki cell line and shRNA for E6 and E7 HPV16 silencing, ChIP-seq, qRT-PCR, and Western blot analyses. Selected genes' expression was also assessed in patients. RESULTS: Several genes have been identified to exhibit altered transcriptional activity due to the influence of HPV16 E6/E7 viral oncogenes acting through the MBD2/MBD3 NuRD complex, linking them to viral infection and cervical oncogenesis. CONCLUSIONS: The impacted genes primarily play roles in governing gene transcription, mRNA processing, and regulation of translation. Understanding these mechanisms offers valuable insights into the process of HPV-induced oncogenesis.


Asunto(s)
Ensamble y Desensamble de Cromatina , Proteínas de Unión al ADN , Complejo Desacetilasa y Remodelación del Nucleosoma Mi-2 , Proteínas Oncogénicas Virales , Proteínas E7 de Papillomavirus , Proteínas Represoras , Neoplasias del Cuello Uterino , Humanos , Complejo Desacetilasa y Remodelación del Nucleosoma Mi-2/metabolismo , Complejo Desacetilasa y Remodelación del Nucleosoma Mi-2/genética , Neoplasias del Cuello Uterino/virología , Neoplasias del Cuello Uterino/genética , Neoplasias del Cuello Uterino/metabolismo , Neoplasias del Cuello Uterino/patología , Proteínas E7 de Papillomavirus/genética , Proteínas E7 de Papillomavirus/metabolismo , Proteínas Oncogénicas Virales/genética , Proteínas Oncogénicas Virales/metabolismo , Proteínas de Unión al ADN/genética , Proteínas de Unión al ADN/metabolismo , Femenino , Ensamble y Desensamble de Cromatina/genética , Proteínas Represoras/genética , Proteínas Represoras/metabolismo , Línea Celular Tumoral , Papillomavirus Humano 16/genética , Papillomavirus Humano 16/metabolismo , Papillomavirus Humano 16/patogenicidad , Carcinogénesis/genética , Infecciones por Papillomavirus/virología , Infecciones por Papillomavirus/genética , Infecciones por Papillomavirus/metabolismo , Regulación Neoplásica de la Expresión Génica
13.
Genes (Basel) ; 15(5)2024 May 17.
Artículo en Inglés | MEDLINE | ID: mdl-38790268

RESUMEN

Lysine acetyltransferase 8, also known as KAT8, is an enzyme involved in epigenetic regulation, primarily recognized for its ability to modulate histone acetylation. This review presents an overview of KAT8, emphasizing its biological functions, which impact many cellular processes and range from chromatin remodeling to genetic and epigenetic regulation. In many model systems, KAT8's acetylation of histone H4 lysine 16 (H4K16) is critical for chromatin structure modification, which influences gene expression, cell proliferation, differentiation, and apoptosis. Furthermore, this review summarizes the observed genetic variability within the KAT8 gene, underscoring the implications of various single nucleotide polymorphisms (SNPs) that affect its functional efficacy and are linked to diverse phenotypic outcomes, ranging from metabolic traits to neurological disorders. Advanced insights into the structural biology of KAT8 reveal its interaction with multiprotein assemblies, such as the male-specific lethal (MSL) and non-specific lethal (NSL) complexes, which regulate a wide range of transcriptional activities and developmental functions. Additionally, this review focuses on KAT8's roles in cellular homeostasis, stem cell identity, DNA damage repair, and immune response, highlighting its potential as a therapeutic target. The implications of KAT8 in health and disease, as evidenced by recent studies, affirm its importance in cellular physiology and human pathology.


Asunto(s)
Epigénesis Genética , Histona Acetiltransferasas , Humanos , Histona Acetiltransferasas/metabolismo , Histona Acetiltransferasas/genética , Acetilación , Histonas/metabolismo , Histonas/genética , Polimorfismo de Nucleótido Simple , Animales , Ensamble y Desensamble de Cromatina
14.
Nat Struct Mol Biol ; 31(5): 742-746, 2024 May.
Artículo en Inglés | MEDLINE | ID: mdl-38769465

RESUMEN

Hexasomes are non-canonical nucleosomes that package DNA with six instead of eight histones. First discovered 40 years ago as a consequence of transcription, two near-atomic-resolution cryo-EM structures of the hexasome in complex with the chromatin remodeler INO80 have now started to unravel its mechanistic impact on the regulatory landscape of chromatin. Loss of one histone H2A-H2B dimer converts inactive nucleosomes into distinct and favorable substrates for ATP-dependent chromatin remodeling.


