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1.
Cell ; 186(4): 683-685, 2023 02 16.
Artículo en Inglés | MEDLINE | ID: mdl-36803599

RESUMEN

Transgenerational epigenetic inheritance in mammals has long been debatable. In this issue of Cell, Takahashi et al. induce DNA methylation at promoter-associated CpG islands (CGIs) of two metabolism-related genes and show that the acquired epigenetic changes and associated metabolic phenotypes are stably propagated across several generations in transgenic mice.


Asunto(s)
Metilación de ADN , Epigénesis Genética , Ratones , Animales , Mamíferos/genética , Patrón de Herencia , Islas de CpG/genética
2.
Cell ; 186(4): 715-731.e19, 2023 02 16.
Artículo en Inglés | MEDLINE | ID: mdl-36754048

RESUMEN

Transgenerational epigenetic inheritance in mammals remains a debated subject. Here, we demonstrate that DNA methylation of promoter-associated CpG islands (CGIs) can be transmitted from parents to their offspring in mice. We generated DNA methylation-edited mouse embryonic stem cells (ESCs), in which CGIs of two metabolism-related genes, the Ankyrin repeat domain 26 and the low-density lipoprotein receptor, were specifically methylated and silenced. DNA methylation-edited mice generated by microinjection of the methylated ESCs exhibited abnormal metabolic phenotypes. Acquired methylation of the targeted CGI and the phenotypic traits were maintained and transmitted across multiple generations. The heritable CGI methylation was subjected to reprogramming in parental PGCs and subsequently reestablished in the next generation at post-implantation stages. These observations provide a concrete step toward demonstrating transgenerational epigenetic inheritance in mammals, which may have implications in our understanding of evolutionary biology as well as the etiology, diagnosis, and prevention of non-genetically inherited human diseases.


Asunto(s)
Metilación de ADN , Epigénesis Genética , Ratones , Humanos , Animales , Islas de CpG , Patrón de Herencia , Mamíferos/genética
3.
Cell ; 184(9): 2503-2519.e17, 2021 04 29.
Artículo en Inglés | MEDLINE | ID: mdl-33838111

RESUMEN

A general approach for heritably altering gene expression has the potential to enable many discovery and therapeutic efforts. Here, we present CRISPRoff-a programmable epigenetic memory writer consisting of a single dead Cas9 fusion protein that establishes DNA methylation and repressive histone modifications. Transient CRISPRoff expression initiates highly specific DNA methylation and gene repression that is maintained through cell division and differentiation of stem cells to neurons. Pairing CRISPRoff with genome-wide screens and analysis of chromatin marks establishes rules for heritable gene silencing. We identify single guide RNAs (sgRNAs) capable of silencing the large majority of genes including those lacking canonical CpG islands (CGIs) and reveal a wide targeting window extending beyond annotated CGIs. The broad ability of CRISPRoff to initiate heritable gene silencing even outside of CGIs expands the canonical model of methylation-based silencing and enables diverse applications including genome-wide screens, multiplexed cell engineering, enhancer silencing, and mechanistic exploration of epigenetic inheritance.


Asunto(s)
Sistemas CRISPR-Cas , Reprogramación Celular , Epigénesis Genética , Epigenoma , Edición Génica , Células Madre Pluripotentes Inducidas/citología , Neuronas/citología , Diferenciación Celular , Islas de CpG , Metilación de ADN , Silenciador del Gen , Código de Histonas , Humanos , Células Madre Pluripotentes Inducidas/metabolismo , Neuronas/metabolismo , Procesamiento Proteico-Postraduccional
4.
Annu Rev Biochem ; 89: 135-158, 2020 06 20.
Artículo en Inglés | MEDLINE | ID: mdl-31815535

RESUMEN

DNA methylation at the 5-position of cytosine (5mC) plays vital roles in mammalian development. DNA methylation is catalyzed by DNA methyltransferases (DNMTs), and the two DNMT families, DNMT3 and DNMT1, are responsible for methylation establishment and maintenance, respectively. Since their discovery, biochemical and structural studies have revealed the key mechanisms underlying how DNMTs catalyze de novo and maintenance DNA methylation. In particular, recent development of low-input genomic and epigenomic technologies has deepened our understanding of DNA methylation regulation in germ lines and early stage embryos. In this review, we first describe the methylation machinery including the DNMTs and their essential cofactors. We then discuss how DNMTs are recruited to or excluded from certain genomic elements. Lastly, we summarize recent understanding of the regulation of DNA methylation dynamics in mammalian germ lines and early embryos with a focus on both mice and humans.


