RESUMEN
Bi-allelic hypomorphic mutations in DNMT3B disrupt DNA methyltransferase activity and lead to immunodeficiency, centromeric instability, facial anomalies syndrome, type 1 (ICF1). Although several ICF1 phenotypes have been linked to abnormally hypomethylated repetitive regions, the unique genomic regions responsible for the remaining disease phenotypes remain largely uncharacterized. Here we explored two ICF1 patient-derived induced pluripotent stem cells (iPSCs) and their CRISPR-Cas9-corrected clones to determine whether DNMT3B correction can globally overcome DNA methylation defects and related changes in the epigenome. Hypomethylated regions throughout the genome are highly comparable between ICF1 iPSCs carrying different DNMT3B variants, and significantly overlap with those in ICF1 patient peripheral blood and lymphoblastoid cell lines. These regions include large CpG island domains, as well as promoters and enhancers of several lineage-specific genes, in particular immune-related, suggesting that they are premarked during early development. CRISPR-corrected ICF1 iPSCs reveal that the majority of phenotype-related hypomethylated regions reacquire normal DNA methylation levels following editing. However, at the most severely hypomethylated regions in ICF1 iPSCs, which also display the highest increases in H3K4me3 levels and/or abnormal CTCF binding, the epigenetic memory persists, and hypomethylation remains uncorrected. Overall, we demonstrate that restoring the catalytic activity of DNMT3B can reverse the majority of the aberrant ICF1 epigenome. However, a small fraction of the genome is resilient to this rescue, highlighting the challenge of reverting disease states that are due to genome-wide epigenetic perturbations. Uncovering the basis for the persistent epigenetic memory will promote the development of strategies to overcome this obstacle.
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Células Madre Pluripotentes Inducidas , Células Madre Pluripotentes Inducidas/metabolismo , Epigenoma , Memoria Epigenética , Histonas/metabolismo , Metilación de ADN , ADN (Citosina-5-)-Metiltransferasas/genéticaRESUMEN
MOTIVATION: methyLImp, a method we recently introduced for the missing value estimation of DNA methylation data, has demonstrated competitive performance in data imputation compared to the existing, general-purpose, approaches. However, imputation running time was considerably long and unfeasible in case of large datasets with numerous missing values. RESULTS: methyLImp2 made possible computations that were previously unfeasible. We achieved this by introducing two important modifications that have significantly reduced the original running time without sacrificing prediction performance. First, we implemented a chromosome-wise parallel version of methyLImp. This parallelization reduced the runtime by several 10-fold in our experiments. Then, to handle large datasets, we also introduced a mini-batch approach that uses only a subset of the samples for the imputation. Thus, it further reduces the running time from days to hours or even minutes in large datasets. AVAILABILITY AND IMPLEMENTATION: The R package methyLImp2 is under review for Bioconductor. It is currently freely available on Github https://github.com/annaplaksienko/methyLImp2.
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Biología Computacional , Metilación de ADNRESUMEN
PURPOSE: Common Variable Immunodeficiency (CVID) is characterized by hypogammaglobulinemia and failure of specific antibody production due to B-cell defects. However, studies have documented various T-cell abnormalities, potentially linked to viral complications. The frequency of Cytomegalovirus (CMV) replication in CVID cohorts is poorly studied. To address this gap in knowledge, we set up an observational study with the objectives of identifying CVID patients with active viraemia (CMV, Epstein-Barr virus (EBV)), evaluating potential correlations with immunophenotypic characteristics, clinical outcome, and the dynamic progression of clinical phenotypes over time. METHODS: 31 CVID patients were retrospectively analysed according to viraemia, clinical and immunologic characteristics. 21 patients with non CVID humoral immunodeficiency were also evaluated as control. RESULTS: Active viral replication of CMV and/or EBV was observed in 25% of all patients. CMV replication was detected only in CVID patients (16%). CVID patients with active viral replication showed reduced HLA-DR+ NK counts when compared with CMV-DNA negative CVID patients. Viraemic patients had lower counts of LIN-DNAMbright and LIN-CD16+ inflammatory lymphoid precursors which correlated with NK-cell subsets. Analysis of the dynamic progression of CVID clinical phenotypes over time, showed that the initial infectious phenotype progressed to complicated phenotypes with time. All CMV viraemic patients had complicated disease. CONCLUSION: Taken together, an impaired production of inflammatory precursors and NK activation is present in CVID patients with active viraemia. Since "Complicated" CVID occurs as a function of disease duration, there is need for an accurate evaluation of this aspect to improve classification and clinical management of CVID patients.
