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The contribution of three-dimensional genome organization to physiological ageing is not well known. Here we show that large-scale chromatin reorganization distinguishes young and old bone marrow progenitor (pro-) B cells. These changes result in increased interactions at the compartment level and reduced interactions within topologically associated domains (TADs). The gene encoding Ebf1, a key B cell regulator, switches from compartment A to B with age. Genetically reducing Ebf1 recapitulates some features of old pro-B cells. TADs that are most reduced with age contain genes important for B cell development, including the immunoglobulin heavy chain (Igh) locus. Weaker intra-TAD interactions at Igh correlate with altered variable (V), diversity (D) and joining (J) gene recombination. Our observations implicate three-dimensional chromatin reorganization as a major driver of pro-B cell phenotypes that impair B lymphopoiesis with age.
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Envelhecimento , Linfócitos B , Montagem e Desmontagem da Cromatina , Cadeias Pesadas de Imunoglobulinas , Linfopoese , Animais , Envelhecimento/genética , Envelhecimento/metabolismo , Linfócitos B/metabolismo , Linfopoese/genética , Cadeias Pesadas de Imunoglobulinas/genética , Cadeias Pesadas de Imunoglobulinas/metabolismo , Transativadores/metabolismo , Transativadores/genética , Cromatina/metabolismo , Cromatina/genética , Células Precursoras de Linfócitos B/metabolismo , Células Precursoras de Linfócitos B/citologia , Células Precursoras de Linfócitos B/imunologia , Camundongos Endogâmicos C57BL , Camundongos , Diferenciação Celular , Camundongos KnockoutRESUMO
The pair of transcription factors Bcl6-Blimp1 is well-known for follicular T helper (Tfh) cell fate determination, however, the mechanism(s) for Bcl6-independent regulation of CXCR5 during Tfh migration into germinal center (GC) is still unclear. In this study, we uncovered another pair of transcription factors, Bhlhe40-Pou2af1, that regulates CXCR5 expression. Pou2af1 was specifically expressed in Tfh cells whereas Bhlhe40 expression was found high in non-Tfh cells. Pou2af1 promoted Tfh formation and migration into GC by upregulating CXCR5 but not Bcl6, while Bhlhe40 repressed this process by inhibiting Pou2af1 expression. RNA-Seq analysis of antigen-specific Tfh cells generated in vivo confirmed the role of Bhlhe40-Pou2af1 axis in regulating optimal CXCR5 expression. Thus, the regulation of CXCR5 expression and migration of Tfh cells into GC involves a transcriptional regulatory circuit consisting of Bhlhe40 and Pou2af1, which operates independent of the Bcl6-Blimp1 circuit that determines the Tfh cell fate.
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The development and function of the immune system are controlled by temporospatial gene expression programs, which are regulated by cis-regulatory elements, chromatin structure, and trans-acting factors. In this study, we cataloged the dynamic histone modifications and chromatin interactions at regulatory regions during T helper (Th) cell differentiation. Our data revealed that the H3K4me1 landscape established by MLL4 in naive CD4+ T cells is critical for restructuring the regulatory interaction network and orchestrating gene expression during the early phase of Th differentiation. GATA3 plays a crucial role in further configuring H3K4me1 modification and the chromatin interaction network during Th2 differentiation. Furthermore, we demonstrated that HSS3-anchored chromatin loops function to restrict the activity of the Th2 locus control region (LCR), thus coordinating the expression of Th2 cytokines. Our results provide insights into the mechanisms of how the interplay between histone modifications, chromatin looping, and trans-acting factors contributes to the differentiation of Th cells.