Asunto(s)
ADN (Citosina-5-)-Metiltransferasa 1/genética , ADN (Citosina-5-)-Metiltransferasas/genética , ADN/genética , Regulación del Desarrollo de la Expresión Génica , Genoma , Animales , Coenzimas/química , Coenzimas/metabolismo , Islas de CpG , ADN/metabolismo , ADN (Citosina-5-)-Metiltransferasa 1/metabolismo , ADN (Citosina-5-)-Metiltransferasas/metabolismo , Metilación de ADN , ADN Metiltransferasa 3A , Embrión de Mamíferos , Humanos , Isoenzimas/genética , Isoenzimas/metabolismo , Masculino , Ratones , Oocitos/citología , Oocitos/enzimología , Oocitos/crecimiento & desarrollo , Transducción de Señal , Espermatozoides/citología , Espermatozoides/enzimología , Espermatozoides/crecimiento & desarrollo
5.
Cell ; 183(6): 1551-1561.e12, 2020 12 10.
Artículo en Inglés | MEDLINE | ID: mdl-33157039

RESUMEN

Retrons are bacterial genetic elements comprised of a reverse transcriptase (RT) and a non-coding RNA (ncRNA). The RT uses the ncRNA as template, generating a chimeric RNA/DNA molecule in which the RNA and DNA components are covalently linked. Although retrons were discovered three decades ago, their function remained unknown. We report that retrons function as anti-phage defense systems. The defensive unit is composed of three components: the RT, the ncRNA, and an effector protein. We examined multiple retron systems and show that they confer defense against a broad range of phages via abortive infection. Focusing on retron Ec48, we show evidence that it "guards" RecBCD, a complex with central anti-phage functions in bacteria. Inhibition of RecBCD by phage proteins activates the retron, leading to abortive infection and cell death. Thus, the Ec48 retron forms a second line of defense that is triggered if the first lines of defense have collapsed.


Asunto(s)
Bacterias/genética , Bacterias/inmunología , Bacteriófagos/fisiología , ARN no Traducido/genética , ADN Polimerasa Dirigida por ARN/genética , Bacterias/virología , Islas de CpG/genética , ADN/metabolismo , Escherichia coli/genética , Escherichia coli/inmunología , Escherichia coli/virología , Proteínas de Escherichia coli/metabolismo , Filogenia
6.
Cell ; 183(7): 1826-1847.e31, 2020 12 23.
Artículo en Inglés | MEDLINE | ID: mdl-33296702

RESUMEN

Inborn errors of human interferon gamma (IFN-γ) immunity underlie mycobacterial disease. We report a patient with mycobacterial disease due to inherited deficiency of the transcription factor T-bet. The patient has extremely low counts of circulating Mycobacterium-reactive natural killer (NK), invariant NKT (iNKT), mucosal-associated invariant T (MAIT), and Vδ2+ γδ T lymphocytes, and of Mycobacterium-non reactive classic TH1 lymphocytes, with the residual populations of these cells also producing abnormally small amounts of IFN-γ. Other lymphocyte subsets develop normally but produce low levels of IFN-γ, with the exception of CD8+ αß T and non-classic CD4+ αß TH1∗ lymphocytes, which produce IFN-γ normally in response to mycobacterial antigens. Human T-bet deficiency thus underlies mycobacterial disease by preventing the development of innate (NK) and innate-like adaptive lymphocytes (iNKT, MAIT, and Vδ2+ γδ T cells) and IFN-γ production by them, with mycobacterium-specific, IFN-γ-producing, purely adaptive CD8+ αß T, and CD4+ αß TH1∗ cells unable to compensate for this deficit.


