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1.
Dev Cell ; 56(5): 602-612.e4, 2021 Mar 08.
Artigo em Inglês | MEDLINE | ID: mdl-33636105

RESUMO

Tissue-specific DNA methylation patterns are created by transcription factors that recruit methylation and demethylation enzymes to cis-regulatory elements. To date, it is not known whether transcription factors are needed to continuously maintain methylation profiles in development and mature tissues or whether they only establish these marks during organ development. We queried the role of the pioneer factor FoxA in generating hypomethylated DNA at liver enhancers. We discovered a set of FoxA-binding sites that undergo regional, FoxA-dependent demethylation during organ development. Conditional ablation of FoxA genes in the adult liver demonstrated that continued FoxA presence was not required to maintain the hypomethylated state, even when massive cell proliferation was induced. This study provides strong evidence for the stable, epigenetic nature of tissue-specific DNA methylation patterns directed by lineage-determining transcription factors during organ development.

2.
Sci Adv ; 6(49)2020 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-33277249

RESUMO

Here, we selectively target pancreatic ductal adenocarcinoma (PDAC) cells harboring a hemizygous gene essential for cell growth. MYB binding protein 1A (MYBBP1A), encoding a chromatin-bound protein, is hemizygous in most of the PDAC due to a chromosome 17p deletion that also spans TP53 We find that hemizygous MYBBP1A loss in isogenic PDAC cells promotes tumorigenesis but, paradoxically, homozygous MYBBP1A loss is associated with impaired cell growth and decreased tumorigenesis. Poly-adenosine 5'-diphosphate-ribose polymerase 1 (PARP1) interacts with MYBBP1A and displaces it from chromatin. Small molecules, such as olaparib, that trap PARP1 to chromatin are able to evict the minimal pool of chromatin-bound MYBBP1A protein in MYBBP1A hemizygous cells and impair cell growth, greater than its impact on wild-type cells. Our findings reveal how a cell essential gene with one allele lost in cancer cells can be preferentially susceptible to a specific molecular therapy, when compared to wild-type cells.

4.
Nat Genet ; 52(10): 1024-1035, 2020 10.
Artigo em Inglês | MEDLINE | ID: mdl-32989324

RESUMO

Protein aggregation is the hallmark of neurodegeneration, but the molecular mechanisms underlying late-onset Alzheimer's disease (AD) are unclear. Here we integrated transcriptomic, proteomic and epigenomic analyses of postmortem human brains to identify molecular pathways involved in AD. RNA sequencing analysis revealed upregulation of transcription- and chromatin-related genes, including the histone acetyltransferases for H3K27ac and H3K9ac. An unbiased proteomic screening singled out H3K27ac and H3K9ac as the main enrichments specific to AD. In turn, epigenomic profiling revealed gains in the histone H3 modifications H3K27ac and H3K9ac linked to transcription, chromatin and disease pathways in AD. Increasing genome-wide H3K27ac and H3K9ac in a fly model of AD exacerbated amyloid-ß42-driven neurodegeneration. Together, these findings suggest that AD involves a reconfiguration of the epigenome, wherein H3K27ac and H3K9ac affect disease pathways by dysregulating transcription- and chromatin-gene feedback loops. The identification of this process highlights potential epigenetic strategies for early-stage disease treatment.


Assuntos
Doença de Alzheimer/genética , Agregação Patológica de Proteínas/genética , Proteoma/genética , Transcriptoma/genética , Acetilação , Doença de Alzheimer/patologia , Peptídeos beta-Amiloides/genética , Cromatina/genética , Epigenoma/genética , Histona Acetiltransferases/genética , Código das Histonas/genética , Histonas/genética , Humanos , Fragmentos de Peptídeos/genética , Agregação Patológica de Proteínas/patologia , Transdução de Sinais/genética , Ativação Transcricional/genética
5.
Nat Genet ; 52(4): 418-427, 2020 04.
Artigo em Inglês | MEDLINE | ID: mdl-32203463

RESUMO

Gene network transitions in embryos and other fate-changing contexts involve combinations of transcription factors. A subset of fate-changing transcription factors act as pioneers; they scan and target nucleosomal DNA and initiate cooperative events that can open the local chromatin. However, a gap has remained in understanding how molecular interactions with the nucleosome contribute to the chromatin-opening phenomenon. Here we identified a short α-helical region, conserved among FOXA pioneer factors, that interacts with core histones and contributes to chromatin opening in vitro. The same domain is involved in chromatin opening in early mouse embryos for normal development. Thus, local opening of chromatin by interactions between pioneer factors and core histones promotes genetic programming.


