RESUMEN
Alternative histone acylations integrate gene expression with cellular metabolic states. Recent measurements of cellular acyl-coenzyme A (acyl-CoA) pools highlight the potential that histone post-translational modifications (PTMs) contribute directly to the regulation of metabolite pools. A metabolite-centric view throws new light onto roles and evolution of histone PTMs.
Asunto(s)
Cromatina , Histonas , Acilcoenzima A/metabolismo , Acilación , Histonas/metabolismo , Procesamiento Proteico-PostraduccionalRESUMEN
BACKGROUND: Aging is characterized by loss of function of the adaptive immune system, but the underlying causes are poorly understood. To assess the molecular effects of aging on B cell development, we profiled gene expression and chromatin features genome-wide, including histone modifications and chromosome conformation, in bone marrow pro-B and pre-B cells from young and aged mice. RESULTS: Our analysis reveals that the expression levels of most genes are generally preserved in B cell precursors isolated from aged compared with young mice. Nonetheless, age-specific expression changes are observed at numerous genes, including microRNA encoding genes. Importantly, these changes are underpinned by multi-layered alterations in chromatin structure, including chromatin accessibility, histone modifications, long-range promoter interactions, and nuclear compartmentalization. Previous work has shown that differentiation is linked to changes in promoter-regulatory element interactions. We find that aging in B cell precursors is accompanied by rewiring of such interactions. We identify transcriptional downregulation of components of the insulin-like growth factor signaling pathway, in particular downregulation of Irs1 and upregulation of Let-7 microRNA expression, as a signature of the aged phenotype. These changes in expression are associated with specific alterations in H3K27me3 occupancy, suggesting that Polycomb-mediated repression plays a role in precursor B cell aging. CONCLUSIONS: Changes in chromatin and 3D genome organization play an important role in shaping the altered gene expression profile of aged precursor B cells. Components of the insulin-like growth factor signaling pathways are key targets of epigenetic regulation in aging in bone marrow B cell precursors.
Asunto(s)
Envejecimiento/genética , Linfocitos B/metabolismo , Cromatina/química , Epigénesis Genética , Somatomedinas/fisiología , Transcriptoma , Envejecimiento/inmunología , Animales , Linfocitos B/inmunología , Regulación hacia Abajo , Genoma , Masculino , Ratones Endogámicos C57BL , Transducción de Señal/genética , Células Madre/inmunología , Células Madre/metabolismoRESUMEN
Disruption of chromatin organization during replication poses a major challenge to the maintenance and integrity of genome organization. It creates the need to accurately reconstruct the chromatin landscape following DNA duplication but there is little mechanistic understanding of how chromatin based modifications are restored on newly synthesized DNA. ATP-dependent chromatin remodeling activities serve multiple roles during replication and recent work underscores their requirement in the maintenance of proper chromatin organization. A new component of chromatin replication, the SWI/SNF-like chromatin remodeler SMARCAD1, acts at replication sites to facilitate deacetylation of newly assembled histones. Deacetylation is a pre-requisite for the restoration of epigenetic signatures in heterochromatin regions following replication. In this way, SMARCAD1, in concert with histone modifying activities and transcriptional repressors, reinforces epigenetic instructions to ensure that silenced loci are correctly perpetuated in each replication cycle. The emerging concept is that remodeling of nucleosomes is an early event imperative to promote the re-establishment of histone modifications following DNA replication.
Asunto(s)
Cromatina/química , Reparación del ADN , Replicación del ADN , Regulación Enzimológica de la Expresión Génica , Heterocromatina/química , Nucleosomas/química , Acetilación , Adenosina Trifosfato/química , Cromatina/genética , Ensamble y Desensamble de Cromatina , ADN Helicasas/química , ADN Helicasas/genética , Activación Enzimática , Epigénesis Genética , Silenciador del Gen , Heterocromatina/genética , Histonas/química , Humanos , Nucleosomas/genética , Mapeo de Interacción de ProteínasAsunto(s)
Núcleo Celular/metabolismo , Ensamble y Desensamble de Cromatina , Proteínas Nucleares/metabolismo , Adenosina Trifosfatasas/química , Adenosina Trifosfatasas/metabolismo , Animales , Proteínas Cromosómicas no Histona/química , Proteínas Cromosómicas no Histona/metabolismo , Humanos , Ratones , Modelos Biológicos , Nucleosomas/metabolismoRESUMEN
Nucleosome-remodelling factors are key facilitators of chromatin dynamics. At the level of single nucleosomes, they are involved in nucleosome-repositioning, altering histone-DNA interactions, disassembly of nucleosomes, and the exchange of histones with variants of different properties. The fundamental nature of chromatin dictates that nucleosome-remodelling affects all aspects of eukaryotic DNA metabolism, but much less is known about the functional interactions of nucleosome-remodelling factors with folded chromatin fibres. Because remodelling machines are abundant constituents of eukaryotic nuclei and, therefore, have ample potential to interact with chromatin, they might also affect higher-order chromatin architecture. Recent observations support roles for nucleosome-remodelling factors at the supra-nucleosomal level.