Asunto(s)
Inmunidad Adaptativa , Inmunidad Innata , Interferón gamma/inmunología , Mycobacterium/inmunología , Proteínas de Dominio T Box/metabolismo , Secuencia de Aminoácidos , Secuencia de Bases , Linaje de la Célula , Preescolar , Cromatina/metabolismo , Islas de CpG/genética , Metilación de ADN/genética , Células Dendríticas/metabolismo , Epigénesis Genética , Femenino , Homocigoto , Humanos , Mutación INDEL/genética , Lactante , Interferón gamma/metabolismo , Células Asesinas Naturales/citología , Células Asesinas Naturales/metabolismo , Mutación con Pérdida de Función/genética , Masculino , Infecciones por Mycobacterium/genética , Infecciones por Mycobacterium/inmunología , Infecciones por Mycobacterium/microbiología , Linaje , Proteínas de Dominio T Box/química , Proteínas de Dominio T Box/deficiencia , Proteínas de Dominio T Box/genética , Linfocitos T Colaboradores-Inductores/inmunología , Transcriptoma/genética
7.
Cell ; 173(2): 291-304.e6, 2018 04 05.
Artículo en Inglés | MEDLINE | ID: mdl-29625048

RESUMEN

We conducted comprehensive integrative molecular analyses of the complete set of tumors in The Cancer Genome Atlas (TCGA), consisting of approximately 10,000 specimens and representing 33 types of cancer. We performed molecular clustering using data on chromosome-arm-level aneuploidy, DNA hypermethylation, mRNA, and miRNA expression levels and reverse-phase protein arrays, of which all, except for aneuploidy, revealed clustering primarily organized by histology, tissue type, or anatomic origin. The influence of cell type was evident in DNA-methylation-based clustering, even after excluding sites with known preexisting tissue-type-specific methylation. Integrative clustering further emphasized the dominant role of cell-of-origin patterns. Molecular similarities among histologically or anatomically related cancer types provide a basis for focused pan-cancer analyses, such as pan-gastrointestinal, pan-gynecological, pan-kidney, and pan-squamous cancers, and those related by stemness features, which in turn may inform strategies for future therapeutic development.


Asunto(s)
Neoplasias/patología , Aneuploidia , Cromosomas/genética , Análisis por Conglomerados , Islas de CpG , Metilación de ADN , Bases de Datos Factuales , Humanos , MicroARNs/metabolismo , Mutación , Proteínas de Neoplasias/genética , Proteínas de Neoplasias/metabolismo , Neoplasias/genética , ARN Mensajero/metabolismo
8.
Cell ; 175(1): 224-238.e15, 2018 09 20.
Artículo en Inglés | MEDLINE | ID: mdl-30173918

RESUMEN

More than 25 inherited human disorders are caused by the unstable expansion of repetitive DNA sequences termed short tandem repeats (STRs). A fundamental unresolved question is why some STRs are susceptible to pathologic expansion, whereas thousands of repeat tracts across the human genome are relatively stable. Here, we discover that nearly all disease-associated STRs (daSTRs) are located at boundaries demarcating 3D chromatin domains. We identify a subset of boundaries with markedly higher CpG island density compared to the rest of the genome. daSTRs specifically localize to ultra-high-density CpG island boundaries, suggesting they might be hotspots for epigenetic misregulation or topological disruption linked to STR expansion. Fragile X syndrome patients exhibit severe boundary disruption in a manner that correlates with local loss of CTCF occupancy and the degree of FMR1 silencing. Our data uncover higher-order chromatin architecture as a new dimension in understanding repeat expansion disorders.


Asunto(s)
Cromatina/genética , Repeticiones de Microsatélite/fisiología , Expansión de Repetición de Trinucleótido/fisiología , Adulto , Encéfalo/citología , Encéfalo/patología , Factor de Unión a CCCTC/genética , Factor de Unión a CCCTC/fisiología , Línea Celular , Cromatina/fisiología , Ensamble y Desensamble de Cromatina/genética , Ensamble y Desensamble de Cromatina/fisiología , Islas de CpG/genética , Islas de CpG/fisiología , ADN/genética , Enfermedad/etiología , Enfermedad/genética , Femenino , Proteína de la Discapacidad Intelectual del Síndrome del Cromosoma X Frágil/genética , Proteína de la Discapacidad Intelectual del Síndrome del Cromosoma X Frágil/metabolismo , Proteína de la Discapacidad Intelectual del Síndrome del Cromosoma X Frágil/fisiología , Síndrome del Cromosoma X Frágil/genética , Síndrome del Cromosoma X Frágil/metabolismo , Genoma Humano/genética , Humanos , Masculino , Repeticiones de Microsatélite/genética , Expansión de Repetición de Trinucleótido/genética
9.
Cell ; 173(1): 248-259.e15, 2018 03 22.
Artículo en Inglés | MEDLINE | ID: mdl-29526463