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Inmunodeficiencia Variable Común , Infecciones por Citomegalovirus , Citomegalovirus , Herpesvirus Humano 4 , Replicación Viral , Humanos , Inmunodeficiencia Variable Común/inmunología , Inmunodeficiencia Variable Común/complicaciones , Masculino , Femenino , Infecciones por Citomegalovirus/inmunología , Citomegalovirus/inmunología , Citomegalovirus/fisiología , Adulto , Persona de Mediana Edad , Herpesvirus Humano 4/fisiología , Herpesvirus Humano 4/inmunología , Estudios Retrospectivos , Células Asesinas Naturales/inmunología , Adulto Joven , Viremia/inmunología , Infecciones por Virus de Epstein-Barr/inmunología , Inmunofenotipificación , Anciano , AdolescenteRESUMEN
The T-BOX transcription factor TBX1 is essential for the development of the pharyngeal apparatus and it is haploinsufficient in DiGeorge syndrome (DGS), a developmental anomaly associated with congenital heart disease and other abnormalities. The murine model recapitulates the heart phenotype and showed collagen accumulation. We first used a cellular model to study gene expression during cardiogenic differentiation of WT and Tbx1-/- mouse embryonic stem cells. Then we used a mouse model of DGS to test whether interfering with collagen accumulation using an inhibitor of lysyl hydroxylase would modify the cardiac phenotype of the mutant. We found that loss of Tbx1 in a precardiac differentiation model was associated with up regulation of a subset of ECM-related genes, including several collagen genes. In the in vivo model, early prenatal treatment with Minoxidil, a lysyl hydroxylase inhibitor, ameliorated the cardiac outflow tract septation phenotype in Tbx1 mutant fetuses, but it had no effect on septation in WT fetuses. We conclude that TBX1 suppresses a defined subset of ECM-related genes. This function is critical for OFT septation because the inhibition of collagen cross-linking in the mutant reduces significantly the penetrance of septation defects.
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Síndrome de DiGeorge , Modelos Animales de Enfermedad , Minoxidil , Proteínas de Dominio T Box , Animales , Síndrome de DiGeorge/genética , Síndrome de DiGeorge/metabolismo , Síndrome de DiGeorge/tratamiento farmacológico , Síndrome de DiGeorge/patología , Ratones , Proteínas de Dominio T Box/genética , Proteínas de Dominio T Box/metabolismo , Minoxidil/farmacología , Colágeno/metabolismo , Diferenciación Celular/efectos de los fármacosRESUMEN
BACKGROUND: Aggressive malignancies, such as pancreatic cancer, are increasingly impacting young, female populations. Our investigation centered on whether the observed trends in cancer incidence were unique to pancreatic cancer or indicative of a broader trend across various cancer types. To delve deeper into this phenomenon, we analyzed cancer incidence trends across different age and sex groups. Furthermore, we explored differences in cancer incidence within specific young subgroups aged 18 to 26 and 27 to 34, to better understand the emerging incidence trend among young individuals. METHODS: This study collected cancer incidence data from one of the Surveillance, Epidemiology, and End Results cancer registry databases (SEER22), with 10,183,928 total cases from 2000 to 2020. Data were analyzed through Joinpoint trend analysis approach to evaluate sex- and age-specific trends in cancer incidence. Exposure rates were reported as Average Annual Percentage Changes (AAPCs). RESULTS: The analysis revealed significant age and sex-specific disparities, particularly among individuals aged 18-26 and 27-34. Pancreatic cancer incidence rates increased more in females aged 18-26 (AAPC, 9.37% [95% CI, 7.36-11.41%]; p < .0001) than in males (4.43% [95% CI, 2.36-6.53%]; p < .0001). Notably, among gender, age, and other malignancies, young females had the highest AAPCs for pancreatic cancer. Additionally, the incidence of gastric cancer, myeloma, and colorectal malignancies also showed higher AAPCs in young females compared to males. CONCLUSIONS: Recognizing emerging risk populations for highly lethal malignancies is crucial for early detection and effective disease management.