Assuntos
Redes Reguladoras de Genes/genética , Histonas/genética , Fatores de Transcrição/genética , Sequência de Aminoácidos , Animais , Linhagem Celular , Cromatina/genética , DNA/genética , Feminino , Regulação da Expressão Gênica no Desenvolvimento/genética , Humanos , Camundongos , Camundongos Endogâmicos C57BL , Nucleossomos/genética , Transcrição Genética/genética
6.
Dev Cell ; 51(6): 745-758.e6, 2019 12 16.
Artigo em Inglês | MEDLINE | ID: mdl-31761669

RESUMO

During mammalian spermatogenesis, germ cell chromatin undergoes dramatic histone acetylation-mediated reorganization, whereby 90%-99% of histones are evicted. Given the potential role of retained histones in fertility and embryonic development, the genomic location of retained nucleosomes is of great interest. However, the ultimate position and mechanisms underlying nucleosome eviction or retention are poorly understood, including several studies utilizing micrococcal-nuclease sequencing (MNase-seq) methodologies reporting remarkably dissimilar locations. We utilized assay for transposase accessible chromatin sequencing (ATAC-seq) in mouse sperm and found nucleosome enrichment at promoters but also retention at inter- and intragenic regions and repetitive elements. We further generated germ-cell-specific, conditional knockout mice for the key histone acetyltransferase Gcn5, which resulted in abnormal chromatin dynamics leading to increased sperm histone retention and severe reproductive phenotypes. Our findings demonstrate that Gcn5-mediated histone acetylation promotes chromatin accessibility and nucleosome eviction in spermiogenesis and that loss of histone acetylation leads to defects that disrupt male fertility and potentially early embryogenesis.


Assuntos
Histonas/metabolismo , Nucleossomos/metabolismo , Espermatogênese/fisiologia , Fatores de Transcrição de p300-CBP/metabolismo , Acetilação , Animais , Cromatina/metabolismo , Masculino , Camundongos , Regiões Promotoras Genéticas/genética , Processamento de Proteína Pós-Traducional/fisiologia , Espermatozoides/metabolismo
7.
Nature ; 571(7764): 211-218, 2019 07.
Artigo em Inglês | MEDLINE | ID: mdl-31207603

RESUMO

Exhausted CD8+ T (Tex) cells in chronic infections and cancer have limited effector function, high co-expression of inhibitory receptors and extensive transcriptional changes compared with effector (Teff) or memory (Tmem) CD8+ T cells. Tex cells are important clinical targets of checkpoint blockade and other immunotherapies. Epigenetically, Tex cells are a distinct immune subset, with a unique chromatin landscape compared with Teff and Tmem cells. However, the mechanisms that govern the transcriptional and epigenetic development of Tex cells remain unknown. Here we identify the HMG-box transcription factor TOX as a central regulator of Tex cells in mice. TOX is largely dispensable for the formation of Teff and Tmem cells, but it is critical for exhaustion: in the absence of TOX, Tex cells do not form. TOX is induced by calcineurin and NFAT2, and operates in a feed-forward loop in which it becomes calcineurin-independent and sustained in Tex cells. Robust expression of TOX therefore results in commitment to Tex cells by translating persistent stimulation into a distinct Tex cell transcriptional and epigenetic developmental program.


Assuntos
Linfócitos T CD8-Positivos/imunologia , Linfócitos T CD8-Positivos/patologia , Epistasia Genética , Proteínas de Homeodomínio/metabolismo , Transcrição Genética , Animais , Calcineurina/metabolismo , Sinalização do Cálcio , Retroalimentação Fisiológica , Feminino , Regulação da Expressão Gênica/imunologia , Genótipo , Memória Imunológica , Masculino , Camundongos , Camundongos Endogâmicos BALB C , Camundongos Endogâmicos C57BL , Fatores de Transcrição NFATC/metabolismo , Evasão Tumoral
8.
Mol Cell ; 73(4): 684-698.e8, 2019 02 21.
Artigo em Inglês | MEDLINE | ID: mdl-30773298

