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1.
Immunohorizons ; 6(9): 671-683, 2022 Sep 13.
Artigo em Inglês | MEDLINE | ID: mdl-36100367

RESUMO

T cells experience varying intensities of tonic or basal TCR signaling in response to self-peptides presented by MHC (self-pMHC) in vivo. We analyzed four subpopulations of mouse naive CD4+ cells that express different levels of Nur77-GFP and Ly6C, surrogate markers that positively and inversely correlate with the strength of tonic TCR signaling, respectively. Adoptive transfer studies suggest that relatively weak or strong Nur77-GFP intensity in thymocytes tends to be maintained in mature T cells. Two-dimensional affinity measurements were lowest for Nur77-GFPloLy6C+ cells and highest for Nur77-GFPhiLy6C- cells, highlighting a positive correlation between apparent TCR affinity and tonic TCR signal strength. Despite experiencing the strongest tonic TCR signaling, Nur77-GFPhiLy6C- cells were least responsive to multiple concentrations of a cognate or suboptimal pMHC. Gene expression analyses suggest that Nur77-GFPhiLy6C- cells induce a gene expression program that has similarities with that of acutely stimulated T cells. However, strong tonic TCR signaling also correlates with increased expression of genes with inhibitory functions, including coinhibitory receptors. Similarly, assay for transposase-accessible chromatin with sequencing analyses suggested that increased tonic TCR signal strength correlated with increased chromatin accessibility associated with genes that have positive and inhibitory roles in T cell activation. Strikingly, Nur77-GFPhiLy6C- cells exhibited differential accessibility within regions of Cd200r1 and Tox that were similar in location to differentially accessible regions previously identified in exhausted CD8+ T cells. We propose that constitutive strong tonic TCR signaling triggers adaptations detectable at both the transcriptional and epigenetic levels, ultimately contributing to the tuning of T cell responsiveness.


Assuntos
Linfócitos T CD8-Positivos , Receptores de Antígenos de Linfócitos T , Animais , Linfócitos T CD4-Positivos/metabolismo , Linfócitos T CD8-Positivos/metabolismo , Cromatina/metabolismo , Camundongos , Receptores de Antígenos de Linfócitos T/genética , Transdução de Sinais
2.
J Exp Med ; 219(11)2022 Nov 07.
Artigo em Inglês | MEDLINE | ID: mdl-36048018

RESUMO

Group 3 innate lymphoid cells (ILC3s) are crucial for the maintenance of host-microbiota homeostasis in gastrointestinal mucosal tissues. The mechanisms that maintain lineage identity of intestinal ILC3s and ILC3-mediated orchestration of microbiota and mucosal T cell immunity are elusive. Here, we identified BATF as a gatekeeper of ILC3 homeostasis in the gut. Depletion of BATF in ILC3s resulted in excessive interferon-γ production, dysbiosis, aberrant T cell immune responses, and spontaneous inflammatory bowel disease (IBD), which was considerably ameliorated by the removal of adaptive immunity, interferon-γ blockade, or antibiotic treatment. Mechanistically, BATF directly binds to the cis-regulatory elements of type 1 effector genes, restrains their chromatin accessibility, and inhibits their expression. Conversely, BATF promotes chromatin accessibility of genes involved in MHCII antigen processing and presentation pathways, which in turn directly promotes the transition of precursor ILC3s to MHCII+ ILC3s. Collectively, our findings reveal that BATF is a key transcription factor for maintaining ILC3 stability and coordinating ILC3-mediated control of intestinal homeostasis.


Assuntos
Fatores de Transcrição de Zíper de Leucina Básica/metabolismo , Imunidade Inata , Linfócitos , Animais , Fatores de Transcrição de Zíper de Leucina Básica/genética , Cromatina/metabolismo , Homeostase , Interferon gama/metabolismo , Mucosa Intestinal , Camundongos
3.
Genome Biol ; 23(1): 185, 2022 Sep 01.
Artigo em Inglês | MEDLINE | ID: mdl-36050765