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Neoplasias , Humanos , Femenino , Masculino , Incidencia , Adulto , Adulto Joven , Adolescente , Neoplasias/epidemiología , Programa de VERF , Factores Sexuales , Estados Unidos/epidemiología , Factores de Edad , Neoplasias Pancreáticas/epidemiologíaRESUMEN
BACKGROUND: Osteoarthritis (OA) is a multifactorial, hypertrophic, and degenerative condition involving the whole joint and affecting a high percentage of middle-aged people. It is due to a combination of factors, although the pivotal mechanisms underlying the disease are still obscure. Moreover, current treatments are still poorly effective, and patients experience a painful and degenerative disease course. METHODS: We used an integrative approach that led us to extract a consensus signature from a meta-analysis of three different OA cohorts. We performed a network-based drug prioritization to detect the most relevant drugs targeting these genes and validated in vitro the most promising candidates. We also proposed a risk score based on a minimal set of genes to predict the OA clinical stage from RNA-Seq data. RESULTS: We derived a consensus signature of 44 genes that we validated on an independent dataset. Using network analysis, we identified Resveratrol, Tenoxicam, Benzbromarone, Pirinixic Acid, and Mesalazine as putative drugs of interest for therapeutics in OA for anti-inflammatory properties. We also derived a list of seven gene-targets validated with functional RT-qPCR assays, confirming the in silico predictions. Finally, we identified a predictive subset of genes composed of DNER, TNFSF11, THBS3, LOXL3, TSPAN2, DYSF, ASPN and HTRA1 to compute the patient's risk score. We validated this risk score on an independent dataset with a high AUC (0.875) and compared it with the same approach computed using the entire consensus signature (AUC 0.922). CONCLUSIONS: The consensus signature highlights crucial mechanisms for disease progression. Moreover, these genes were associated with several candidate drugs that could represent potential innovative therapeutics. Furthermore, the patient's risk scores can be used in clinical settings.
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Osteoartritis , Persona de Mediana Edad , Humanos , Osteoartritis/tratamiento farmacológico , Osteoartritis/genéticaRESUMEN
SUMMARY: ADViSELipidomics is a novel Shiny app for preprocessing, analyzing and visualizing lipidomics data. It handles the outputs from LipidSearch and LIQUID for lipid identification and quantification and the data from the Metabolomics Workbench. ADViSELipidomics extracts information by parsing lipid species (using LIPID MAPS classification) and, together with information available on the samples, performs several exploratory and statistical analyses. When the experiment includes internal lipid standards, ADViSELipidomics can normalize the data matrix, providing normalized concentration values per lipids and samples. Moreover, it identifies differentially abundant lipids in simple and complex experimental designs, dealing with batch effect correction. Finally, ADViSELipidomics has a user-friendly graphical user interface and supports an extensive series of interactive graphics. AVAILABILITY AND IMPLEMENTATION: ADViSELipidomics is freely available at https://github.com/ShinyFabio/ADViSELipidomics. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Asunto(s)
Lipidómica , Programas Informáticos , Flujo de Trabajo , Metabolómica , Lípidos/análisisRESUMEN
OBJECTIVE: The immune response arises from a fine balance of mechanisms that provide for surveillance, tolerance, and elimination of dangers. Sulfavant A (SULF A) is a sulfolipid with a promising adjuvant activity. Here we studied the mechanism of action of SULF A and addressed the identification of its molecular target in human dendritic cells (hDCs). METHODS: Adjuvant effect and immunological response to SULF A were assessed on DCs derived from human donors. In addition to testing various reporter cells, target identification and downstream signalling was supported by a reverse pharmacology approach based on antibody blocking and gene silencing, crosstalk with TLR pathways, use of human allogeneic mixed lymphocyte reaction. RESULTS: SULF A binds to the Triggering Receptor Expressed on Myeloid cells-2 (TREM2) and initiates an unconventional maturation of hDCs leading to enhanced migration activity and up-regulation of MHC and co-stimulatory molecules without release of conventional cytokines. This response involves the SYK-NFAT axis and is compromised by blockade or gene silencing of TREM2. Activation by SULF A preserved the DC functions to excite the allogeneic T cell response, and increased interleukin-10 release after lipopolysaccharide stimulation. CONCLUSION: SULF A is the first synthetic small molecule that binds to TREM2. The receptor engagement drives differentiation of an unprecedented DC phenotype (homeDCs) that contributes to immune homeostasis without compromising lymphocyte activation and immunogenic response. This mechanism fully supports the adjuvant and immunoregulatory activity of SULF A. We also propose that the biological properties of SULF A can be of interest in various physiopathological mechanisms and therapies involving TREM2.