RESUMO

Accumulation of senescent cells during aging contributes to chronic inflammation and age-related diseases. While senescence is associated with profound alterations of the epigenome, a systematic view of epigenetic factors in regulating senescence is lacking. Here, we curated a library of short hairpin RNAs for targeted silencing of all known epigenetic proteins and performed a high-throughput screen to identify key candidates whose downregulation can delay replicative senescence of primary human cells. This screen identified multiple new players including the histone acetyltransferase p300 that was found to be a primary driver of the senescent phenotype. p300, but not the paralogous CBP, induces a dynamic hyper-acetylated chromatin state and promotes the formation of active enhancer elements in the non-coding genome, leading to a senescence-specific gene expression program. Our work illustrates a causal role of histone acetyltransferases and acetylation in senescence and suggests p300 as a potential therapeutic target for senescence and age-related diseases.


Assuntos
Proliferação de Células , Senescência Celular , Montagem e Desmontagem da Cromatina , Cromatina/enzimologia , Fibroblastos/enzimologia , Histonas/metabolismo , Processamento de Proteína Pós-Traducional , Fatores de Transcrição de p300-CBP/metabolismo , Acetilação , Proliferação de Células/genética , Senescência Celular/genética , Cromatina/genética , Montagem e Desmontagem da Cromatina/genética , Repressão Epigenética , Células HEK293 , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Histonas/genética , Humanos , Interferência de RNA , RNA Interferente Pequeno/genética , RNA Interferente Pequeno/metabolismo , Transdução de Sinais , Fatores de Tempo , Transcrição Genética , Fatores de Transcrição de p300-CBP/genética
9.
Gastroenterology ; 156(6): 1834-1848, 2019 05.
Artigo em Inglês | MEDLINE | ID: mdl-30689973

RESUMO

BACKGROUND & AIMS: Little is known about mechanisms that underlie postnatal hepatocyte maturation and fibrosis at the chromatin level. We investigated the transcription of genes involved in maturation and fibrosis in postnatal hepatocytes of mice, focusing on the chromatin compaction the roles of the Polycomb repressive complex 2 histone methyltransferases EZH1 and EZH2. METHODS: Hepatocytes were isolated from mixed background C57BL/6J-C3H mice, as well as mice with liver-specific disruption of Ezh1 and/or Ezh2, at postnatal day 14 and 2 months after birth. Liver tissues were collected and analyzed by RNA sequencing, H3K27me3 chromatin immunoprecipitation sequencing, and sonication-resistant heterochromatin sequencing (a method to map heterochromatin and euchromatin). Liver damage was characterized by histologic analysis. RESULTS: We found more than 3000 genes differentially expressed in hepatocytes during liver maturation from postnatal day 14 to month 2 after birth. Disruption of Ezh1 and Ezh2 in livers caused perinatal hepatocytes to differentiate prematurely and to express genes at postnatal day 14 that would normally be induced by month 2 and differentiate prematurely. Loss of Ezh1 and Ezh2 also resulted in liver fibrosis. Genes with H3K27me3-postive and H3K4me3-positive euchromatic promoters were prematurely induced in hepatocytes with loss of Ezh1 and Ezh2-these genes included those that regulate hepatocyte maturation, fibrosis, and genes not specifically associated with the liver lineage. CONCLUSIONS: The Polycomb repressive complex 2 proteins EZH1 and EZH2 regulate genes that control hepatocyte maturation and fibrogenesis and genes not specifically associated with the liver lineage by acting at euchromatic promoter regions. EZH1 and EZH2 thereby promote liver homeostasis and prevent liver damage. Strategies to manipulate Polycomb proteins might be used to improve hepatocyte derivation protocols or developed for treatment of patients with liver fibrosis.