RESUMO

BACKGROUND: Lamina-associated domains (LADs) are large genomic regions that are positioned at the nuclear lamina. It has remained largely unclear what drives the positioning and demarcation of LADs. Because the insulator protein CTCF is enriched at LAD borders, it was postulated that CTCF binding could position some LAD boundaries, possibly through its function in stalling cohesin and hence preventing cohesin invading into the LAD. To test this, we mapped genome-nuclear lamina interactions in mouse embryonic stem cells after rapid depletion of CTCF and other perturbations of cohesin dynamics. RESULTS: CTCF and cohesin contribute to a sharp transition in lamina interactions at LAD borders, while LADs are maintained after depletion of these proteins, also at borders marked by CTCF. CTCF and cohesin may thus reinforce LAD borders, but do not position these. CTCF binding sites within LADs are locally detached from the lamina and enriched for accessible DNA and active histone modifications. Remarkably, despite lamina positioning being strongly correlated with genome inactivity, this DNA remains accessible after the local detachment is lost following CTCF depletion. At a chromosomal scale, cohesin depletion and cohesin stabilization by depletion of the unloading factor WAPL quantitatively affect lamina interactions, indicative of perturbed chromosomal positioning in the nucleus. Finally, while H3K27me3 is locally enriched at CTCF-marked LAD borders, we find no evidence for an interplay between CTCF and H3K27me3 on lamina interactions. CONCLUSIONS: These findings illustrate that CTCF and cohesin are not primary determinants of LAD patterns. Rather, these proteins locally modulate NL interactions.


Assuntos
Fator de Ligação a CCCTC/metabolismo , Proteínas Cromossômicas não Histona/metabolismo , Histonas , Lâmina Nuclear , Animais , Proteínas de Ciclo Celular/genética , Cromatina/metabolismo , DNA/metabolismo , Histonas/metabolismo , Camundongos , Lâmina Nuclear/química
4.
Commun Biol ; 5(1): 967, 2022 Sep 15.
Artigo em Inglês | MEDLINE | ID: mdl-36109650

RESUMO

Singapore's National Flower, Papilionanthe (Ple.) Miss Joaquim 'Agnes' (PMJ) is highly prized as a horticultural flower from the Orchidaceae family. A combination of short-read sequencing, single-molecule long-read sequencing and chromatin contact mapping was used to assemble the PMJ genome, spanning 2.5 Gb and 19 pseudo-chromosomal scaffolds. Genomic resources and chemical profiling provided insights towards identifying, understanding and elucidating various classes of secondary metabolite compounds synthesized by the flower. For example, presence of the anthocyanin pigments detected by chemical profiling coincides with the expression of ANTHOCYANIN SYNTHASE (ANS), an enzyme responsible for the synthesis of the former. Similarly, the presence of vandaterosides (a unique class of glycosylated organic acids with the potential to slow skin aging) discovered using chemical profiling revealed the involvement of glycosyltransferase family enzymes candidates in vandateroside biosynthesis. Interestingly, despite the unnoticeable scent of the flower, genes involved in the biosynthesis of volatile compounds and chemical profiling revealed the combination of oxygenated hydrocarbons, including traces of linalool, beta-ionone and vanillin, forming the scent profile of PMJ. In summary, by combining genomics and biochemistry, the findings expands the known biodiversity repertoire of the Orchidaceae family and insights into the genome and secondary metabolite processes of PMJ.


Assuntos
Antocianinas , Orchidaceae , Cromatina/metabolismo , Flores/genética , Flores/metabolismo , Regulação da Expressão Gênica de Plantas , Glicosiltransferases/genética , Redes e Vias Metabólicas , Orchidaceae/genética , Singapura
5.
Sci Immunol ; 7(75): eabj0140, 2022 Sep 16.
Artigo em Inglês | MEDLINE | ID: mdl-36112694

RESUMO

Pulmonary alveolar proteinosis (PAP) is a syndrome characterized by accumulation of surfactant lipoproteins within the lung alveoli. Alveolar macrophages (AMs) are crucial for surfactant clearance, and their differentiation depends on colony-stimulating factor 2 (CSF2), which regulates the establishment of an AM-characteristic gene regulatory network. Here, we report that the transcription factor CCAAT/enhancer binding protein ß (C/EBPß) is essential for the development of the AM identity, as demonstrated by transcriptome and chromatin accessibility analysis. Furthermore, C/EBPß-deficient AMs showed severe defects in proliferation, phagocytosis, and lipid metabolism, collectively resulting in a PAP-like syndrome. Mechanistically, the long C/EBPß protein variants LAP* and LAP together with CSF2 signaling induced the expression of Pparg isoform 2 but not Pparg isoform 1, a molecular regulatory mechanism that was also observed in other CSF2-primed macrophages. These results uncover C/EBPß as a key regulator of AM cell fate and shed light on the molecular networks controlling lipid metabolism in macrophages.