Assuntos
Diferenciação Celular , Cromatina , Código das Histonas , Histonas , Células Th2 , Diferenciação Celular/imunologia , Animais , Cromatina/metabolismo , Camundongos , Células Th2/imunologia , Histonas/metabolismo , Fator de Transcrição GATA3/metabolismo , Regulação da Expressão Gênica , Camundongos Endogâmicos C57BL , Linfócitos T Auxiliares-Indutores/imunologia , Linfócitos T Auxiliares-Indutores/metabolismo , Histona-Lisina N-Metiltransferase/metabolismo , Histona-Lisina N-Metiltransferase/genética , Região de Controle de Locus Gênico , Citocinas/metabolismoRESUMO
The spatial folding of eukaryotic genome plays a key role in genome function. We report here that our recently developed method, Hi-TrAC, which specializes in detecting chromatin loops among accessible genomic regions, can detect active sub-TADs with a median size of 100 kb, most of which harbor one or two cell specifically expressed genes and regulatory elements such as super-enhancers organized into nested interaction domains. These active sub-TADs are characterized by highly enriched histone mark H3K4me1 and chromatin-binding proteins, including Cohesin complex. Deletion of selected sub-TAD boundaries have different impacts, such as decreased chromatin interaction and gene expression within the sub-TADs or compromised insulation between the sub-TADs, depending on the specific chromatin environment. We show that knocking down core subunit of the Cohesin complex using shRNAs in human cells or decreasing the H3K4me1 modification by deleting the H3K4 methyltransferase Mll4 gene in mouse Th17 cells disrupted the sub-TADs structure. Our data also suggest that super-enhancers exist as an equilibrium globule structure, while inaccessible chromatin regions exist as a fractal globule structure. In summary, Hi-TrAC serves as a highly sensitive and inexpensive approach to study dynamic changes of active sub-TADs, providing more explicit insights into delicate genome structures and functions.
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Cromatina , Elementos Facilitadores Genéticos , Técnicas Genéticas , Sequências Reguladoras de Ácido Nucleico , Animais , Humanos , Camundongos , Montagem e Desmontagem da Cromatina , GenomaRESUMO
Mounting evidence has shown that ambient PM2.5 exposure is closely associated with the development of obesity, and adipose tissue represents an important endocrine target for PM2.5. In this study, the 3T3-L1 preadipocyte differentiation model was employed to comprehensively explore the adipogenic potential of PM2.5. After 8 days of PM2.5 exposure, adipocyte fatty acid uptake and lipid accumulation were significantly increased, and adipogenic differentiation of 3T3-L1 cells was promoted in a concentration-dependent manner. Transcriptome and lipidome analyses revealed the systematic disruption of transcriptional and lipid profiling at 10 µg/mL PM2.5. Functional enrichment and visualized network analyses showed that the peroxisome proliferator-activated receptor (PPAR) pathway and the metabolism of glycerophospholipids, glycerolipids, and sphingolipids were most significantly affected during adipocyte differentiation. Reporter gene assays indicated that PPARγ was activated by PM2.5, demonstrating that PM2.5 promoted adipogenesis by activating PPARγ. The increased transcriptional and protein expressions of PPARγ and downstream adipogenesis-associated markers (e.g., Fabp4 and CD36) were further cross-validated using qRT-PCR and western blot. PM2.5-induced adipogenesis, PPARγ pathway activation, and lipid remodeling were significantly attenuated by the supplementation of a PPARγ antagonist (T0070907). Overall, this study yielded mechanistic insights into PM2.5-induced adipogenesis in vitro by identifying the potential biomolecular targets for the prevention of PM2.5-induced obesity and related metabolic diseases.
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Adipogenia , PPAR gama , Animais , Camundongos , PPAR gama/genética , PPAR gama/metabolismo , Células 3T3-L1 , Lipídeos , Obesidade , Diferenciação CelularRESUMO
Interferon-γ (IFN-γ) is a key cytokine in response to viral or intracellular bacterial infection in mammals. While a number of enhancers are described to promote IFN-γ responses, to the best of our knowledge, no silencers for the Ifng gene have been identified. By examining H3K4me1 histone modification in naive CD4+ T cells within Ifng locus, we identified a silencer (CNS-28) that restrains Ifng expression. Mechanistically, CNS-28 maintains Ifng silence by diminishing enhancer-promoter interactions within Ifng locus in a GATA3-dependent but T-bet-independent manner. Functionally, CNS-28 restrains Ifng transcription in NK cells, CD4+ cells, and CD8+ T cells during both innate and adaptive immune responses. Moreover, CNS-28 deficiency resulted in repressed type 2 responses due to elevated IFN-γ expression, shifting Th1 and Th2 paradigm. Thus, CNS-28 activity ensures immune cell quiescence by cooperating with other regulatory cis elements within the Ifng gene locus to minimize autoimmunity.