Asunto(s)
Ensamble y Desensamble de Cromatina , Microscopía por Crioelectrón , Histonas , Nucleosomas , Nucleosomas/metabolismo , Nucleosomas/química , Nucleosomas/ultraestructura , Histonas/metabolismo , Histonas/química , Modelos Moleculares , Humanos , Proteínas de Saccharomyces cerevisiae/metabolismo , Proteínas de Saccharomyces cerevisiae/química , ADN/metabolismo , ADN/química
15.
Cell Rep ; 43(5): 114170, 2024 May 28.
Artículo en Inglés | MEDLINE | ID: mdl-38700983

RESUMEN

During cell fate transitions, cells remodel their transcriptome, chromatin, and epigenome; however, it has been difficult to determine the temporal dynamics and cause-effect relationship between these changes at the single-cell level. Here, we employ the heterokaryon-mediated reprogramming system as a single-cell model to dissect key temporal events during early stages of pluripotency conversion using super-resolution imaging. We reveal that, following heterokaryon formation, the somatic nucleus undergoes global chromatin decompaction and removal of repressive histone modifications H3K9me3 and H3K27me3 without acquisition of active modifications H3K4me3 and H3K9ac. The pluripotency gene OCT4 (POU5F1) shows nascent and mature RNA transcription within the first 24 h after cell fusion without requiring an initial open chromatin configuration at its locus. NANOG, conversely, has significant nascent RNA transcription only at 48 h after cell fusion but, strikingly, exhibits genomic reopening early on. These findings suggest that the temporal relationship between chromatin compaction and gene activation during cellular reprogramming is gene context dependent.


Asunto(s)
Reprogramación Celular , Ensamble y Desensamble de Cromatina , Histonas , Humanos , Reprogramación Celular/genética , Histonas/metabolismo , Análisis de la Célula Individual , Activación Transcripcional , Factor 3 de Transcripción de Unión a Octámeros/metabolismo , Factor 3 de Transcripción de Unión a Octámeros/genética , Cromatina/metabolismo , Proteína Homeótica Nanog/metabolismo , Proteína Homeótica Nanog/genética , Células Madre Pluripotentes Inducidas/metabolismo , Células Madre Pluripotentes Inducidas/citología
16.
Open Biol ; 14(5): 230358, 2024 May.
Artículo en Inglés | MEDLINE | ID: mdl-38689555

RESUMEN

The nucleolus is the most prominent liquid droplet-like membrane-less organelle in mammalian cells. Unlike the nucleolus in terminally differentiated somatic cells, those in totipotent cells, such as murine zygotes or two-cell embryos, have a unique nucleolar structure known as nucleolus precursor bodies (NPBs). Previously, it was widely accepted that NPBs in zygotes are simply passive repositories of materials that will be gradually used to construct a fully functional nucleolus after zygotic genome activation (ZGA). However, recent research studies have challenged this simplistic view and demonstrated that functions of the NPBs go beyond ribosome biogenesis. In this review, we provide a snapshot of the functions of NPBs in zygotes and early two-cell embryos in mice. We propose that these membrane-less organelles function as a regulatory hub for chromatin organization. On the one hand, NPBs provide the structural platform for centric and pericentric chromatin remodelling. On the other hand, the dynamic changes in nucleolar structure control the release of the pioneer factors (i.e. double homeobox (Dux)). It appears that during transition from totipotency to pluripotency, decline of totipotency and initiation of fully functional nucleolus formation are not independent events but are interconnected. Consequently, it is reasonable to hypothesize that dissecting more unknown functions of NPBs may shed more light on the enigmas of early embryonic development and may ultimately provide novel approaches to improve reprogramming efficiency.