Assuntos
Macrófagos Alveolares , Surfactantes Pulmonares , Cromatina/metabolismo , Metabolismo dos Lipídeos , Lipoproteínas/metabolismo , Macrófagos Alveolares/metabolismo , PPAR gama/metabolismo , Isoformas de Proteínas/metabolismo , Surfactantes Pulmonares/metabolismo , Tensoativos/metabolismo
6.
Front Immunol ; 13: 938240, 2022.
Artigo em Inglês | MEDLINE | ID: mdl-36072607

RESUMO

Common variable immunodeficiency (CVID) is the most prevalent form of symptomatic primary immunodeficiency in humans. The genetic cause of CVID is still unknown in about 70% of cases. Ten percent of CVID patients carry heterozygous mutations in the tumor necrosis factor receptor superfamily member 13B gene (TNFRSF13B), encoding TACI. Mutations in TNFRSF13B alone may not be sufficient for the development of CVID, as 1% of the healthy population carry these mutations. The common hypothesis is that TACI mutations are not fully penetrant and additional factors contribute to the development of CVID. To determine these additional factors, we investigated the perturbations of transcription factor (TF) binding and the transcriptome profiles in unstimulated and CD40L/IL21-stimulated naïve B cells from CVID patients harboring the C104R mutation in TNFRSF13B and compared them to their healthy relatives with the same mutation. In addition, the proteome of stimulated naïve B cells was investigated. For functional validation, intracellular protein concentrations were measured by flow cytometry. Our analysis revealed 8% less accessible chromatin in unstimulated naïve B cells and 25% less accessible chromatin in class-switched memory B cells from affected and unaffected TACI mutation carriers compared to healthy donors. The most enriched TF binding motifs in TACI mutation carriers involved members from the ETS, IRF, and NF-κB TF families. Validation experiments supported dysregulation of the NF-κB and MAPK pathways. In steady state, naïve B cells had increased cell death pathways and reduced cell metabolism pathways, while after stimulation, enhanced immune responses and decreased cell survival were detected. Using a multi-omics approach, our findings provide valuable insights into the impaired biology of naïve B cells from TACI mutation carriers.


Assuntos
Imunodeficiência de Variável Comum , NF-kappa B , Linfócitos B , Cromatina/metabolismo , Humanos , Mutação , NF-kappa B/metabolismo
7.
Int J Mol Sci ; 23(17)2022 Sep 01.
Artigo em Inglês | MEDLINE | ID: mdl-36077381

RESUMO

Although significant advancement has been made in the study of adipogenesis, knowledge about how chromatin accessibility regulates yak adipogenesis is lacking. We here described genome-wide dynamic chromatin accessibility in preadipocytes and adipocytes by using the assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq), and thus revealed the unique characteristics of open chromatin during yak adipocyte differentiation. The chromatin accessibility of preadipocytes and adipocytes exhibited a similar genomic distribution, displaying a preferential location within the intergenic region, intron, and promoter. The pathway enrichment analysis identified that genes with differential chromatin accessibility were involved in adipogenic metabolism regulation pathways, such as the peroxisome proliferator activated receptor-γ (PPAR) signaling pathway, wingless-type MMTV integration site (Wnt) signaling pathway, and extracellular matrix-receptor (ECM-receptor) interaction. Integration of ATAC-seq and mRNA-seq revealed that genes with a high expression were associated with high levels of chromatin accessibility, especially within 1 kb upstream and downstream of the transcription start site. In addition, we identified a series of transcription factors (TFs) related to adipogenesis and created the TF regulatory network, providing the possible interactions between TFs during yak adipogenesis. This study is crucial for advancing the understanding of transcriptional regulatory mechanisms of adipogenesis and provides valuable information for understanding the adaptation of plateau species to high-altitude environments by maintaining whole body homeostasis through fat metabolism.


Assuntos
Adipogenia , Cromatina , Adipócitos/metabolismo , Adipogenia/genética , Animais , Bovinos , Cromatina/genética , Cromatina/metabolismo , Sequenciamento de Cromatina por Imunoprecipitação , Sequenciamento de Nucleotídeos em Larga Escala
8.
Cells ; 11(17)2022 Aug 28.
Artigo em Inglês | MEDLINE | ID: mdl-36078081