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Células Dendríticas , Activación de Linfocitos , Citocinas/metabolismo , Células Dendríticas/metabolismo , Homeostasis , LigandosRESUMEN
The highly conserved zinc finger CCCTC-binding factor (CTCF) regulates genomic imprinting and gene expression by acting as a transcriptional activator or repressor of promoters and insulator of enhancers. The multiple functions of CTCF are accomplished by co-association with other protein partners and are dependent on genomic context and tissue specificity. Despite the critical role of CTCF in the organization of genome structure, to date, only a subset of CTCF interaction partners have been identified. Here we present a large-scale identification of CTCF-binding partners using affinity purification and high-resolution LC-MS/MS analysis. In addition to functional enrichment of specific protein families such as the ribosomal proteins and the DEAD box helicases, we identified novel high-confidence CTCF interactors that provide a still unexplored biochemical context for CTCF's multiple functions. One of the newly validated CTCF interactors is BRG1, the major ATPase subunit of the chromatin remodeling complex SWI/SNF, establishing a relationship between two master regulators of genome organization. This work significantly expands the current knowledge of the human CTCF interactome and represents an important resource to direct future studies aimed at uncovering molecular mechanisms modulating CTCF pleiotropic functions throughout the genome.
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Factor de Unión a CCCTC/metabolismo , Ensamble y Desensamble de Cromatina , ADN Helicasas/metabolismo , Complejos Multiproteicos/metabolismo , Proteínas Nucleares/metabolismo , Factores de Transcripción/metabolismo , Factor de Unión a CCCTC/genética , Línea Celular Tumoral , ADN Helicasas/genética , Humanos , Complejos Multiproteicos/genética , Proteínas Nucleares/genética , Factores de Transcripción/genéticaRESUMEN
The transcription factor CCCTC-binding factor (CTCF) modulates pleiotropic functions mostly related to gene expression regulation. The role of CTCF in large scale genome organization is also well established. A unifying model to explain relationships among many CTCF-mediated activities involves direct or indirect interactions with numerous protein cofactors recruited to specific binding sites. The co-association of CTCF with other architectural proteins such as cohesin, chromodomain helicases, and BRG1, further supports the interplay between master regulators of mammalian genome folding. Here, we report a comprehensive LC-MS/MS mapping of the components of the switch/sucrose nonfermentable (SWI/SNF) chromatin remodeling complex co-associated with CTCF including subunits belonging to the core, signature, and ATPase modules. We further show that the localization patterns of representative SWI/SNF members significantly overlap with CTCF sites on transcriptionally active chromatin regions. Moreover, we provide evidence of a direct binding of the BRK-BRG1 domain to the zinc finger motifs 4-8 of CTCF, thus, suggesting that these domains mediate the interaction of CTCF with the SWI/SNF complex. These findings provide an updated view of the cooperative nature between CTCF and the SWI/SNF ATP-dependent chromatin remodeling complexes, an important step for understanding how these architectural proteins collaborate to shape the genome.
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Factor de Unión a CCCTC/genética , Ensamble y Desensamble de Cromatina/genética , Proteínas Cromosómicas no Histona/genética , ADN Helicasas/genética , Proteínas Nucleares/genética , Factores de Transcripción/genética , Dedos de Zinc/genética , Adenosina Trifosfatasas/genética , Sitios de Unión/genética , Proteínas de Ciclo Celular/genética , Regulación de la Expresión Génica/genética , Genoma Humano/genética , Humanos , Complejos Multiproteicos/genética , Mapas de Interacción de Proteínas/genética , Espectrometría de Masas en Tándem , CohesinasRESUMEN
PURPOSE: Beckwith-Wiedemann syndrome (BWS) is a developmental disorder caused by dysregulation of the imprinted gene cluster of chromosome 11p15.5 and often associated with loss of methylation (LOM) of the imprinting center 2 (IC2) located in KCNQ1 intron 10. To unravel the etiological mechanisms underlying these epimutations, we searched for genetic variants associated with IC2 LOM. METHODS: We looked for cases showing the clinical features of both BWS and long QT syndrome (LQTS), which is often associated with KCNQ1 variants. Pathogenic variants were identified by genomic analysis and targeted sequencing. Functional experiments were performed to link these pathogenic variants to the imprinting defect. RESULTS: We found three rare cases in which complete IC2 LOM is associated with maternal transmission of KCNQ1 variants, two of which were demonstrated to affect KCNQ1 transcription upstream of IC2. As a consequence of KCNQ1 haploinsufficiency, these variants also cause LQTS on both maternal and paternal transmission. CONCLUSION: These results are consistent with the hypothesis that, similar to what has been demonstrated in mouse, lack of transcription across IC2 results in failure of methylation establishment in the female germline and BWS later in development, and also suggest a new link between LQTS and BWS that is important for genetic counseling.