Asunto(s)
Nucléolo Celular , Cromatina , Desarrollo Embrionario , Animales , Humanos , Ratones , Nucléolo Celular/metabolismo , Cromatina/metabolismo , Ensamble y Desensamble de Cromatina , Regulación del Desarrollo de la Expresión Génica , Cigoto/metabolismo , Cigoto/citología
17.
Proc Natl Acad Sci U S A ; 121(18): e2311374121, 2024 Apr 30.
Artículo en Inglés | MEDLINE | ID: mdl-38648478

RESUMEN

The control of eukaryotic gene expression is intimately connected to highly dynamic chromatin structures. Gene regulation relies on activator and repressor transcription factors (TFs) that induce local chromatin opening and closing. However, it is unclear how nucleus-wide chromatin organization responds dynamically to the activity of specific TFs. Here, we examined how two TFs with opposite effects on local chromatin accessibility modulate chromatin dynamics nucleus-wide. We combine high-resolution diffusion mapping and dense flow reconstruction and correlation in living cells to obtain an imaging-based, nanometer-scale analysis of local diffusion processes and long-range coordinated movements of both chromatin and TFs. We show that the expression of either an individual transcriptional activator (CDX2) or repressor (SIX6) with large numbers of binding sites increases chromatin mobility nucleus-wide, yet they induce opposite coherent chromatin motions at the micron scale. Hi-C analysis of higher-order chromatin structures shows that induction of the pioneer factor CDX2 leads both to changes in local chromatin interactions and the distribution of A and B compartments, thus relating the micromovement of chromatin with changes in compartmental structures. Given that inhibition of transcription initiation and elongation by RNA Pol II has a partial impact on the global chromatin dynamics induced by CDX2, we suggest that CDX2 overexpression alters chromatin structure dynamics both dependently and independently of transcription. Our biophysical analysis shows that sequence-specific TFs can influence chromatin structure on multiple architectural levels, arguing that local chromatin changes brought by TFs alter long-range chromatin mobility and its organization.


Asunto(s)
Cromatina , Factores de Transcripción , Cromatina/metabolismo , Cromatina/genética , Factores de Transcripción/metabolismo , Factores de Transcripción/genética , Humanos , Factor de Transcripción CDX2/metabolismo , Factor de Transcripción CDX2/genética , Regulación de la Expresión Génica , Núcleo Celular/metabolismo , Sitios de Unión , Ensamble y Desensamble de Cromatina
18.
Cardiovasc Diabetol ; 23(1): 139, 2024 Apr 25.
Artículo en Inglés | MEDLINE | ID: mdl-38664790

RESUMEN

BACKGROUND: Diabetic cardiomyopathy (DCM) poses a growing health threat, elevating heart failure risk in diabetic individuals. Understanding DCM is crucial, with fibroblasts and endothelial cells playing pivotal roles in driving myocardial fibrosis and contributing to cardiac dysfunction. Advances in Multimodal single-cell profiling, such as scRNA-seq and scATAC-seq, provide deeper insights into DCM's unique cell states and molecular landscape for targeted therapeutic interventions. METHODS: Single-cell RNA and ATAC data from 10x Multiome libraries were processed using Cell Ranger ARC v2.0.1. Gene expression and ATAC data underwent Seurat and Signac filtration. Differential gene expression and accessible chromatin regions were identified. Transcription factor activity was estimated with chromVAR, and Cis-coaccessibility networks were calculated using Cicero. Coaccessibility connections were compared to the GeneHancer database. Gene Ontology analysis, biological process scoring, cell-cell communication analysis, and gene-motif correlation was performed to reveal intricate molecular changes. Immunofluorescent staining utilized various antibodies on paraffin-embedded tissues to verify the findings. RESULTS: This study integrated scRNA-seq and scATAC-seq data obtained from hearts of WT and DCM mice, elucidating molecular changes at the single-cell level throughout the diabetic cardiomyopathy progression. Robust and accurate clustering analysis of the integrated data revealed altered cell proportions, showcasing decreased endothelial cells and macrophages, coupled with increased fibroblasts and myocardial cells in the DCM group, indicating enhanced fibrosis and endothelial damage. Chromatin accessibility analysis unveiled unique patterns in cell types, with heightened transcriptional activity in myocardial cells. Subpopulation analysis highlighted distinct changes in cardiomyocytes and fibroblasts, emphasizing pathways related to fatty acid metabolism and cardiac contraction. Fibroblast-centered communication analysis identified interactions with endothelial cells, implicating VEGF receptors. Endothelial cell subpopulations exhibited altered gene expressions, emphasizing contraction and growth-related pathways. Candidate regulators, including Tcf21, Arnt, Stat5a, and Stat5b, were identified, suggesting their pivotal roles in DCM development. Immunofluorescence staining validated marker genes of cell subpopulations, confirming PDK4, PPARγ and Tpm1 as markers for metabolic pattern-altered cardiomyocytes, activated fibroblasts and endothelial cells with compromised proliferation. CONCLUSION: Our integrated scRNA-seq and scATAC-seq analysis unveils intricate cell states and molecular alterations in diabetic cardiomyopathy. Identified cell type-specific changes, transcription factors, and marker genes offer valuable insights. The study sheds light on potential therapeutic targets for DCM.