RESUMO

In domestic mammals, cold stress decreases the survival rate of newborns and increases the cost of management. Brown adipose tissue (BAT) is the main thermogenic organ for cubs, and well-developed fetal BAT (FBAT) is beneficial for newborns to maintain core temperatures during the first several days of life. However, our knowledge of the epigenetic mechanisms during the early development of FBAT remains largely unknown. Rabbits (Oryctolagus cuniculus) are economically important domestic animals. In this study, a histological analysis shows that the tissue content, thermogenic capacity, and lipid content of FBAT dramatically increases from gestational day 21 (G21) to gestational day 24 (G24) in rabbits. RNA-seq, microRNA-seq (miRNA-seq), and the assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) show that many genes, miRNAs, and chromatin-accessible regions (referred to as peaks) were identified as significantly changed from G21 to G24, respectively. The upregulated genes from G21 to G24 were significantly enriched in the mitochondrial metabolism and thermogenesis-related signal pathways. The integrated analysis of transcriptome and chromatin accessibility reveals that the peaks in the promoters have a more regulatory effect than peaks in other genomic elements on the expression of their nearby genes in FBATs. The upregulated genes that are associated with increased chromatin accessibility in the promoter regions are involved in the energy metabolism-related signaling pathways. The genes that have a greater tendency to be regulated by miRNAs than the chromatin accessibility in gene promoters are involved in the apelin, insulin, and endocytosis signaling pathways. Furthermore, genome-wide transcription factor (TF) footprinting analysis identifies early B-cell factor1 (EBF1) as playing a key role during early FBAT development. The carbon metabolism, citrate cycle, and PPAR signaling pathways are significantly enriched by the predicted EBF1-regulated cascade TF-network. In conclusion, our work provides a framework for understanding epigenetics regulatory mechanisms underlying the early development of FBAT and identifies potential TF involved in the early development of FBAT in rabbits.


Assuntos
Cromatina , MicroRNAs , Tecido Adiposo Marrom/metabolismo , Animais , Cromatina/metabolismo , Redes Reguladoras de Genes , Mamíferos/metabolismo , MicroRNAs/genética , MicroRNAs/metabolismo , Coelhos , Fatores de Transcrição/genética , Fatores de Transcrição/metabolismo , Transcriptoma/genética
9.
Cells ; 11(17)2022 Sep 03.
Artigo em Inglês | MEDLINE | ID: mdl-36078161

RESUMO

Ageing is accompanied by dramatic changes in chromatin structure organization and genome function. Two essential components of chromatin, the linker histone Hho1p and actin-related protein 4 (Arp4p), have been shown to physically interact in Saccharomyces cerevisiae cells, thus maintaining chromatin dynamics and function, as well as genome stability and cellular morphology. Disrupting this interaction has been proven to influence the stability of the yeast genome and the way cells respond to stress during chronological ageing. It has also been proven that the abrogated interaction between these two chromatin proteins elicited premature ageing phenotypes. Alterations in chromatin compaction have also been associated with replicative ageing, though the main players are not well recognized. Based on this knowledge, here, we examine how the interaction between Hho1p and Arp4p impacts the ageing of mitotically active yeast cells. For this purpose, two sets of strains were used-haploids (WT(n), arp4, hho1Δ and arp4 hho1Δ) and their heterozygous diploid counterparts (WT(2n), ARP4/arp4, HHO1/hho1Δ and ARP4 HHO1/arp4 hho1Δ)-for the performance of extensive morphological and physiological analyses during replicative ageing. These analyses included a comparative examination of the yeast cells' chromatin structure, proliferative and reproductive potential, and resilience to stress, as well as polysome profiles and chemical composition. The results demonstrated that the haploid chromatin mutants arp4 and arp4 hho1Δ demonstrated a significant reduction in replicative and total lifespan. These findings lead to the conclusion that the importance of a healthy interaction between Arp4p and Hho1p in replicative ageing is significant. This is proof of the concomitant importance of Hho1p and Arp4p in chronological and replicative ageing.


Assuntos
Proteínas de Saccharomyces cerevisiae , Saccharomyces cerevisiae , Actinas/metabolismo , Cromatina/metabolismo , Histonas/metabolismo , Saccharomyces cerevisiae/metabolismo , Proteínas de Saccharomyces cerevisiae/metabolismo , Fatores de Transcrição/metabolismo
10.
Cell Rep ; 40(10): 111315, 2022 Sep 06.
Artigo em Inglês | MEDLINE | ID: mdl-36070691