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Linfócitos T CD8-Positivos , Interferon gama , Animais , Interferon gama/genética , Interferon gama/metabolismo , Linfócitos T CD8-Positivos/metabolismo , Diferenciação Celular , Sequências Reguladoras de Ácido Nucleico , Homeostase , Células Th1 , MamíferosRESUMO
High concentrations of elemental lead (Pb) in the atmosphere pose a serious threat to human health. This study presents and summarizes data obtained from relevant literature on Pb concentrations within fine particulate matter (PM2.5) recorded in major cities in China from 2008 to 2019. An environmental health risk assessment model was then used to evaluate the health hazards of inhaling Pb among adults and children in China. Owing to the promulgation and implementation of a series of air pollution control measures, the Pb concentrations within PM2.5 measured in major cities in China showed a downward trend after peaking in 2013. The concentrations were higher in winter than in summer, and higher in northern cities than in southern cities. Although the Pb concentrations in most cities did not exceed the limit (500 ng/m3) set by China, they remained much higher than concentrations recorded in developed countries. The results of the environmental health risk analysis showed that the non-carcinogenic risk from atmospheric Pb exposure was higher in children than in adults (adult females > adult males), while the carcinogenic risk was higher in adults than in children. This study shows that even if the health risk of Pb in PM2.5 does not exceed the acceptable limit, stricter Pb pollution control measures are required to safeguard population health due to the dangers of Pb.
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Poluentes Atmosféricos , Poluição do Ar , Masculino , Adulto , Criança , Feminino , Humanos , Poluentes Atmosféricos/análise , Cidades , Chumbo/análise , Monitoramento Ambiental , Material Particulado/análise , Poluição do Ar/análise , China , Medição de Risco , Estações do AnoRESUMO
The three-dimensional genomic structure plays a critical role in gene expression, cellular differentiation, and pathological conditions. It is pivotal to elucidate fine-scale chromatin architectures, especially interactions of regulatory elements, to understand the temporospatial regulation of gene expression. In this study, we report Hi-TrAC as a proximity ligation-free, robust, and sensitive technique to profile genome-wide chromatin interactions at high-resolution among regulatory elements. Hi-TrAC detects chromatin looping among accessible regions at single nucleosome resolution. With almost half-million identified loops, we reveal a comprehensive interaction network of regulatory elements across the genome. After integrating chromatin binding profiles of transcription factors, we discover that cohesin complex and CTCF are responsible for organizing long-range chromatin loops, related to domain formation; whereas ZNF143 and HCFC1 are involved in structuring short-range chromatin loops between regulatory elements, which directly regulate gene expression. Thus, we introduce a methodology to identify a delicate and comprehensive network of cis-regulatory elements, revealing the complexity and a division of labor of transcription factors in organizing chromatin loops for genome organization and gene expression.
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Cromatina , Fatores de Transcrição , Fatores de Transcrição/genética , Fatores de Transcrição/metabolismo , Cromatina/genética , Cromossomos/metabolismo , Sequências Reguladoras de Ácido Nucleico , Genoma , Fator de Ligação a CCCTC/genética , Fator de Ligação a CCCTC/metabolismoRESUMO
BACKGROUND: Air pollution is associated with accelerated biological ages determined by DNA methylation (DNAm) patterns, imposing further risks of age-related adverse effects. However, little is known about the independent and joint effects of exposure to gaseous organic chemicals that may share a common source. METHODS: We conducted a panel study with the 3-day exposure assessment monthly among 73 Chinese healthy elderly people aged 60 to 69 years in Jinan, Shandong province during September 2018 to January 2019.Exposure to 26 ambient organic chemical contaminants were measured by wearable passive samplers, including volatile organic compounds, polycyclic aromatic hydrocarbons (PAHs), phthalates (PAEs), nitroaromatics (NIs), polybrominated diphenyl ethers, chlorinated hydrocarbons, and organophosphate esters. The Illumina MethylationEPIC BeadChip was used to measure DNA methylation levels in blood samples, and based on which, epigenetic ageing biomarkers, including Hannum clock, Horvath clock, DNAm PhenoAge, DNAm GrimAge, and DNAm estimator of telomere length (DNAmTL) were calculated. Linear mixed effect models were used to estimate the linear associations between 3-day personal chemical exposure and the epigenetic biomarkers, Weighted quantile sum (WQS) regression and the Bayesian kernel machine regression (BKMR) model were further used to evaluate the effect of chemical mixtures. RESULTS: Multiple linear mixed effects regression models showed that DNAmPhenoAge acceleration was significantly and positively associated with exposure to PAEs, NIs, and PAHs in healthy elderly individuals. Both WQS regression and BKMR models showed a significant positive association with DNAmPhenoAge acceleration with chemical exposures, in which the effect of di-n-butyl phthalate exposure showed the greatest importance. CONCLUSION: These findings suggest that exposure to a mixture of airborne chemicals significantly increase the acceleration of the epigenetic biomarker of phenotypic age. These findings serve to identify toxic chemicals in the air and facilitate the evaluation of their potentially severe health effects.