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Síndrome de Beckwith-Wiedemann/genética , Metilación de ADN/genética , Canal de Potasio KCNQ1/genética , Adolescente , Adulto , Animales , Síndrome de Beckwith-Wiedemann/epidemiología , Síndrome de Beckwith-Wiedemann/patología , Niño , Preescolar , Cromosomas Humanos Par 11/genética , Femenino , Impresión Genómica/genética , Humanos , Lactante , Intrones/genética , Masculino , Herencia Materna/genética , Ratones , Linaje , Adulto JovenRESUMEN
Hypomorphic mutations in DNA-methyltransferase DNMT3B cause majority of the rare disorder Immunodeficiency, Centromere instability and Facial anomalies syndrome cases (ICF1). By unspecified mechanisms, mutant-DNMT3B interferes with lymphoid-specific pathways resulting in immune response defects. Interestingly, recent findings report that DNMT3B shapes intragenic CpG-methylation of highly-transcribed genes. However, how the DNMT3B-dependent epigenetic network modulates transcription and whether ICF1-specific mutations impair this process remains unknown. We performed a transcriptomic and epigenomic study in patient-derived B-cell lines to investigate the genome-scale effects of DNMT3B dysfunction. We highlighted that altered intragenic CpG-methylation impairs multiple aspects of transcriptional regulation, like alternative TSS usage, antisense transcription and exon splicing. These defects preferentially associate with changes of intragenic H3K4me3 and at lesser extent of H3K27me3 and H3K36me3. In addition, we highlighted a novel DNMT3B activity in modulating the self-regulatory circuit of sense-antisense pairs and the exon skipping during alternative splicing, through interacting with RNA molecules. Strikingly, altered transcription affects disease relevant genes, as for instance the memory-B cell marker CD27 and PTPRC genes, providing us with biological insights into the ICF1-syndrome pathogenesis. Our genome-scale approach sheds light on the mechanisms still poorly understood of the intragenic function of DNMT3B and DNA methylation in gene expression regulation.
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Empalme Alternativo , Anorexia/genética , Caquexia/genética , ADN (Citosina-5-)-Metiltransferasas/genética , Anomalías del Ojo/genética , Histonas/genética , Síndromes de Inmunodeficiencia/genética , Mutación , ARN Mensajero/genética , Enfermedades de la Piel/genética , Anorexia/inmunología , Anorexia/patología , Linfocitos B/inmunología , Linfocitos B/patología , Caquexia/inmunología , Caquexia/patología , Línea Celular Transformada , Islas de CpG , ADN (Citosina-5-)-Metiltransferasas/inmunología , Metilación de ADN , Epigénesis Genética , Anomalías del Ojo/inmunología , Anomalías del Ojo/patología , Facies , Femenino , Histonas/inmunología , Humanos , Síndromes de Inmunodeficiencia/inmunología , Síndromes de Inmunodeficiencia/patología , Memoria Inmunológica , Antígenos Comunes de Leucocito/genética , Antígenos Comunes de Leucocito/inmunología , Masculino , Regiones Promotoras Genéticas , ARN Mensajero/inmunología , Enfermedades de la Piel/inmunología , Enfermedades de la Piel/patología , Transcripción Genética , Miembro 7 de la Superfamilia de Receptores de Factores de Necrosis Tumoral/genética , Miembro 7 de la Superfamilia de Receptores de Factores de Necrosis Tumoral/inmunología , ADN Metiltransferasa 3BRESUMEN
Imprinting Control Regions (ICRs) need to maintain their parental allele-specific DNA methylation during early embryogenesis despite genome-wide demethylation and subsequent de novo methylation. ZFP57 and KAP1 are both required for maintaining the repressive DNA methylation and H3-lysine-9-trimethylation (H3K9me3) at ICRs. In vitro, ZFP57 binds a specific hexanucleotide motif that is enriched at its genomic binding sites. We now demonstrate in mouse embryonic stem cells (ESCs) that SNPs disrupting closely-spaced hexanucleotide motifs are associated with lack of ZFP57 binding and H3K9me3 enrichment. Through a transgenic approach in mouse ESCs, we further demonstrate that an ICR fragment containing three ZFP57 motif sequences recapitulates the original methylated or unmethylated status when integrated into the genome at an ectopic position. Mutation of Zfp57 or the hexanucleotide motifs led to loss of ZFP57 binding and DNA methylation of the transgene. Finally, we identified a sequence variant of the hexanucleotide motif that interacts with ZFP57 both in vivo and in vitro. The presence of multiple and closely located copies of ZFP57 motif variants emerges as a distinct characteristic that is required for the faithful maintenance of repressive epigenetic marks at ICRs and other ZFP57 binding sites.