RESUMEN

The dynamics of the chromatin regulatory landscape during human early embryogenesis remains unknown. Using DNase I hypersensitive site (DHS) sequencing, we report that the chromatin accessibility landscape is gradually established during human early embryogenesis. Interestingly, the DHSs with OCT4 binding motifs are enriched at the timing of zygotic genome activation (ZGA) in humans, but not in mice. Consistently, OCT4 contributes to ZGA in humans, but not in mice. We further find that lower CpG promoters usually establish DHSs at later stages. Similarly, younger genes tend to establish promoter DHSs and are expressed at later embryonic stages, while older genes exhibit these features at earlier stages. Moreover, our data show that human active transposons SVA and HERV-K harbor DHSs and are highly expressed in early embryos, but not in differentiated tissues. In summary, our data provide an evolutionary developmental view for understanding the regulation of gene and transposon expression.


Asunto(s)
Cromatina/metabolismo , Embrión de Mamíferos/metabolismo , Evolución Molecular , Animales , Sitios de Unión , Islas de CpG , Metilación de ADN , Elementos Transponibles de ADN/genética , Desoxirribonucleasa I/metabolismo , Regulación hacia Abajo , Desarrollo Embrionario , Humanos , Ratones , Factor 3 de Transcripción de Unión a Octámeros/antagonistas & inhibidores , Factor 3 de Transcripción de Unión a Octámeros/genética , Factor 3 de Transcripción de Unión a Octámeros/metabolismo , Regiones Promotoras Genéticas , Interferencia de ARN , ARN Interferente Pequeño/metabolismo , Cigoto/metabolismo
10.
Cell ; 168(5): 801-816.e13, 2017 02 23.
Artículo en Inglés | MEDLINE | ID: mdl-28215704

RESUMEN

DNMT3A mutations occur in ∼25% of acute myeloid leukemia (AML) patients. The most common mutation, DNMT3AR882H, has dominant negative activity that reduces DNA methylation activity by ∼80% in vitro. To understand the contribution of DNMT3A-dependent methylation to leukemogenesis, we performed whole-genome bisulfite sequencing of primary leukemic and non-leukemic cells in patients with or without DNMT3AR882 mutations. Non-leukemic hematopoietic cells with DNMT3AR882H displayed focal methylation loss, suggesting that hypomethylation antedates AML. Although virtually all AMLs with wild-type DNMT3A displayed CpG island hypermethylation, this change was not associated with gene silencing and was essentially absent in AMLs with DNMT3AR882 mutations. Primary hematopoietic stem cells expanded with cytokines were hypermethylated in a DNMT3A-dependent manner, suggesting that hypermethylation may be a response to, rather than a cause of, cellular proliferation. Our findings suggest that hypomethylation is an initiating phenotype in AMLs with DNMT3AR882, while DNMT3A-dependent CpG island hypermethylation is a consequence of AML progression.


Asunto(s)
Islas de CpG , ADN (Citosina-5-)-Metiltransferasas/metabolismo , Metilación de ADN , Leucemia Mieloide Aguda/genética , Células de la Médula Ósea/patología , ADN (Citosina-5-)-Metiltransferasas/genética , ADN Metiltransferasa 3A , Epigénesis Genética , Humanos , Leucemia Mieloide Aguda/patología , Mutación , Análisis de Secuencia de ADN
11.
Cell ; 170(2): 367-381.e20, 2017 Jul 13.
Artículo en Inglés | MEDLINE | ID: mdl-28709003

RESUMEN

High-order chromatin structure plays important roles in gene expression regulation. Knowledge of the dynamics of 3D chromatin structures during mammalian embryo development remains limited. We report the 3D chromatin architecture of mouse gametes and early embryos using an optimized Hi-C method with low-cell samples. We find that mature oocytes at the metaphase II stage do not have topologically associated domains (TADs). In sperm, extra-long-range interactions (>4 Mb) and interchromosomal interactions occur frequently. The high-order structures of both the paternal and maternal genomes in zygotes and two-cell embryos are obscure but are gradually re-established through development. The establishment of the TAD structure requires DNA replication but not zygotic genome activation. Furthermore, unmethylated CpGs are enriched in A compartment, and methylation levels are decreased to a greater extent in A compartment than in B compartment in embryos. In summary, the global reprogramming of chromatin architecture occurs during early mammalian development.