RESUMO

The transcriptional regulator Runx2 (runt-related transcription factor 2) has essential but distinct roles in osteoblasts and chondrocytes in skeletal development. However, Runx2-mediated regulatory mechanisms underlying the distinctive programming of osteoblasts and chondrocytes are not well understood. Here, we perform an integrative analysis to investigate Runx2-DNA binding and chromatin accessibility ex vivo using neonatal osteoblasts and chondrocytes. We find that Runx2 engages with cell-type-distinct chromatin-accessible regions, potentially interacting with different combinations of transcriptional regulators, forming cell-type-specific hotspots, and potentiating chromatin accessibility. Genetic analysis and direct cellular reprogramming studies suggest that Runx2 is essential for establishment of chromatin accessibility in osteoblasts. Functional enhancer studies identify an Sp7 distal enhancer driven by Runx2-dependent binding and osteoblast-specific chromatin accessibility, contributing to normal osteoblast differentiation. Our findings provide a framework for understanding the regulatory landscape encompassing Runx2-mediated and cell-type-distinct enhancer networks that underlie the specification of osteoblasts.


Assuntos
Cromatina , Subunidade alfa 1 de Fator de Ligação ao Core , Osteoblastos , Animais , Diferenciação Celular/fisiologia , Cromatina/metabolismo , Subunidade alfa 1 de Fator de Ligação ao Core/genética , Subunidade alfa 1 de Fator de Ligação ao Core/metabolismo , Camundongos , Osteoblastos/metabolismo , Osteogênese
11.
PLoS Genet ; 18(9): e1010351, 2022 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-36048878

RESUMO

Advances in genomic technology led to a more focused pattern for the distribution of chromosomal proteins and a better understanding of their functions. The recent development of the CUT&RUN technique marks one of the important such advances. Here we develop a modified CUT&RUN technique that we termed nanoCUT&RUN, in which a high affinity nanobody to GFP is used to bring micrococcal nuclease to the binding sites of GFP-tagged chromatin proteins. Subsequent activation of the nuclease cleaves the chromatin, and sequencing of released DNA identifies binding sites. We show that nanoCUT&RUN efficiently produces high quality data for the TRL transcription factor in Drosophila embryos, and distinguishes binding sites specific between two TRL isoforms. We further show that nanoCUT&RUN dissects the distributions of the HipHop and HOAP telomere capping proteins, and uncovers unexpected binding of telomeric proteins at centromeres. nanoCUT&RUN can be readily applied to any system in which a chromatin protein of interest, or its isoforms, carries the GFP tag.


Assuntos
Proteínas de Drosophila , Drosophila , Animais , Cromatina/genética , Cromatina/metabolismo , Proteínas Cromossômicas não Histona/genética , Proteínas de Ligação a DNA/genética , Proteínas de Ligação a DNA/metabolismo , Drosophila/genética , Proteínas de Drosophila/metabolismo , Telômero/genética , Telômero/metabolismo , Fatores de Transcrição/genética
12.
Cell ; 185(18): 3390-3407.e18, 2022 Sep 01.
Artigo em Inglês | MEDLINE | ID: mdl-36055200

RESUMO

Chemical synapses between axons and dendrites mediate neuronal intercellular communication. Here, we describe a synapse between axons and primary cilia: the axo-ciliary synapse. Using enhanced focused ion beam-scanning electron microscopy on samples with optimally preserved ultrastructure, we discovered synapses between brainstem serotonergic axons and the primary cilia of hippocampal CA1 pyramidal neurons. Functionally, these cilia are enriched in a ciliary-restricted serotonin receptor, the 5-hydroxytryptamine receptor 6 (5-HTR6). Using a cilia-targeted serotonin sensor, we show that opto- and chemogenetic stimulation of serotonergic axons releases serotonin onto cilia. Ciliary 5-HTR6 stimulation activates a non-canonical Gαq/11-RhoA pathway, which modulates nuclear actin and increases histone acetylation and chromatin accessibility. Ablation of this pathway reduces chromatin accessibility in CA1 pyramidal neurons. As a signaling apparatus with proximity to the nucleus, axo-ciliary synapses short circuit neurotransmission to alter the postsynaptic neuron's epigenetic state.