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Poluição do Ar , Hidrocarbonetos Policíclicos Aromáticos , Idoso , Humanos , Teorema de Bayes , População do Leste Asiático , Poluição do Ar/efeitos adversos , Envelhecimento , Epigenômica , Biomarcadores , Hidrocarbonetos Policíclicos Aromáticos/toxicidadeRESUMO
Transposon (de)repression and heterochromatin reorganization are dynamically regulated during cell fate determination and are hallmarks of cellular senescence. However, whether they are sequence specifically regulated remains unknown. Here we uncover that the KCNQ1OT1 lncRNA, by sequence-specific Hoogsteen base pairing with double-stranded genomic DNA via its repeat-rich region and binding to the heterochromatin protein HP1α, guides, induces and maintains epigenetic silencing at specific repetitive DNA elements. Repressing KCNQ1OT1 or deleting its repeat-rich region reduces DNA methylation and H3K9me3 on KCNQ1OT1-targeted transposons. Engineering a fusion KCNQ1OT1 with an ectopically targeting guiding triplex sequence induces de novo DNA methylation at the target site. Phenotypically, repressing KCNQ1OT1 induces senescence-associated heterochromatin foci, transposon activation and retrotransposition as well as cellular senescence, demonstrating an essential role of KCNQ1OT1 to safeguard against genome instability and senescence.
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Heterocromatina , RNA Guia de Cinetoplastídeos , Heterocromatina/genética , RNA Guia de Cinetoplastídeos/metabolismo , Metilação de DNA , DNA/metabolismo , Homólogo 5 da Proteína CromoboxRESUMO
A set of one-dimensional experimental device for solute transport in non-penetrating fractured clay are developed, which can study the laws of groundwater flow and solute transport under different hydraulic heads, fractured aperture, and thickness of non-penetrating zones. The experimental results show that the solute will quickly reach the bottom of the clay along the non-penetrating fracture, and there is an obvious dominant flow phenomenon compared with the intact clay. According to the experimental data and numerical calculation results, the model parameters of the fracture and each soil layer were identified, and the verified numerical model was used to simulate the solute transport in the non-penetrating fractured clay. The numerical results show that the increase of the thickness for the non-penetrating zone has a significant improvement on the anti-seepage ability of clay, and the increase of the hydraulic head pressure and fractured aperture leads to a faster growth rate of the solute concentration, which indicates that the solute breaks down the lower impermeable clay layer under high head pressure. The research results are of great significance for the bottom anti-seepage layer similar to landfill projects.
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Mammalian genomes have multiple enhancers spanning an ultralong distance (>megabases) to modulate important genes, but it is unclear how these enhancers coordinate to achieve this task. We combine multiplexed CRISPRi screening with machine learning to define quantitative enhancer-enhancer interactions. We find that the ultralong distance enhancer network has a nested multilayer architecture that confers functional robustness of gene expression. Experimental characterization reveals that enhancer epistasis is maintained by three-dimensional chromosomal interactions and BRD4 condensation. Machine learning prediction of synergistic enhancers provides an effective strategy to identify noncoding variant pairs associated with pathogenic genes in diseases beyond genome-wide association studies analysis. Our work unveils nested epistasis enhancer networks, which can better explain enhancer functions within cells and in diseases.