Asunto(s)
Cromatina/metabolismo , Embrión de Mamíferos/metabolismo , Desarrollo Embrionario , Animales , Cromatina/química , Islas de CpG , Metilación de ADN , Replicación del ADN , Embrión de Mamíferos/química , Epigénesis Genética , Femenino , Células Germinativas/metabolismo , Masculino , Metafase , Ratones , Ratones Endogámicos C57BL , Ratones Endogámicos DBA , Oocitos/citología , Espermatozoides/metabolismo , Cigoto/metabolismo
12.
Mol Cell ; 84(20): 3950-3966.e6, 2024 Oct 17.
Artículo en Inglés | MEDLINE | ID: mdl-39383879

RESUMEN

The role of long non-coding RNAs (lncRNAs) in malignant cell transformation remains elusive. We previously identified an enhancer-associated lncRNA, LINC01116 (named HOXDeRNA), as a transformative factor converting human astrocytes into glioma-like cells. Employing a combination of CRISPR editing, chromatin isolation by RNA purification coupled with sequencing (ChIRP-seq), in situ mapping RNA-genome interactions (iMARGI), chromatin immunoprecipitation sequencing (ChIP-seq), HiC, and RNA/DNA FISH, we found that HOXDeRNA directly binds to CpG islands within the promoters of 35 glioma-specific transcription factors (TFs) distributed throughout the genome, including key stem cell TFs SOX2, OLIG2, POU3F2, and ASCL1, liberating them from PRC2 repression. This process requires a distinct RNA quadruplex structure and other segments of HOXDeRNA, interacting with EZH2 and CpGs, respectively. Subsequent transformation activates multiple oncogenes (e.g., EGFR, miR-21, and WEE1), driven by the SOX2- and OLIG2-dependent glioma-specific super enhancers. These results help reconstruct the sequence of events underlying the process of astrocyte transformation, highlighting HOXDeRNA's central genome-wide activity and suggesting a shared RNA-dependent mechanism in otherwise heterogeneous and multifactorial gliomagenesis.


Asunto(s)
Elementos de Facilitación Genéticos , Regulación Neoplásica de la Expresión Génica , Glioma , ARN Largo no Codificante , Humanos , ARN Largo no Codificante/genética , ARN Largo no Codificante/metabolismo , Glioma/genética , Glioma/patología , Glioma/metabolismo , Astrocitos/metabolismo , Factores de Transcripción/metabolismo , Factores de Transcripción/genética , Regiones Promotoras Genéticas , Islas de CpG , Transformación Celular Neoplásica/genética , Transformación Celular Neoplásica/metabolismo , Línea Celular Tumoral , Transcripción Genética , Sitios de Unión , Súper Potenciadores
13.
Cell ; 167(1): 233-247.e17, 2016 Sep 22.
Artículo en Inglés | MEDLINE | ID: mdl-27662091

RESUMEN

Mammalian DNA methylation is a critical epigenetic mechanism orchestrating gene expression networks in many biological processes. However, investigation of the functions of specific methylation events remains challenging. Here, we demonstrate that fusion of Tet1 or Dnmt3a with a catalytically inactive Cas9 (dCas9) enables targeted DNA methylation editing. Targeting of the dCas9-Tet1 or -Dnmt3a fusion protein to methylated or unmethylated promoter sequences caused activation or silencing, respectively, of an endogenous reporter. Targeted demethylation of the BDNF promoter IV or the MyoD distal enhancer by dCas9-Tet1 induced BDNF expression in post-mitotic neurons or activated MyoD facilitating reprogramming of fibroblasts into myoblasts, respectively. Targeted de novo methylation of a CTCF loop anchor site by dCas9-Dnmt3a blocked CTCF binding and interfered with DNA looping, causing altered gene expression in the neighboring loop. Finally, we show that these tools can edit DNA methylation in mice, demonstrating their wide utility for functional studies of epigenetic regulation.