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Metilación de ADN , Impresión Genómica , Células Madre Embrionarias de Ratones/metabolismo , Proteínas Represoras/genética , Alelos , Animales , Secuencia de Bases , Línea Celular , Inmunoprecipitación de Cromatina , Histonas/metabolismo , Lisina/metabolismo , Metilación , Ratones , Ratones Endogámicos C57BL , Ratones Noqueados , Ratones Transgénicos , Mutación , Proteínas Nucleares/genética , Proteínas Nucleares/metabolismo , Motivos de Nucleótidos/genética , Polimorfismo de Nucleótido Simple , Unión Proteica/genética , Proteínas Represoras/metabolismo , Proteína 28 que Contiene Motivos TripartitoRESUMEN
ZFP57 is necessary for maintaining repressive epigenetic modifications at Imprinting control regions (ICRs). In mouse embryonic stem cells (ESCs), ZFP57 binds ICRs (ICRBS) and many other loci (non-ICRBS). To address the role of ZFP57 on all its target sites, we performed high-throughput and multi-locus analyses of inbred and hybrid mouse ESC lines carrying different gene knockouts. By using an allele-specific RNA-seq approach, we demonstrate that ZFP57 loss results in derepression of the imprinted allele of multiple genes in the imprinted clusters. We also find marked epigenetic differences between ICRBS and non-ICRBS suggesting that different cis-acting regulatory functions are repressed by ZFP57 at these two classes of target loci. Overall, these data demonstrate that ZFP57 is pivotal to maintain the allele-specific epigenetic modifications of ICRs that in turn are necessary for maintaining the imprinted expression over long distances. At non-ICRBS, ZFP57 inactivation results in acquisition of epigenetic features that are characteristic of poised enhancers, suggesting that another function of ZFP57 in early embryogenesis is to repress cis-acting regulatory elements whose activity is not yet required.
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Regulación del Desarrollo de la Expresión Génica , Impresión Genómica , Células Madre Embrionarias de Ratones/metabolismo , Proteínas Nucleares/metabolismo , Proteínas Represoras/metabolismo , Animales , Sitios de Unión/genética , Diferenciación Celular/genética , Islas de CpG/genética , Epigénesis Genética , Sitios Genéticos , Histonas/metabolismo , Lisina/metabolismo , Metilación , Ratones , Modelos GenéticosRESUMEN
The human retina is a specialized tissue involved in light stimulus transduction. Despite its unique biology, an accurate reference transcriptome is still missing. Here, we performed gene expression analysis (RNA-seq) of 50 retinal samples from non-visually impaired post-mortem donors. We identified novel transcripts with high confidence (Observed Transcriptome (ObsT)) and quantified the expression level of known transcripts (Reference Transcriptome (RefT)). The ObsT included 77 623 transcripts (23 960 genes) covering 137 Mb (35 Mb new transcribed genome). Most of the transcripts (92%) were multi-exonic: 81% with known isoforms, 16% with new isoforms and 3% belonging to new genes. The RefT included 13 792 genes across 94 521 known transcripts. Mitochondrial genes were among the most highly expressed, accounting for about 10% of the reads. Of all the protein-coding genes in Gencode, 65% are expressed in the retina. We exploited inter-individual variability in gene expression to infer a gene co-expression network and to identify genes specifically expressed in photoreceptor cells. We experimentally validated the photoreceptors localization of three genes in human retina that had not been previously reported. RNA-seq data and the gene co-expression network are available online (http://retina.tigem.it).