Assuntos
Axônios/fisiologia , Cromatina/química , Cílios , Sinapses , Núcleo Celular/metabolismo , Cromatina/metabolismo , Cílios/metabolismo , Hipocampo/citologia , Hipocampo/fisiologia , Serotonina/metabolismo , Transdução de Sinais , Sinapses/fisiologia
13.
Proc Natl Acad Sci U S A ; 119(34): e2207009119, 2022 Aug 23.
Artigo em Inglês | MEDLINE | ID: mdl-35969760

RESUMO

Classical dendritic cells (cDCs) are essential for immune responses and differentiate from hematopoietic stem cells via intermediate progenitors, such as monocyte-DC progenitors (MDPs) and common DC progenitors (CDPs). Upon infection, cDCs are activated and rapidly express host defense-related genes, such as those encoding cytokines and chemokines. Chromatin structures, including nuclear compartments and topologically associating domains (TADs), have been implicated in gene regulation. However, the extent and dynamics of their reorganization during cDC development and activation remain unknown. In this study, we comprehensively determined higher-order chromatin structures by Hi-C in DC progenitors and cDC subpopulations. During cDC differentiation, chromatin activation was initially induced at the MDP stage. Subsequently, a shift from inactive to active nuclear compartments occurred at the cDC gene loci in CDPs, which was followed by increased intra-TAD interactions and loop formation. Mechanistically, the transcription factor IRF8, indispensable for cDC differentiation, mediated chromatin activation and changes into the active compartments in DC progenitors, thereby possibly leading to cDC-specific gene induction. Using an infection model, we found that the chromatin structures of host defense-related gene loci were preestablished in unstimulated cDCs, indicating that the formation of higher-order chromatin structures prior to infection may contribute to the rapid responses to pathogens. Overall, these results suggest that chromatin structure reorganization is closely related to the establishment of cDC-specific gene expression and immune functions. This study advances the fundamental understanding of chromatin reorganization in cDC differentiation and activation.


Assuntos
Montagem e Desmontagem da Cromatina , Células Dendríticas , Células-Tronco Hematopoéticas , Animais , Diferenciação Celular/genética , Cromatina/genética , Cromatina/metabolismo , Células Dendríticas/citologia , Regulação da Expressão Gênica , Camundongos
14.
Sci Rep ; 12(1): 14137, 2022 Aug 19.
Artigo em Inglês | MEDLINE | ID: mdl-35986039

RESUMO

We recently mapped a genetic susceptibility locus on chromosome 6q22.33 for type 1 diabetes (T1D) diagnosed below the age of 7 years between the PTPRK and thymocyte-selection-associated (THEMIS) genes. As the thymus plays a central role in shaping the T cell repertoire, we aimed to identify the most likely causal genetic factors behind this association using thymocyte genomic data. In four thymocyte populations, we identified 253 DNA sequence motifs underlying histone modifications. The G insertion allele of rs138300818, associated with protection from diabetes, created thymocyte motifs for multiple histone modifications and thymocyte types. In a parallel approach to identifying variants that alter transcription factor binding motifs, the same variant disrupted a predicted motif for Rfx7, which is abundantly expressed in the thymus. Chromatin state and RNA sequencing data suggested strong transcription overlapping rs138300818 in fetal thymus, while expression quantitative trait locus and chromatin conformation data associate the insertion with lower THEMIS expression. Extending the analysis to other T1D loci further highlighted rs66733041 affecting the GATA3 transcription factor binding in the AFF3 locus. Taken together, our results support a role for thymic THEMIS gene expression and the rs138300818 variant in promoting the development of early-onset T1D.


Assuntos
Diabetes Mellitus Tipo 1 , Timócitos , Criança , Cromatina/genética , Cromatina/metabolismo , Diabetes Mellitus Tipo 1/genética , Diabetes Mellitus Tipo 1/metabolismo , Predisposição Genética para Doença , Humanos , Lactente , Locos de Características Quantitativas , Timócitos/metabolismo
15.
Cell Rep ; 40(8): 111250, 2022 Aug 23.
Artigo em Inglês | MEDLINE | ID: mdl-36001970

RESUMO

Nucleosome-displacing-factors (NDFs) in yeast, similar to pioneer factors in higher eukaryotes, can open closed chromatin and generate nucleosome-depleted regions (NDRs). NDRs in yeast are also affected by ATP-dependent chromatin remodelers (CRs). However, how NDFs and CRs coordinate in nucleosome invasion and NDR formation is still unclear. Here, we design a high-throughput method to systematically study the interplay between NDFs and CRs. By combining an integrated synthetic oligonucleotide library with DNA methyltransferase-based, single-molecule nucleosome mapping, we measure the impact of CRs on NDRs generated by individual NDFs. We find that CRs are dispensable for nucleosome invasion by NDFs, and they function downstream of NDF binding to modulate the NDR length. A few CRs show high specificity toward certain NDFs; however, in most cases, CRs are recruited in a factor-nonspecific and NDR length-dependent manner. Overall, our study provides a framework to investigate how NDFs and CRs cooperate to regulate chromatin opening.