Asunto(s)
Repeticiones Palindrómicas Cortas Agrupadas y Regularmente Espaciadas , ADN (Citosina-5-)-Metiltransferasas/metabolismo , Metilación de ADN/genética , Proteínas de Unión al ADN/metabolismo , Epigénesis Genética , Edición Génica/métodos , Proteínas Proto-Oncogénicas/metabolismo , Animales , Proteínas Bacterianas/genética , Proteínas Bacterianas/metabolismo , Factor Neurotrófico Derivado del Encéfalo/genética , Factor de Unión a CCCTC , Proteína 9 Asociada a CRISPR , Línea Celular , Islas de CpG , ADN (Citosina-5-)-Metiltransferasas/genética , ADN Metiltransferasa 3A , Proteínas de Unión al ADN/genética , Endonucleasas/genética , Endonucleasas/metabolismo , Elementos de Facilitación Genéticos , Genoma , Ratones , Proteína MioD/metabolismo , Neuronas/metabolismo , Regiones Promotoras Genéticas , Unión Proteica , Proteínas Proto-Oncogénicas/genética , Proteínas Recombinantes de Fusión/genética , Proteínas Recombinantes de Fusión/metabolismo , Proteínas Represoras/metabolismo
14.
Cell ; 163(1): 218-29, 2015 Sep 24.
Artículo en Inglés | MEDLINE | ID: mdl-26406378

RESUMEN

Mammalian DNA methylation plays an essential role in development. To date, only snapshots of different mouse and human cell types have been generated, providing a static view on DNA methylation. To enable monitoring of methylation status as it changes over time, we establish a reporter of genomic methylation (RGM) that relies on a minimal imprinted gene promoter driving a fluorescent protein. We show that insertion of RGM proximal to promoter-associated CpG islands reports the gain or loss of DNA methylation. We further utilized RGM to report endogenous methylation dynamics of non-coding regulatory elements, such as the pluripotency-specific super enhancers of Sox2 and miR290. Loci-specific DNA methylation changes and their correlation with transcription were visualized during cell-state transition following differentiation of mouse embryonic stem cells and during reprogramming of somatic cells to pluripotency. RGM will allow the investigation of dynamic methylation changes during development and disease at single-cell resolution.


Asunto(s)
Metilación de ADN , Análisis de la Célula Individual , Animales , Islas de CpG , Metilasas de Modificación del ADN/metabolismo , Células Madre Embrionarias , Elementos de Facilitación Genéticos , Humanos , Ratones , MicroARNs/metabolismo , Regiones Promotoras Genéticas , Factores de Transcripción SOXB1/metabolismo
15.
Nature ; 628(8007): 373-380, 2024 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-38448583

RESUMEN

Pervasive transcriptional activity is observed across diverse species. The genomes of extant organisms have undergone billions of years of evolution, making it unclear whether these genomic activities represent effects of selection or 'noise'1-4. Characterizing default genome states could help understand whether pervasive transcriptional activity has biological meaning. Here we addressed this question by introducing a synthetic 101-kb locus into the genomes of Saccharomyces cerevisiae and Mus musculus and characterizing genomic activity. The locus was designed by reversing but not complementing human HPRT1, including its flanking regions, thus retaining basic features of the natural sequence but ablating evolved coding or regulatory information. We observed widespread activity of both reversed and native HPRT1 loci in yeast, despite the lack of evolved yeast promoters. By contrast, the reversed locus displayed no activity at all in mouse embryonic stem cells, and instead exhibited repressive chromatin signatures. The repressive signature was alleviated in a locus variant lacking CpG dinucleotides; nevertheless, this variant was also transcriptionally inactive. These results show that synthetic genomic sequences that lack coding information are active in yeast, but inactive in mouse embryonic stem cells, consistent with a major difference in 'default genomic states' between these two divergent eukaryotic cell types, with implications for understanding pervasive transcription, horizontal transfer of genetic information and the birth of new genes.