Assuntos
Diferenciação Celular/genética , Proteína Potenciadora do Homólogo 2 de Zeste/genética , Repressão Epigenética , Regulação da Expressão Gênica/genética , Cirrose Hepática/genética , Complexo Repressor Polycomb 2/genética , Animais , Proteína Potenciadora do Homólogo 2 de Zeste/metabolismo , Eucromatina , Feminino , Expressão Gênica , Ontologia Genética , Hepatócitos , Histonas/metabolismo , Cirrose Hepática/patologia , Masculino , Metilação , Camundongos , Complexo Repressor Polycomb 2/metabolismo , Regiões Promotoras Genéticas , Fatores de Tempo
10.
Science ; 363(6424): 294-297, 2019 01 18.
Artigo em Inglês | MEDLINE | ID: mdl-30606806

RESUMO

Gene silencing by chromatin compaction is integral to establishing and maintaining cell fates. Trimethylated histone 3 lysine 9 (H3K9me3)-marked heterochromatin is reduced in embryonic stem cells compared to differentiated cells. However, the establishment and dynamics of closed regions of chromatin at protein-coding genes, in embryologic development, remain elusive. We developed an antibody-independent method to isolate and map compacted heterochromatin from low-cell number samples. We discovered high levels of compacted heterochromatin, H3K9me3-decorated, at protein-coding genes in early, uncommitted cells at the germ-layer stage, undergoing profound rearrangements and reduction upon differentiation, concomitant with cell type-specific gene expression. Perturbation of the three H3K9me3-related methyltransferases revealed a pivotal role for H3K9me3 heterochromatin during lineage commitment at the onset of organogenesis and for lineage fidelity maintenance.


Assuntos
Diferenciação Celular , Linhagem da Célula , Células-Tronco Embrionárias/citologia , Heterocromatina/genética , Histonas/química , Animais , Embrião de Mamíferos , Feminino , Regulação da Expressão Gênica no Desenvolvimento , Inativação Gênica , Camadas Germinativas/citologia , Hepatócitos/citologia , Células Secretoras de Insulina/citologia , Metilação , Camundongos , Camundongos Endogâmicos C57BL , Camundongos Knockout , Organogênese
11.
Nat Neurosci ; 21(4): 497-505, 2018 04.
Artigo em Inglês | MEDLINE | ID: mdl-29507413

RESUMO

Aging is the strongest risk factor for Alzheimer's disease (AD), although the underlying mechanisms remain unclear. The chromatin state, in particular through the mark H4K16ac, has been implicated in aging and thus may play a pivotal role in age-associated neurodegeneration. Here we compare the genome-wide enrichment of H4K16ac in the lateral temporal lobe of AD individuals against both younger and elderly cognitively normal controls. We found that while normal aging leads to H4K16ac enrichment, AD entails dramatic losses of H4K16ac in the proximity of genes linked to aging and AD. Our analysis highlights the presence of three classes of AD-related changes with distinctive functional roles. Furthermore, we discovered an association between the genomic locations of significant H4K16ac changes with genetic variants identified in prior AD genome-wide association studies and with expression quantitative trait loci. Our results establish the basis for an epigenetic link between aging and AD.


Assuntos
Envelhecimento , Doença de Alzheimer , Encéfalo/patologia , Epigênese Genética/fisiologia , Epigenômica/métodos , Histona Desacetilase 1/metabolismo , Idoso , Doença de Alzheimer/genética , Doença de Alzheimer/patologia , Doença de Alzheimer/fisiopatologia , Análise de Variância , Encéfalo/metabolismo , Imunoprecipitação da Cromatina , Feminino , Estudo de Associação Genômica Ampla , Histona Desacetilase 1/genética , Humanos , Masculino , Pessoa de Meia-Idade
12.
Nat Neurosci ; 21(7): 1018, 2018 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-29556027

RESUMO

In the version of this article initially published online, the fifth author's name was given as Alexander Amlie-Wolf. The correct name is Alexandre Amlie-Wolf. The error has been corrected in the print, PDF and HTML versions of this article.

13.
Genes Dev ; 32(2): 181-193, 2018 01 15.
Artigo em Inglês | MEDLINE | ID: mdl-29440247

RESUMO

Epithelial tissues rely on a highly coordinated balance between self-renewal, proliferation, and differentiation, disruption of which may drive carcinogenesis. The epigenetic regulator KMT2D (MLL4) is one of the most frequently mutated genes in all cancers, particularly epithelial cancers, yet its normal function in these tissues is unknown. Here, we identify a novel role for KMT2D in coordinating this fine balance, as depletion of KMT2D from undifferentiated epidermal keratinocytes results in reduced proliferation, premature spurious activation of terminal differentiation genes, and disorganized epidermal stratification. Genome-wide, KMT2D interacts with p63 and is enriched at its target enhancers. Depletion of KMT2D results in a broad loss of enhancer histone modifications H3 Lys 4 (H3K4) monomethylation (H3K4me1) and H3K27 acetylation (H3K27ac) as well as reduced expression of p63 target genes, including key genes involved in epithelial development and adhesion. Together, these results reveal a critical role for KMT2D in the control of epithelial enhancers and p63 target gene expression, including the requirement of KMT2D for the maintenance of epithelial progenitor gene expression and the coordination of proper terminal differentiation.