Assuntos
Nucleossomos , Proteínas de Saccharomyces cerevisiae , Cromatina/metabolismo , Montagem e Desmontagem da Cromatina , Nucleossomos/metabolismo , Saccharomyces cerevisiae/metabolismo , Proteínas de Saccharomyces cerevisiae/genética , Proteínas de Saccharomyces cerevisiae/metabolismo
16.
Int J Mol Sci ; 23(16)2022 Aug 11.
Artigo em Inglês | MEDLINE | ID: mdl-36012213

RESUMO

Growing evidence indicates that transposons or transposable elements (TEs)-derived accessible chromatin regions (ACRs) play essential roles in multiple biological processes by interacting with trans-acting factors. However, the function of TE-derived ACRs in the regulation of gene expression in the rice genome has not been well characterized. In this study, we examined the chromatin dynamics in six types of rice tissues and found that ~8% of ACRs were derived from TEs and exhibited distinct levels of accessibility and conservation as compared to those without TEs. TEs exhibited a TE subtype-dependent impact on ACR formation, which can be mediated by changes in the underlying DNA methylation levels. Moreover, we found that tissue-specific TE-derived ACRs might function in the tissue development through the modulation of nearby gene expression. Interestingly, many genes in domestication sweeps were found to overlap with TE-derived ACRs, suggesting their potential functions in the rice domestication. In addition, we found that the expression divergence of 1070 duplicate gene pairs were associated with TE-derived ACRs and had distinct distributions of TEs and ACRs around the transcription start sites (TSSs), which may experience different selection pressures. Thus, our study provides some insights into the biological implications of TE-derived ACRs in the rice genome. Our results imply that these ACRs are likely involved in the regulation of tissue development, rice domestication and functional divergence of duplicated genes.


Assuntos
Oryza , Cromatina/genética , Cromatina/metabolismo , Metilação de DNA , Elementos de DNA Transponíveis/genética , Domesticação , Genoma de Planta , Oryza/metabolismo
17.
Curr Opin Struct Biol ; 75: 102430, 2022 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-35914496

RESUMO

DNA methylation plays a vital role in epigenetic regulation in both plants and animals, and typically occurs at the 5-carbon position of the cytosine pyrimidine ring within the CpG dinucleotide steps. Cytosine methylation can alter DNA's geometry, mechanical and physico-chemical properties - thus influencing the molecular signaling events vital for transcription, replication and chromatin remodeling. Despite the profound effect cytosine methylation can have on DNA, the underlying atomistic mechanisms remain enigmatic. Many studies so far have produced controversial findings on how cytosine methylation dictates DNA flexibility and accessibility, nucleosome stability and dynamics. Here, we review the most recent experimental and computational studies that provide precise characterization of structure and function of cytosine methylation and its versatile roles in modulating DNA mechanics, nucleosome and chromatin structure, stability and dynamics. Moreover, the review briefly discusses the relationship between DNA methylation and nucleosome positioning, and the crosstalk between DNA methylation and histone tail modifications.


Assuntos
Metilação de DNA , Nucleossomos , Animais , Cromatina/química , Cromatina/metabolismo , Montagem e Desmontagem da Cromatina , Ilhas de CpG , Citosina/química , Citosina/metabolismo , DNA/química , Epigênese Genética
18.
Nat Plants ; 8(8): 940-953, 2022 08.
Artigo em Inglês | MEDLINE | ID: mdl-35915144

RESUMO

The arrangement of centromeres within the nucleus differs among species and cell types. However, neither the mechanisms determining centromere distribution nor its biological significance are currently well understood. In this study, we demonstrate the importance of centromere distribution for the maintenance of genome integrity through the cytogenic and molecular analysis of mutants defective in centromere distribution. We propose a two-step regulatory mechanism that shapes the non-Rabl-like centromere distribution in Arabidopsis thaliana through condensin II and the linker of the nucleoskeleton and cytoskeleton (LINC) complex. Condensin II is enriched at centromeres and, in cooperation with the LINC complex, induces the scattering of centromeres around the nuclear periphery during late anaphase/telophase. After entering interphase, the positions of the scattered centromeres are then stabilized by nuclear lamina proteins of the CROWDED NUCLEI (CRWN) family. We also found that, despite their strong impact on centromere distribution, condensin II and CRWN proteins have little effect on chromatin organization involved in the control of gene expression, indicating a robustness of chromatin organization regardless of the type of centromere distribution.