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Proteínas del Ojo/genética , Redes Reguladoras de Genes , Genoma Humano , Proteínas Mitocondriales/genética , Retina/metabolismo , Transcriptoma , Adulto , Anciano , Empalme Alternativo , Atlas como Asunto , Mapeo Cromosómico , Exones , Proteínas del Ojo/metabolismo , Femenino , Perfilación de la Expresión Génica , Ontología de Genes , Secuenciación de Nucleótidos de Alto Rendimiento , Humanos , Masculino , Persona de Mediana Edad , Proteínas Mitocondriales/metabolismo , Anotación de Secuencia Molecular , Isoformas de Proteínas/genética , Isoformas de Proteínas/metabolismo , Retina/citologíaRESUMEN
Vaccination is the most successful and cost-effective method to prevent infectious diseases. However, many vaccine antigens have poor in vivo immunogenic potential and need adjuvants to enhance immune response. The application of systems biology to immunity and vaccinology has yielded crucial insights about how vaccines and adjuvants work. We have previously characterized two safe and powerful delivery systems derived from non-pathogenic prokaryotic organisms: E2 and fd filamentous bacteriophage systems. They elicit an in vivo immune response inducing CD8+ T-cell responses, even in absence of adjuvants or stimuli for dendritic cells' maturation. Nonetheless, a systematic and comparative analysis of the complex gene expression network underlying such activation is missing. Therefore, we compared the transcriptomes of ex vivo isolated bone marrow-derived dendritic cells exposed to these antigen delivery systems. Significant differences emerged, especially for genes involved in innate immunity, co-stimulation, and cytokine production. Results indicate that E2 drives polarization toward the Th2 phenotype, mainly mediated by Irf4, Ccl17, and Ccr4 over-expression. Conversely, fd-scαDEC-205 triggers Th1 T cells' polarization through the induction of Il12b, Il12rb, Il6, and other molecules involved in its signal transduction. The data analysis was performed using RNASeqGUI, hence, addressing the increasing need of transparency and reproducibility of computational analysis.
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Presentación de Antígeno/inmunología , Antígenos/inmunología , Biología Computacional , Células Dendríticas/inmunología , Células Dendríticas/metabolismo , Transcripción Genética , Animales , Análisis por Conglomerados , Biología Computacional/métodos , Perfilación de la Expresión Génica , Regulación de la Expresión Génica , Redes Reguladoras de Genes , Secuenciación de Nucleótidos de Alto Rendimiento , Inmunidad/genética , Redes y Vías Metabólicas , Ratones , Reproducibilidad de los Resultados , Transcriptoma , Interfaz Usuario-Computador , Vacunas , Flujo de TrabajoRESUMEN
Free-living bacteria grown under aerobic conditions were used to investigate, by next-generation RNA sequencing analysis, the transcriptional profiles of Sinorhizobium meliloti wild-type 1021 and its derivative, RD64, overproducing the main auxin indole-3-acetic acid (IAA). Among the upregulated genes in RD64 cells, we detected the main nitrogen-fixation regulator fixJ, the two intermediate regulators fixK and nifA, and several other genes known to be FixJ targets. The gene coding for the sigma factor RpoH1 and other genes involved in stress response, regulated in a RpoH1-dependent manner in S. meliloti, were also induced in RD64 cells. Under microaerobic condition, quantitative real-time polymerase chain reaction analysis revealed that the genes fixJL and nifA were up-regulated in RD64 cells as compared with 1021 cells. This work provided evidence that the overexpression of IAA in S. meliloti free-living cells induced many of the transcriptional changes that normally occur in nitrogen-fixing root nodule.
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Regulación Bacteriana de la Expresión Génica , Ácidos Indolacéticos/metabolismo , Sinorhizobium meliloti/fisiología , Proteínas Bacterianas/genética , Proteínas Bacterianas/metabolismo , Fijación del Nitrógeno/genética , Análisis de Secuencia de ARN , Factor sigma/genética , Factor sigma/metabolismoRESUMEN
BACKGROUND: The DNA base composition is well known to be highly variable among organisms. Bio-physic studies on the effect of the GC increments on the DNA structure have shown that GC-richer DNA sequences are more bendable. The result was the keystone of the hypothesis proposing the metabolic rate as the major force driving the GC content variability, since an increased resistance to the torsion stress is mainly required during the transcription process to avoid DNA breakage. Hence, the aim of the present work is to test if both salinity and migration, suggested to affect the metabolic rate of teleostean fishes, affect the average genomic GC content as well. Moreover, since the gill surface has been reported to be a major morphological expression of metabolic rate, this parameter was also analyzed in the light of the above hypothesis. RESULTS: Teleosts living in different environments (freshwater and seawater) and with different lifestyles (migratory and non-migratory) were analyzed studying three variables: routine metabolic rate, gill area and genomic GC-content, none of them showing a phylogenetic signal among fish species. Routine metabolic rate, specific gill area and average genomic GC were higher in seawater than freshwater species. The same trend was observed comparing migratory versus non-migratory species. Crossing salinity and lifestyle, the active migratory species living in seawater show coincidentally the highest routine metabolic rate, the highest specific gill area and the highest average genomic GC content. CONCLUSIONS: The results clearly highlight that environmental factors (salinity) and lifestyle (migration) affect not only the physiology (i.e. the routine metabolic rate), and the morphology (i.e. gill area) of teleosts, but also basic genome feature (i.e. the GC content), thus opening to an interesting liaison among the three variables in the light of the metabolic rate hypothesis.