Assuntos
Proteínas de Ligação a DNA/fisiologia , Elementos Facilitadores Genéticos , Queratinócitos/metabolismo , Proteínas de Neoplasias/fisiologia , Fatores de Transcrição/metabolismo , Proteínas Supressoras de Tumor/metabolismo , Proliferação de Células , Células Cultivadas , Proteínas de Ligação a DNA/metabolismo , Código das Histonas , Homeostase , Humanos , Proteínas de Neoplasias/metabolismo
14.
Mol Cell ; 68(6): 1023-1037.e15, 2017 12 21.
Artigo em Inglês | MEDLINE | ID: mdl-29272703

RESUMO

Heterochromatin is integral to cell identity maintenance by impeding the activation of genes for alternate cell fates. Heterochromatic regions are associated with histone 3 lysine 9 trimethylation (H3K9me3) or H3K27me3, but these modifications are also found in euchromatic regions that permit transcription. We discovered that resistance to sonication is a reliable indicator of the heterochromatin state, and we developed a biophysical method (gradient-seq) to discriminate subtypes of H3K9me3 and H3K27me3 domains in sonication-resistant heterochromatin (srHC) versus euchromatin. These classifications are more accurate than the histone marks alone in predicting transcriptional silence and resistance of alternate fate genes to activation during direct cell conversion. Our proteomics of H3K9me3-marked srHC and functional screens revealed diverse proteins, including RBMX and RBMXL1, that impede gene induction during cellular reprogramming. Isolation of srHC with gradient-seq provides a genome-wide map of chromatin structure, elucidating subtypes of repressed domains that are uniquely predictive of diverse other chromatin properties.


Assuntos
Biomarcadores/análise , Reprogramação Celular , Proteínas Cromossômicas não Histona/metabolismo , Genômica/métodos , Heterocromatina/genética , Heterocromatina/metabolismo , Proteômica/métodos , Esclerose Amiotrófica Lateral/genética , Esclerose Amiotrófica Lateral/metabolismo , Esclerose Amiotrófica Lateral/patologia , Células Cultivadas , Proteínas Cromossômicas não Histona/genética , Mapeamento Cromossômico , Fibroblastos/citologia , Fibroblastos/metabolismo , Sequenciamento de Nucleotídeos em Larga Escala , Histonas/genética , Histonas/metabolismo , Humanos
15.
Science ; 358(6359): 119-122, 2017 10 06.
Artigo em Inglês | MEDLINE | ID: mdl-28912132

RESUMO

Although the genome is generally thought to be transcriptionally silent during mitosis, technical limitations have prevented sensitive mapping of transcription during mitosis and mitotic exit. Thus, the means by which the interphase expression pattern is transduced to daughter cells have been unclear. We used 5-ethynyluridine to pulse-label transcripts during mitosis and mitotic exit and found that many genes exhibit transcription during mitosis, as confirmed with fluorescein isothiocyanate-uridine 5'-triphosphate labeling, RNA fluorescence in situ hybridization, and quantitative reverse transcription polymerase chain reaction. The first round of transcription immediately after mitosis primarily activates genes involved in the growth and rebuilding of daughter cells, rather than cell type-specific functions. We propose that the cell's transcription pattern is largely retained at a low level through mitosis, whereas the amplitude of transcription observed in interphase is reestablished during mitotic exit.