Assuntos
Centrômero , Membrana Nuclear , Adenosina Trifosfatases/metabolismo , Cromatina/metabolismo , Proteínas de Ligação a DNA , Complexos Multiproteicos , Membrana Nuclear/metabolismo
19.
Proc Natl Acad Sci U S A ; 119(33): e2204338119, 2022 Aug 16.
Artigo em Inglês | MEDLINE | ID: mdl-35939709

RESUMO

Despite the recent discovery of tissue regeneration enhancers in highly regenerative animals, upstream and downstream genetic programs connected by these enhancers still remain unclear. Here, we performed a genome-wide analysis of enhancers and associated genes in regenerating nephric tubules of Xenopus laevis. Putative enhancers were identified using assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) and H3K27ac chromatin immunoprecipitation sequencing (ChIP-seq) analyses. Their target genes were predicted based on their proximity to enhancers on genomic DNA and consistency of their transcriptome profiles to ATAC-seq/ChIP-seq profiles of the enhancers. Motif enrichment analysis identified the central role of Krüppel-like factors (Klf) in the enhancer. Klf15, a member of the Klf family, directly binds enhancers and stimulates expression of regenerative genes, including adrenoreceptor alpha 1A (adra1a), whereas inhibition of Klf15 activity results in failure of nephric tubule regeneration. Moreover, pharmacological inhibition of Adra1a-signaling suppresses nephric tubule regeneration, while its activation promotes nephric tubule regeneration and restores organ size. These results indicate that Klf15-dependent adrenergic receptor signaling through regeneration enhancers plays a central role in the genetic network for kidney regeneration.


Assuntos
Elementos Facilitadores Genéticos , Túbulos Renais , Fatores de Transcrição Kruppel-Like , Receptores Adrenérgicos , Regeneração , Animais , Cromatina/metabolismo , Regulação da Expressão Gênica , Redes Reguladoras de Genes , Túbulos Renais/fisiologia , Fatores de Transcrição Kruppel-Like/genética , Fatores de Transcrição Kruppel-Like/metabolismo , Receptores Adrenérgicos/metabolismo , Regeneração/genética , Xenopus laevis
20.
Proc Natl Acad Sci U S A ; 119(33): e2208522119, 2022 Aug 16.
Artigo em Inglês | MEDLINE | ID: mdl-35939714

RESUMO

Apoptosis is a genetically regulated program of cell death that plays a key role in immune disease processes. We identified EBF4, a little-studied member of the early B cell factor (EBF) family of transcription factors, in a whole-genome CRISPR screen for regulators of Fas/APO-1/CD95-mediated T cell death. Loss of EBF4 increases the half-life of the c-FLIP protein, and its presence in the Fas signaling complex impairs caspase-8 cleavage and apoptosis. Transcriptome analysis revealed that EBF4 regulates molecules such as TBX21, EOMES, granzyme, and perforin that are important for human natural killer (NK) and CD8+ T cell functions. Proximity-dependent biotin identification (Bio-ID) mass spectrometry analyses showed EBF4 binding to STAT3, STAT5, and MAP kinase 3 and a strong pathway relationship to interleukin-2 regulated genes, which are known to govern cytotoxicity pathways. Chromatin immunoprecipitation and DNA sequencing analysis defined a canonical EBF4 binding motif, 5'-CCCNNGG/AG-3', closely related to the EBF1 binding site; using a luciferase-based reporter, we found a dose-dependent transcriptional response of this motif to EBF4. We also conducted assay for transposase-accessible chromatin sequencing in EBF4-overexpressing cells and found increased chromatin accessibility upstream of granzyme and perforin and in topologically associated domains in human lymphocytes. Finally, we discovered that the EBF4 has basal expression in human but not mouse NK cells and CD8+ T cells and vanishes following activating stimulation. Together, our data reveal key features of a previously unknown transcriptional regulator of human cytotoxic immune function.


Assuntos
Apoptose , Linfócitos T CD8-Positivos , Citotoxicidade Imunológica , Proteína Ligante Fas , Linfócitos T Citotóxicos , Fatores de Transcrição , Animais , Apoptose/fisiologia , Cromatina/metabolismo , Citotoxicidade Imunológica/genética , Proteína Ligante Fas/metabolismo , Granzimas/genética , Humanos , Camundongos , Perforina/metabolismo , Fatores de Transcrição/genética , Fatores de Transcrição/metabolismo
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