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Doença , Elementos Facilitadores Genéticos , Epistasia Genética , Aprendizado de Máquina , Proteínas de Ciclo Celular , Doença/genética , Estudo de Associação Genômica Ampla , Humanos , Células K562 , Proteínas Nucleares/genética , Fatores de Transcrição/genéticaRESUMO
The differentiation of innate lymphoid cells (ILCs) from hematopoietic stem cells needs to go through several multipotent progenitor stages. However, it remains unclear whether the fates of multipotent progenitors are predefined by epigenetic states. Here, we report the identification of distinct accessible chromatin regions in all lymphoid progenitors (ALPs), EILPs, and ILC precursors (ILCPs). Single-cell MNase-seq analyses revealed that EILPs contained distinct subpopulations epigenetically primed toward either dendritic cell lineages or ILC lineages. We found that TCF-1 and GATA3 co-bound to the lineage-defining sites for ILCs (LDS-Is), whereas PU.1 binding was enriched in the LDSs for alternative dendritic cells (LDS-As). TCF-1 and GATA3 were indispensable for the epigenetic priming of LDSs at the EILP stage. Our results suggest that the multipotency of progenitor cells is defined by the existence of a heterogeneous population of cells epigenetically primed for distinct downstream lineages, which are regulated by key transcription factors.
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Imunidade Inata , Linfócitos , Diferenciação Celular , Linhagem da Célula , Epigênese Genética , Células-Tronco HematopoéticasRESUMO
Cell-to-cell variation in gene expression is a widespread phenomenon, which may play important roles in cellular differentiation, function, and disease development1-9. Chromatin is implicated in contributing to the cellular heterogeneity in gene expression10-16. Fully understanding the mechanisms of cellular heterogeneity requires simultaneous measurement of RNA and occupancy of histone modifications and transcription factors on chromatin due to their critical roles in transcriptional regulation17,18. We generally term the occupancy of histone modifications and transcription factors as Chromatin occupancy. Here, we report a technique, termed scPCOR-seq (single-cell Profiling of Chromatin Occupancy and RNAs Sequencing), for simultaneously profiling genome-wide chromatin protein binding or histone modification marks and RNA expression in the same cell. We demonstrated that scPCOR-seq can profile either H3K4me3 or RNAPII and RNAs in a mixture of human H1, GM12878 and 293 T cells at a single-cell resolution and either H3K4me3, RNAPII, or RNA profile can correctly separate the cells. Application of scPCOR-seq to the in vitro differentiation of the erythrocyte precursor CD36 cells from human CD34 stem or progenitor cells revealed that H3K4me3 and RNA exhibit distinct properties in clustering cells during differentiation. Overall, our work provides a promising approach to understand the relationships among different omics layers.
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Cromatina , RNA Polimerase II , Cromatina/genética , Imunoprecipitação da Cromatina , Humanos , RNA/genética , RNA Polimerase II/genética , Fatores de Transcrição/metabolismoRESUMO
Fine particulate matter (PM2.5) exposure and sleep disturbance have been significantly associated with adverse cardiovascular outcomes, however, the combined effects of these two factors are still unclear. We conducted a multi-center cross-sectional study from November 2018 to May 2019 in the Beijing-Tianjin-Hebei region in China to investigate the potential modifying effects of sleep disturbance on associations between cardiac conduction abnormalities and PM2.5 exposure, as well as the combined effects of sleep disturbance and heavy pollution episodes, which were defined based on the PM2.5 mass concentration (≥75⯵g/m3, falling in the 75th/90th percentile) and duration (1â¯day and ≥2â¯days). The sleep quality and sleep duration of all participants were evaluated using the Pittsburgh Sleep Quality Index. Standard 12-lead electrocardiogram (ECG) test was performed to measure the heart rate (HR), QRS duration (time taken for ventricular depolarization), HR corrected QT interval (time for ventricular depolarization and repolarization) and PR interval (time for atrioventricular conduction). Multivariable linear regression models were performed to evaluate the associations of PM2.5 and heavy pollution events on ECG parameters and the joint effects with sleep disturbance. We found PM2.5 exposure was independently associated with prolonged QRS and QTc intervals. Association between PM2.5 and the QTc interval was significantly stronger in participants with poor sleep quality. For each 10-µg/m3 increase in PM2.5 concentration, the QTc interval in the participants with poor sleep quality increased by 0.41â¯% (95â¯% confidence interval: 0.19, 0.64). In addition, heavy PM2.5 pollution episodes, especially extremely heavy pollution of long duration, were found to have synergistic effects with sleep disturbance on ECG parameters. Our findings provide evidence that PM2.5 exposure, especially heavy pollution episodes, may increase abnormal cardiac conduction and have a synergistic effect with sleep disturbance. Improving sleep hygiene is crucial to protect the heart health of the general population.