Asunto(s)
Migración Animal , Composición de Base , Peces/genética , Genoma , Salinidad , Animales , Metabolismo Energético , Peces/clasificación , Peces/metabolismo , Agua Dulce , Branquias/fisiología , Filogenia , Agua de MarRESUMEN
In this study, we investigated by in silico analysis the possible correlation between microRNAs (miRNAs) and Anamnia V-SINEs (a superfamily of short interspersed nuclear elements), which belong to those retroposon families that have been preserved in vertebrate genomes for millions of years and are actively transcribed because they are embedded in the 3' untranslated region (UTR) of several genes. We report the results of the analysis of the genomic distribution of these mobile elements in zebrafish (Danio rerio) and discuss their involvement in generating miRNA gene loci. The computational study showed that the genes predicted to bear V-SINEs can be targeted by miRNAs with a very high hybridization E-value. Gene ontology analysis indicates that these genes are mainly involved in metabolic, membrane, and cytoplasmic signaling pathways. Nearly all the miRNAs that were predicted to target the V-SINEs of these genes, i.e., miR-338, miR-9, miR-181, miR-724, miR-735, and miR-204, have been validated in similar regulatory roles in mammals. The large number of genes bearing a V-SINE involved in metabolic and cellular processes suggests that V-SINEs may play a role in modulating cell responses to different stimuli and in preserving the metabolic balance during cell proliferation and differentiation. Although they need experimental validation, these preliminary results suggest that in the genome of D. rerio, as in other TE families in vertebrates, the preservation of V-SINE retroposons may also have been favored by their putative role in gene network modulation.
Asunto(s)
Regulación de la Expresión Génica , MicroARNs/genética , Elementos de Nucleótido Esparcido Corto/genética , Pez Cebra/genética , Regiones no Traducidas 3' , Animales , Sitios de Unión , Mapeo Cromosómico , Biología Computacional/métodos , Ontología de Genes , Genoma , Genómica , MicroARNs/química , Familia de Multigenes , Interferencia de ARN , ARN Mensajero/química , ARN Mensajero/genética , Análisis de Secuencia de ARNRESUMEN
BACKGROUND: Chip-seq experiments are becoming a standard approach for genome-wide profiling protein-DNA interactions, such as detecting transcription factor binding sites, histone modification marks and RNA Polymerase II occupancy. However, when comparing a ChIP sample versus a control sample, such as Input DNA, normalization procedures have to be applied in order to remove experimental source of biases. Despite the substantial impact that the choice of the normalization method can have on the results of a ChIP-seq data analysis, their assessment is not fully explored in the literature. In particular, there are no diagnostic tools that show whether the applied normalization is indeed appropriate for the data being analyzed. RESULTS: In this work we propose a novel diagnostic tool to examine the appropriateness of the estimated normalization procedure. By plotting the empirical densities of log relative risks in bins of equal read count, along with the estimated normalization constant, after logarithmic transformation, the researcher is able to assess the appropriateness of the estimated normalization constant. We use the diagnostic plot to evaluate the appropriateness of the estimates obtained by CisGenome, NCIS and CCAT on several real data examples. Moreover, we show the impact that the choice of the normalization constant can have on standard tools for peak calling such as MACS or SICER. Finally, we propose a novel procedure for controlling the FDR using sample swapping. This procedure makes use of the estimated normalization constant in order to gain power over the naive choice of constant (used in MACS and SICER), which is the ratio of the total number of reads in the ChIP and Input samples. CONCLUSIONS: Linear normalization approaches aim to estimate a scale factor, r, to adjust for different sequencing depths when comparing ChIP versus Input samples. The estimated scaling factor can easily be incorporated in many peak caller algorithms to improve the accuracy of the peak identification. The diagnostic plot proposed in this paper can be used to assess how adequate ChIP/Input normalization constants are, and thus it allows the user to choose the most adequate estimate for the analysis.