Assuntos
Mitose/genética , Transcrição Genética , Ativação Transcricional , Linhagem Celular Tumoral , Fluoresceína-5-Isotiocianato/química , Humanos , Hibridização in Situ Fluorescente , Interfase/genética , RNA Mensageiro/análise , RNA Mensageiro/biossíntese , RNA Mensageiro/química , Reação em Cadeia da Polimerase Via Transcriptase Reversa , Coloração e Rotulagem , Uridina Trifosfato/química
16.
Sci Transl Med ; 9(398)2017 07 12.
Artigo em Inglês | MEDLINE | ID: mdl-28701476

RESUMO

Markers are needed to facilitate early detection of pancreatic ductal adenocarcinoma (PDAC), which is often diagnosed too late for effective therapy. Starting with a PDAC cell reprogramming model that recapitulated the progression of human PDAC, we identified secreted proteins and tested a subset as potential markers of PDAC. We optimized an enzyme-linked immunosorbent assay (ELISA) using plasma samples from patients with various stages of PDAC, from individuals with benign pancreatic disease, and from healthy controls. A phase 1 discovery study (n = 20), a phase 2a validation study (n = 189), and a second phase 2b validation study (n = 537) revealed that concentrations of plasma thrombospondin-2 (THBS2) discriminated among all stages of PDAC consistently. The receiver operating characteristic (ROC) c-statistic was 0.76 in the phase 1 study, 0.84 in the phase 2a study, and 0.87 in the phase 2b study. The plasma concentration of THBS2 was able to discriminate resectable stage I cancer as readily as stage III/IV PDAC tumors. THBS2 plasma concentrations combined with those for CA19-9, a previously identified PDAC marker, yielded a c-statistic of 0.96 in the phase 2a study and 0.97 in the phase 2b study. THBS2 data improved the ability of CA19-9 to distinguish PDAC from pancreatitis. With a specificity of 98%, the combination of THBS2 and CA19-9 yielded a sensitivity of 87% for PDAC in the phase 2b study. A THBS2 and CA19-9 blood marker panel measured with a conventional ELISA may improve the detection of patients at high risk for PDAC.


Assuntos
Adenocarcinoma/sangue , Adenocarcinoma/diagnóstico , Biomarcadores Tumorais/sangue , Antígeno CA-19-9/sangue , Carcinoma Ductal Pancreático/sangue , Carcinoma Ductal Pancreático/diagnóstico , Detecção Precoce de Câncer , Trombospondinas/sangue , Adenocarcinoma/patologia , Idoso , Carcinoma Ductal Pancreático/patologia , Estudos de Casos e Controles , Demografia , Feminino , Humanos , Masculino , Pessoa de Meia-Idade , Reprodutibilidade dos Testes
17.
Nature ; 546(7658): 381-386, 2017 06 15.
Artigo em Inglês | MEDLINE | ID: mdl-28562591

RESUMO

Metabolic production of acetyl coenzyme A (acetyl-CoA) is linked to histone acetylation and gene regulation, but the precise mechanisms of this process are largely unknown. Here we show that the metabolic enzyme acetyl-CoA synthetase 2 (ACSS2) directly regulates histone acetylation in neurons and spatial memory in mammals. In a neuronal cell culture model, ACSS2 increases in the nuclei of differentiating neurons and localizes to upregulated neuronal genes near sites of elevated histone acetylation. A decrease in ACSS2 lowers nuclear acetyl-CoA levels, histone acetylation, and responsive expression of the cohort of neuronal genes. In adult mice, attenuation of hippocampal ACSS2 expression impairs long-term spatial memory, a cognitive process that relies on histone acetylation. A decrease in ACSS2 in the hippocampus also leads to defective upregulation of memory-related neuronal genes that are pre-bound by ACSS2. These results reveal a connection between cellular metabolism, gene regulation, and neural plasticity and establish a link between acetyl-CoA generation 'on-site' at chromatin for histone acetylation and the transcription of key neuronal genes.


Assuntos
Acetato-CoA Ligase/metabolismo , Hipocampo/enzimologia , Hipocampo/fisiologia , Histonas/metabolismo , Memória/fisiologia , Plasticidade Neuronal/genética , Ativação Transcricional , Acetato-CoA Ligase/deficiência , Acetato-CoA Ligase/genética , Acetilcoenzima A/metabolismo , Acetilação , Animais , Diferenciação Celular , Núcleo Celular/metabolismo , Células Cultivadas , Cromatina/enzimologia , Cromatina/genética , Cromatina/metabolismo , Regulação Enzimológica da Expressão Gênica , Hipocampo/metabolismo , Histonas/química , Consolidação da Memória/fisiologia , Camundongos , Plasticidade Neuronal/fisiologia , Neurônios/citologia , Neurônios/metabolismo , Regulação para Cima
18.
Cell ; 168(1-2): 135-149.e22, 2017 Jan 12.
Artigo em Inglês | MEDLINE | ID: mdl-28086087