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Poluentes Atmosféricos , Poluição do Ar , Transtornos do Sono-Vigília , Poluentes Atmosféricos/análise , Poluentes Atmosféricos/toxicidade , Poluição do Ar/análise , China/epidemiologia , Estudos Transversais , Exposição Ambiental/efeitos adversos , Humanos , Material Particulado/análise , Material Particulado/toxicidade , Sono , Transtornos do Sono-Vigília/induzido quimicamenteRESUMO
BACKGROUND: Exposure to fine particulate matter (PM2.5) is a prominent risk factor for cardiovascular aging in older adults and causes mild syndromes or other comorbidities in otherwise healthy older adults. Accordingly, a precise tool for PM2.5 exposure risk stratification is urgently needed. We aimed to address this need by comparing the performances of seven types of epigenetic age and chronological age to classify the effects of short-term PM2.5 exposure on blood pressure (BP), a typical clinical surrogate marker of cardiovascular aging. METHODS: We conducted a panel study of the Chinese healthy adults aged 60-69 years through five monthly visits. Personal PM2.5 exposures were measured using wearable monitoring devices for three consecutive days, and DNA methylation was determined by the Illumina MethylationEPIC BeadChip using blood samples collected at each visit. Systolic BP, diastolic BP, mean arterial pressure and pulse pressure were measured by the electronic BP monitor. Linear mixed models with interaction terms between PM2.5 and different ages were used to assess their potential usefulness for stratification. RESULTS: DNAmPhenoAge, Skin & blood clock, DNAmGrimAge acceleration, and DunedinPoAm had significant modifying effects on the relationship between PM2.5 and BP. For instance, a 10-µg/m3 increase in the 72-h moving mean PM2.5 was significantly associated with 0.30% (95% CI: 0.10%, 0.51%) and -0.07% (95% CI: -0.32%, 0.18%) increases in systolic BP at higher and lower DNAmPhenoAge acceleration, respectively. Joint models further revealed that using a combination of epigenetic ages could more precisely stratify the effect of PM2.5 on BP. CONCLUSIONS: Our research indicates that epigenetic age may be a useful tool for evaluating the effect of short-term PM2.5 exposure on cardiovascular aging status.
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Poluentes Atmosféricos , Poluição do Ar , Idoso , Poluentes Atmosféricos/análise , Poluição do Ar/análise , Biomarcadores , Pressão Sanguínea/fisiologia , Exposição Ambiental/análise , Epigênese Genética , Humanos , Material Particulado/análise , Material Particulado/toxicidadeRESUMO
Adaptive CD4+ T helper cells and their innate counterparts, innate lymphoid cells, utilize an identical set of transcription factors (TFs) for their differentiation and functions. However, similarities and differences in the induction of these TFs in related lymphocytes are still elusive. Here, we show that T helper-1 (Th1) cells and natural killer (NK) cells displayed distinct epigenomes at the Tbx21 locus, which encodes T-bet, a critical TF for regulating type 1 immune responses. The initial induction of T-bet in NK precursors was dependent on the NK-specific DNase I hypersensitive site Tbx21-CNS-3, and the expression of the interleukin-18 (IL-18) receptor; IL-18 induced T-bet expression through the transcription factor RUNX3, which bound to Tbx21-CNS-3. By contrast, signal transducer and activator of transcription (STAT)-binding motifs within Tbx21-CNS-12 were critical for IL-12-induced T-bet expression during Th1 cell differentiation both in vitro and in vivo. Thus, type 1 innate and adaptive lymphocytes utilize distinct enhancer elements for their development and differentiation.