Asunto(s)
Genes Sintéticos , Genoma , Saccharomyces cerevisiae , Transcripción Genética , Animales , Humanos , Ratones , Cromatina/genética , Islas de CpG , Genes Sintéticos/genética , Genoma/genética , Células Madre Embrionarias de Ratones/metabolismo , Regiones Promotoras Genéticas/genética , Saccharomyces cerevisiae/genética , Hipoxantina Fosforribosiltransferasa/genética , Evolución Molecular
16.
Mol Cell ; 82(6): 1169-1185.e7, 2022 03 17.
Artículo en Inglés | MEDLINE | ID: mdl-35202573

RESUMEN

Polycomb group (PcG) proteins are essential for post-implantation development by depositing repressive histone modifications at promoters, mainly CpG islands (CGIs), of developmental regulator genes. However, promoter PcG marks are erased after fertilization and de novo established in peri-implantation embryos, coinciding with the transition from naive to primed pluripotency. Nevertheless, the molecular basis for this establishment remains unknown. In this study, we show that the expression of the long KDM2B isoform (KDM2BLF), which contains the demethylase domain, is specifically induced at peri-implantation and that its H3K36me2 demethylase activity is required for PcG enrichment at CGIs. Moreover, KDM2BLF interacts with BRG1/BRM-associated factor (BAF) and stabilizes BAF occupancy at CGIs for subsequent gain of accessibility, which precedes PcG enrichment. Consistently, KDM2BLF inactivation results in significantly delayed post-implantation development. In summary, our data unveil dynamic chromatin configuration of CGIs during exit from naive pluripotency and provide a conceptual framework for the spatiotemporal establishment of PcG functions.


Asunto(s)
Cromatina , Proteínas de Drosophila , Islas de CpG , Proteínas de Drosophila/metabolismo , Código de Histonas , Proteínas del Grupo Polycomb/genética , Proteínas del Grupo Polycomb/metabolismo , Regiones Promotoras Genéticas
17.
Nat Immunol ; 18(5): 509-518, 2017 05.
Artículo en Inglés | MEDLINE | ID: mdl-28319098

RESUMEN

The retention of intracellular Toll-like receptors (TLRs) in the endoplasmic reticulum prevents their activation under basal conditions. TLR9 is activated by sensing ligands in specific endosomal-lysosomal compartments. Here we identified IRAP+ endosomes as major cellular compartments for the early steps of TLR9 activation in dendritic cells (DCs). Both TLR9 and its ligand, the dinucleotide CpG, were present as cargo in IRAP+ endosomes. In the absence of the aminopeptidase IRAP, the trafficking of CpG and TLR9 to lysosomes and signaling via TLR9 were enhanced in DCs and in mice following bacterial infection. IRAP stabilized CpG-containing endosomes by interacting with the actin-nucleation factor FHOD4, which slowed the trafficking of TLR9 toward lysosomes. Thus, endosomal retention of TLR9 via the interaction of IRAP with the actin cytoskeleton is a mechanism that prevents hyper-activation of TLR9 in DCs.


Asunto(s)
Cistinil Aminopeptidasa/metabolismo , Citoesqueleto/metabolismo , Células Dendríticas/fisiología , Endosomas/metabolismo , Infecciones por Pseudomonas/inmunología , Pseudomonas aeruginosa/inmunología , Receptor Toll-Like 9/metabolismo , Animales , Células Cultivadas , Islas de CpG/genética , Cistinil Aminopeptidasa/genética , Células Dendríticas/microbiología , Ratones , Ratones Endogámicos C57BL , Ratones Noqueados , Mutación/genética , Oligodesoxirribonucleótidos/inmunología , Unión Proteica , Transducción de Señal
18.
Nat Immunol ; 18(10): 1160-1172, 2017 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-28783152

RESUMEN

Regulatory T cells (Treg cells) perform two distinct functions: they maintain self-tolerance, and they support organ homeostasis by differentiating into specialized tissue Treg cells. We found that epigenetic modifications defined the molecular characteristics of tissue Treg cells. Tagmentation-based whole-genome bisulfite sequencing revealed more than 11,000 regions that were methylated differentially in pairwise comparisons of tissue Treg cell populations and lymphoid T cells. Similarities in the epigenetic landscape led to the identification of a common tissue Treg cell population that was present in many organs and was characterized by gain and loss of DNA methylation that included many gene sites associated with the TH2 subset of helper T cells, such as the gene encoding cytokine IL-33 receptor ST2, as well as the production of tissue-regenerative factors. Furthermore, the ST2-expressing population was dependent on the transcriptional regulator BATF and could be expanded by IL-33. Thus, tissue Treg cells integrate multiple waves of epigenetic reprogramming that define their tissue-restricted specialization.