Asunto(s)
Cromatina/metabolismo , Regulación de la Expresión Génica , Nucleosomas/metabolismo , Animales , Cromatina/genética , Humanos , Modelos Biológicos , Nucleosomas/genéticaRESUMEN
During DNA replication, chromatin states have to be accurately transmitted from the parental to the daughter strands for faithful epigenetic inheritance. Chromatin remodelling factors at the replication site are thought to be involved in this process. Recent work adds ATP-dependent nucleosome remodelling factors to this category of enzymes. The WICH complex, consisting of the ISWI-type ATPase SNF2H and the Williams Syndrome Transcription Factor (WSTF), binds to replication foci using PCNA, a key factor in DNA- and chromatin replication and DNA repair, as an interaction platform. Depletion of WSTF results in decreased chromatin accessibility, which is evident already in newly replicated DNA. This leads to heterochromatin formation on a global scale and a decrease in overall transcriptional activity. Here, we propose that WICH, by keeping nucleosomes mobile, provides access to the newly replicated DNA and may thereby create a window of opportunity after DNA replication for rebinding of factors that maintain the epigenetic state, and thus prevents aberrant heterochromatin formation. Our model may provide an explanation for the long-standing observation of a delay in chromatin "maturation" on newly replicated DNA, by connecting this delay with the action of PCNA-bound WSTF-ISWI, and highlights chromatin remodeling shortly after DNA replication as a critical point for regulation.
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Adenosina Trifosfatasas/fisiología , Cromatina/química , Regulación de la Expresión Génica , Factores de Transcripción/fisiología , Animales , Sitios de Unión , Ciclo Celular , ADN/química , Replicación del ADN , Epigénesis Genética , Heterocromatina/química , Humanos , Modelos Biológicos , Nucleosomas/química , Unión ProteicaRESUMEN
Chromatin states have to be faithfully duplicated during DNA replication to maintain cell identity. It is unclear whether or how ATP-dependent chromatin-remodelling factors are involved in this process. Here we provide evidence that the Williams syndrome transcription factor (WSTF) is targeted to replication foci through direct interaction with the DNA clamp PCNA, an important coordinator of DNA and chromatin replication. WSTF, in turn, recruits imitation switch (ISWI)-type nucleosome-remodelling factor SNF2H to replication sites. These findings reveal a novel recruitment mechanism for ATP-dependent chromatin-remodelling factors that is fundamentally different from the previously documented targeting by sequence-specific transcriptional regulators. RNA-interference-mediated depletion of WSTF or SNF2H causes a compaction of newly replicated chromatin and increases the amount of heterochromatin markers, including HP1beta. This increase in the amount of HP1beta protein is mediated by progression through S phase and is not the result of an increase in HP1beta mRNA levels. We propose that the WSTF-ISWI complex has a role in the maintenance of chromatin structures during DNA replication.