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Imunidade Inata , Interleucina-18 , Células Matadoras Naturais , Células Th1 , Diferenciação Celular , Interleucina-18/metabolismo , Células Matadoras Naturais/imunologia , Proteínas com Domínio T/metabolismo , Células Th1/imunologia , Fatores de Transcrição/metabolismoRESUMO
Investigating chromatin interactions between regulatory regions such as enhancer and promoter elements is vital for understanding the regulation of gene expression. Compared to Hi-C and its variants, the emerging 3D mapping technologies focusing on enriched signals, such as TrAC-looping, reduce the sequencing cost and provide higher interaction resolution for cis-regulatory elements. A robust pipeline is needed for the comprehensive interpretation of these data, especially for loop-centric analysis. Therefore, we have developed a new versatile tool named cLoops2 for the full-stack analysis of these 3D chromatin interaction data. cLoops2 consists of core modules for peak-calling, loop-calling, differentially enriched loops calling and loops annotation. It also contains multiple modules for interaction resolution estimation, data similarity estimation, features quantification, feature aggregation analysis, and visualization. cLoops2 with documentation and example data are open source and freely available at GitHub: https://github.com/KejiZhaoLab/cLoops2.
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Montagem e Desmontagem da Cromatina , Cromatina/química , Software , Linhagem Celular Tumoral , Cromatina/genética , Cromatina/metabolismo , Biologia Computacional/métodos , HumanosRESUMO
Bone metastases frequently occur in NSCLC patients at the late stage, indicating poor survival. However, mechanisms about the initiation of NSCLC bone metastases remain largely unclear. In our previous reports, BMP2 signaling activation has been found to enhance NSCLC bone metastases through enhancing carcinoma cells migration, invasion, osteoclasts differentiation and osteoblasts immature differentiation. Nevertheless, downstream target genes of BMP2 contributing to those processes still remain unknown. In this project, we find that the expression of Pnma5 is higher in metastatic bone tumors of Lewis lung carcinoma than in metastatic lung tumors and parental Lewis lung cells. Pnma5 overexpression not only can promote cell migration and invasion of NSCLC cells but also tumor-induced osteoclasts differentiation. Interestingly, knockdown of Pnma5 in Lewis lung cells blocks BMP2 signaling from inducing Lewis lung cells migration and invasion. Although BMP2 signaling can promote Lewis lung cells-induced osteoclasts differentiation from macrophages, this effect can also be blocked when Pnma5 is knocked down in Lewis lung cells. Moreover, Pnma5 can promote NSCLC bone metastases in vivo as the downstream target of BMP2. Those results above indicate that BMP2 signaling enhances NSCLC bone metastases via its direct downstream target gene Pnma5. This research reveals the detailed molecular mechanism about how BMP2 signaling contributes to NSCLC bone metastases via PNMA5 and provides a new potential therapeutic target for the treatment of NSCLC bone metastases.
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Recently, multiple single-cell assays were developed for detecting histone marks at the single-cell level. These techniques are either limited by the low cell throughput or sparse reads which limit their applications. To address these problems, we introduce indexing single-cell immunocleavage sequencing (iscChIC-seq), a multiplex indexing method based on TdT terminal transferase and T4 DNA ligase-mediated barcoding strategy and single-cell ChIC-seq, which is capable of readily analyzing histone modifications across tens of thousands of single cells in one experiment. Application of iscChIC-seq to profiling H3K4me3 and H3K27me3 in human white blood cells (WBCs) enabled successful detection of more than 10,000 single cells for each histone modification with 11 K and 45 K nonredundant reads per cell, respectively. Cluster analysis of these data allowed identification of monocytes, T cells, B cells, and NK cells from WBCs. The cell types annotated from H3K4me3 single-cell data are specifically correlated with the cell types annotated from H3K27me3 single-cell data. Our data indicate that iscChIC-seq is a reliable technique for profiling histone modifications in a large number of single cells, which may find broad applications in studying cellular heterogeneity and differentiation status in complex developmental and disease systems.