RESUMO

CBP/p300 are transcription co-activators whose binding is a signature of enhancers, cis-regulatory elements that control patterns of gene expression in multicellular organisms. Active enhancers produce bi-directional enhancer RNAs (eRNAs) and display CBP/p300-dependent histone acetylation. Here, we demonstrate that CBP binds directly to RNAs in vivo and in vitro. RNAs bound to CBP in vivo include a large number of eRNAs. Using steady-state histone acetyltransferase (HAT) assays, we show that an RNA binding region in the HAT domain of CBP-a regulatory motif unique to CBP/p300-allows RNA to stimulate CBP's HAT activity. At enhancers where CBP interacts with eRNAs, stimulation manifests in RNA-dependent changes in the histone acetylation mediated by CBP, such as H3K27ac, and by corresponding changes in gene expression. By interacting directly with CBP, eRNAs contribute to the unique chromatin structure at active enhancers, which, in turn, is required for regulation of target genes.


Assuntos
Histona Acetiltransferases/metabolismo , RNA não Traduzido/metabolismo , Fatores de Transcrição de p300-CBP/metabolismo , Acetilação , Animais , Linhagem Celular , Elementos Facilitadores Genéticos , Fibroblastos/metabolismo , Histonas/metabolismo , Camundongos
19.
Front Aging Neurosci ; 8: 208, 2016.
Artigo em Inglês | MEDLINE | ID: mdl-27630559

RESUMO

Aging is a major risk factor for many neurodegenerative disorders. A key feature of aging biology that may underlie these diseases is cellular senescence. Senescent cells accumulate in tissues with age, undergo widespread changes in gene expression, and typically demonstrate altered, pro-inflammatory profiles. Astrocyte senescence has been implicated in neurodegenerative disease, and to better understand senescence-associated changes in astrocytes, we investigated changes in their transcriptome using RNA sequencing. Senescence was induced in human fetal astrocytes by transient oxidative stress. Brain-expressed genes, including those involved in neuronal development and differentiation, were downregulated in senescent astrocytes. Remarkably, several genes indicative of astrocytic responses to injury were also downregulated, including glial fibrillary acidic protein and genes involved in the processing and presentation of antigens by major histocompatibility complex class II proteins, while pro-inflammatory genes were upregulated. Overall, our findings suggest that senescence-related changes in the function of astrocytes may impact the pathogenesis of age-related brain disorders.

20.
Mol Cell ; 62(1): 79-91, 2016 Apr 07.
Artigo em Inglês | MEDLINE | ID: mdl-27058788

RESUMO

Nuclear DNA wraps around core histones to form nucleosomes, which restricts the binding of transcription factors to gene regulatory sequences. Pioneer transcription factors can bind DNA sites on nucleosomes and initiate gene regulatory events, often leading to the local opening of chromatin. However, the nucleosomal configuration of open chromatin and the basis for its regulation is unclear. We combined low and high levels of micrococcal nuclease (MNase) digestion along with core histone mapping to assess the nucleosomal configuration at enhancers and promoters in mouse liver. We find that MNase-accessible nucleosomes, bound by transcription factors, are retained more at liver-specific enhancers than at promoters and ubiquitous enhancers. The pioneer factor FoxA displaces linker histone H1, thereby keeping enhancer nucleosomes accessible in chromatin and allowing other liver-specific transcription factors to bind and stimulate transcription. Thus, nucleosomes are not exclusively repressive to gene regulation when they are retained with, and exposed by, pioneer factors.


Assuntos
Elementos Facilitadores Genéticos , Fator 3-alfa Nuclear de Hepatócito/metabolismo , Fator 3-beta Nuclear de Hepatócito/metabolismo , Fator 3-gama Nuclear de Hepatócito/metabolismo , Nucleossomos/metabolismo , Animais , Histonas/metabolismo , Fígado/metabolismo , Camundongos , Nucleossomos/genética , Especificidade de Órgãos , Regiões Promotoras Genéticas , Transcrição Genética
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