Asunto(s)
Adenosina Trifosfatasas/metabolismo , Ensamble y Desensamble de Cromatina/fisiología , Replicación del ADN/genética , Antígeno Nuclear de Célula en Proliferación/metabolismo , Factores de Transcripción/metabolismo , Síndrome de Williams/genética , Adenosina Trifosfatasas/genética , Adenosina Trifosfato/metabolismo , Cromatina/genética , Cromatina/metabolismo , Ensamble y Desensamble de Cromatina/genética , Homólogo de la Proteína Chromobox 5 , Proteínas Cromosómicas no Histona/genética , Proteínas Cromosómicas no Histona/metabolismo , Cromosomas Humanos Par 7/genética , Marcadores Genéticos/genética , Células HeLa , Humanos , Proteínas Nucleares/genética , Proteínas Nucleares/metabolismo , Antígeno Nuclear de Célula en Proliferación/genética , Interferencia de ARN , Factores de Transcripción/genética , Síndrome de Williams/metabolismoRESUMEN
The histone fold is a structural motif with which two related proteins interact and is found in complexes involved in wrapping DNA, the nucleosome, and transcriptional regulation, as in NC2. We reveal a novel function for histone-fold proteins: facilitation of nucleosome remodeling. ACF1-ISWI complex (ATP-dependent chromatin assembly and remodeling factor [ACF]) associates with histone-fold proteins (CHRAC-15 and CHRAC-17 in the human chromatin accessibility complex [CHRAC]) whose functional relevance has been unclear. We show that these histone-fold proteins facilitate ATP-dependent nucleosome sliding by ACF. Direct interaction of the CHRAC-15/17 complex with the ACF1 subunit is essential for this process. CHRAC-17 interacts with another histone-fold protein, p12, in DNA polymerase epsilon, but CHRAC-15 is essential for interaction with ACF and enhancement of nucleosome sliding. Surprisingly, CHRAC-15/17, p12/CHRAC-17, and NC2 complexes facilitate ACF-mediated chromatin assembly by a mechanism different from nucleosome sliding enhancement, suggesting a general activity of H2A/H2B type histone-fold complexes in chromatin assembly.
Asunto(s)
Histonas/química , Nucleosomas/química , Secuencia de Aminoácidos , Animales , Cromatina/química , ADN/química , ADN Polimerasa II/química , ADN Polimerasa III/química , Proteínas de Unión al ADN/química , Relación Dosis-Respuesta a Droga , Drosophila , Glutatión Transferasa/metabolismo , Humanos , Datos de Secuencia Molecular , Nucleoproteínas/química , Unión Proteica , Pliegue de Proteína , Estructura Terciaria de Proteína , Proteínas Recombinantes de Fusión/metabolismo , Homología de Secuencia de Aminoácido , Factores de TiempoRESUMEN
The mechanism by which the eukaryotic DNA-replication machinery penetrates condensed chromatin structures to replicate the underlying DNA is poorly understood. Here we provide evidence that an ACF1-ISWI chromatin-remodeling complex is required for replication through heterochromatin in mammalian cells. ACF1 (ATP-utilizing chromatin assembly and remodeling factor 1) and an ISWI isoform, SNF2H (sucrose nonfermenting-2 homolog), become specifically enriched in replicating pericentromeric heterochromatin. RNAi-mediated depletion of ACF1 specifically impairs the replication of pericentromeric heterochromatin. Accordingly, depletion of ACF1 causes a delay in cell-cycle progression through the late stages of S phase. In vivo depletion of SNF2H slows the progression of DNA replication throughout S phase, indicating a functional overlap with ACF1. Decondensing the heterochromatin with 5-aza-2-deoxycytidine reverses the effects of ACF1 and SNF2H depletion. Expression of an ACF1 mutant that cannot interact with SNF2H also interferes with replication of condensed chromatin. Our data suggest that an ACF1-SNF2H complex is part of a dedicated mechanism that enables DNA replication through highly condensed regions of chromatin.
Asunto(s)
Adenosina Trifosfatasas/fisiología , Azacitidina/análogos & derivados , Cromatina/fisiología , Replicación del ADN , Heterocromatina/fisiología , Protaminas , Factores de Transcripción/fisiología , Células 3T3 , Adenosina Trifosfatasas/metabolismo , Animales , Afidicolina/farmacología , Azacitidina/farmacología , Células Cultivadas , Centrómero/inmunología , Centrómero/metabolismo , Cromatina/química , Cromatina/genética , Proteínas Cromosómicas no Histona/metabolismo , ADN/metabolismo , ADN-Citosina Metilasas/metabolismo , Decitabina , Inhibidores Enzimáticos/farmacología , Eliminación de Gen , Proteínas Fluorescentes Verdes , Células HeLa , Humanos , Proteínas Luminiscentes/metabolismo , Ratones , Proteínas Nucleares/inmunología , Proteínas Nucleares/metabolismo , ARN Interferente Pequeño/metabolismo , Proteínas Recombinantes de Fusión/metabolismo , Fase S , Factores de Transcripción/genética , Células Tumorales CultivadasRESUMEN
The histone modification repertoire has recently been expanded. Dot1p is a new type of methyltransferase that methylates lysine 79 in the histone H3 core only in its nucleosomal context and has a possible role in marking open chromatin regions.