Asunto(s)
Metilación de ADN , Estudio de Asociación del Genoma Completo , Linfocitos T Reguladores/metabolismo , Animales , Biomarcadores , Análisis por Conglomerados , Biología Computacional/métodos , Islas de CpG , Epigénesis Genética , Perfilación de la Expresión Génica , Regulación de la Expresión Génica , Ontología de Genes , Secuenciación de Nucleótidos de Alto Rendimiento , Inmunofenotipificación , Ratones , Ratones Transgénicos , Anotación de Secuencia Molecular , Especificidad de Órganos/genética , Especificidad de Órganos/inmunología , Regiones Promotoras Genéticas , Células Th2/metabolismo , Sitio de Iniciación de la Transcripción , Transcriptoma
19.
Immunity ; 52(6): 1119-1132.e4, 2020 06 16.
Artículo en Inglés | MEDLINE | ID: mdl-32362325

RESUMEN

The contribution of FOXP3-expressing naturally occurring regulatory T (Treg) cells to common polygenic autoimmune diseases remains ambiguous. Here, we characterized genome-wide epigenetic profiles (CpG methylation and histone modifications) of human Treg and conventional T (Tconv) cells in naive and activated states. We found that single-nucleotide polymorphisms (SNPs) associated with common autoimmune diseases were predominantly enriched in CpG demethylated regions (DRs) specifically present in naive Treg cells but much less enriched in activation-induced DRs common in Tconv and Treg cells. Naive Treg cell-specific DRs were largely included in Treg cell-specific super-enhancers and closely associated with transcription and other epigenetic changes in naive and effector Treg cells. Thus, naive Treg cell-specific CpG hypomethylation had a key role in controlling Treg cell-specific gene transcription and epigenetic modification. The results suggest possible contribution of altered function or development of natural Treg cells to the susceptibility to common autoimmune diseases.


Asunto(s)
Enfermedades Autoinmunes/genética , Enfermedades Autoinmunes/inmunología , Epigénesis Genética , Epigenómica , Predisposición Genética a la Enfermedad , Linfocitos T Reguladores/inmunología , Linfocitos T Reguladores/metabolismo , Biomarcadores , Diferenciación Celular/genética , Diferenciación Celular/inmunología , Biología Computacional , Islas de CpG , Metilación de ADN , Epigenómica/métodos , Perfilación de la Expresión Génica , Variación Genética , Humanos , Inmunofenotipificación , Polimorfismo de Nucleótido Simple , Subgrupos de Linfocitos T , Linfocitos T Reguladores/citología , Transcriptoma
20.
Cell ; 157(4): 979-991, 2014 May 08.
Artículo en Inglés | MEDLINE | ID: mdl-24813617

RESUMEN

The reprogramming of parental methylomes is essential for embryonic development. In mammals, paternal 5-methylcytosines (5mCs) have been proposed to be actively converted to oxidized bases. These paternal oxidized bases and maternal 5mCs are believed to be passively diluted by cell divisions. By generating single-base resolution, allele-specific DNA methylomes from mouse gametes, early embryos, and primordial germ cell (PGC), as well as single-base-resolution maps of oxidized cytosine bases for early embryos, we report the existence of 5hmC and 5fC in both maternal and paternal genomes and find that 5mC or its oxidized derivatives, at the majority of demethylated CpGs, are converted to unmodified cytosines independent of passive dilution from gametes to four-cell embryos. Therefore, we conclude that paternal methylome and at least a significant proportion of maternal methylome go through active demethylation during embryonic development. Additionally, all the known imprinting control regions (ICRs) were classified into germ-line or somatic ICRs.


Asunto(s)
Metilación de ADN , Desarrollo Embrionario , Regulación del Desarrollo de la Expresión Génica , Impresión Genómica , 5-Metilcitosina/metabolismo , Animales , Islas de CpG , Citosina/análogos & derivados , Citosina/metabolismo , Embrión de Mamíferos/metabolismo , Femenino , Masculino , Ratones , Ratones Endogámicos C57BL , Ratones Endogámicos DBA , Regiones Promotoras Genéticas
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