Asunto(s)
Cardiomiopatías Diabéticas , Análisis de la Célula Individual , Transcriptoma , Cardiomiopatías Diabéticas/genética , Cardiomiopatías Diabéticas/metabolismo , Cardiomiopatías Diabéticas/patología , Cardiomiopatías Diabéticas/fisiopatología , Animales , Perfilación de la Expresión Génica , Cromatina/metabolismo , Cromatina/genética , Ratones Endogámicos C57BL , Redes Reguladoras de Genes , Ensamble y Desensamble de Cromatina , Modelos Animales de Enfermedad , Masculino , RNA-Seq , Regulación de la Expresión Génica , Miocitos Cardíacos/metabolismo , Miocitos Cardíacos/patología , Fibroblastos/metabolismo , Fibroblastos/patología , Fibrosis , Ratones , Células Endoteliales/metabolismo , Células Endoteliales/patología
19.
Cell Rep Med ; 5(4): 101504, 2024 Apr 16.
Artículo en Inglés | MEDLINE | ID: mdl-38593809

RESUMEN

Targeted therapies have improved outcomes for certain cancer subtypes, but cytotoxic chemotherapy remains a mainstay for triple-negative breast cancer (TNBC). The epithelial-to-mesenchymal transition (EMT) is a developmental program co-opted by cancer cells that promotes metastasis and chemoresistance. There are no therapeutic strategies specifically targeting mesenchymal-like cancer cells. We report that the US Food and Drug Administration (FDA)-approved chemotherapeutic eribulin induces ZEB1-SWI/SNF-directed chromatin remodeling to reverse EMT that curtails the metastatic propensity of TNBC preclinical models. Eribulin induces mesenchymal-to-epithelial transition (MET) in primary TNBC in patients, but conventional chemotherapy does not. In the treatment-naive setting, but not after acquired resistance to other agents, eribulin sensitizes TNBC cells to subsequent treatment with other chemotherapeutics. These findings provide an epigenetic mechanism of action of eribulin, supporting its use early in the disease process for MET induction to prevent metastatic progression and chemoresistance. These findings warrant prospective clinical evaluation of the chemosensitizing effects of eribulin in the treatment-naive setting.


Asunto(s)
Antineoplásicos , Furanos , Cetonas , Policétidos Poliéteres , Neoplasias de la Mama Triple Negativas , Estados Unidos , Humanos , Neoplasias de la Mama Triple Negativas/patología , Ensamble y Desensamble de Cromatina , Estudios Prospectivos , Antineoplásicos/uso terapéutico
20.
Mol Cell ; 84(10): 1855-1869.e5, 2024 May 16.
Artículo en Inglés | MEDLINE | ID: mdl-38593804

RESUMEN

RNA transcribed from enhancers, i.e., eRNA, has been suggested to directly activate transcription by recruiting transcription factors and co-activators. Although there have been specific examples of eRNA functioning in this way, it is not clear how general this may be. We find that the AT-hook of SWI/SNF preferentially binds RNA and, as part of the esBAF complex, associates with eRNA transcribed from intronic and intergenic regions. Our data suggest that SWI/SNF is globally recruited in cis by eRNA to cell-type-specific enhancers, representative of two distinct stages that mimic early mammalian development, and not at enhancers that are shared between the two stages. In this manner, SWI/SNF facilitates recruitment and/or activation of MLL3/4, p300/CBP, and Mediator to stage-specific enhancers and super-enhancers that regulate the transcription of metabolic and cell lineage priming-related genes. These findings highlight a connection between ATP-dependent chromatin remodeling and eRNA in cell identity and typical- and super-enhancer activation.


Asunto(s)
Linaje de la Célula , ADN Helicasas , Elementos de Facilitación Genéticos , Proteínas Nucleares , Factores de Transcripción , Factores de Transcripción/metabolismo , Factores de Transcripción/genética , ADN Helicasas/metabolismo , ADN Helicasas/genética , Linaje de la Célula/genética , Animales , Proteínas Nucleares/metabolismo , Proteínas Nucleares/genética , Humanos , Ratones , Ensamble y Desensamble de Cromatina , Proteínas Cromosómicas no Histona/metabolismo , Proteínas Cromosómicas no Histona/genética
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