المؤلفون: Hiroko Nomaru, Yang Liu, Christopher De Bono, Dario Righelli, Andrea Cirino, Wei Wang, Hansoo Song, Silvia E. Racedo, Anelisa G. Dantas, Lu Zhang, Chen-Leng Cai, Claudia Angelini, Lionel Christiaen, Robert G. Kelly, Antonio Baldini, Deyou Zheng, Bernice E. Morrow

المصدر: Nature Communications, Vol 12, Iss 1, Pp 1-19 (2021)

مصطلحات موضوعية: Science

الوصف: Perturbations of the cardiopharyngeal mesoderm can lead to congenital defects in individuals with 22q11.2 deletion syndrome. Here the authors use single cell RNA-sequencing to identify a multilineage primed population within the mesoderm, marked by Tbx1, which has bipotent properties to form cardiac and branchiomeric muscle cells.

وصف الملف: electronic resource

العلاقة: https://doaj.org/toc/2041-1723Test

الوصول الحر: https://doaj.org/article/f709a55fc0cc4c0b854e870ae4c8e741Test

المؤلفون: Basilia Acurzio, Ankit Verma, Alessia Polito, Carlo Giaccari, Francesco Cecere, Salvatore Fioriniello, Floriana Della Ragione, Annalisa Fico, Flavia Cerrato, Claudia Angelini, Robert Feil, Andrea Riccio

المصدر: Scientific Reports, Vol 11, Iss 1, Pp 1-17 (2021)

مصطلحات موضوعية: Medicine, Science

الوصف: Abstract ZFP57 is required to maintain the germline-marked differential methylation at imprinting control regions (ICRs) in mouse embryonic stem cells (ESCs). Although DNA methylation has a key role in genomic imprinting, several imprinted genes are controlled by different mechanisms, and a comprehensive study of the relationship between DMR methylation and imprinted gene expression is lacking. To address the latter issue, we differentiated wild-type and Zfp57 -/- hybrid mouse ESCs into neural precursor cells (NPCs) and evaluated allelic expression of imprinted genes. In mutant NPCs, we observed a reduction of allelic bias of all the 32 genes that were imprinted in wild-type cells, demonstrating that ZFP57-dependent methylation is required for maintaining or acquiring imprinted gene expression during differentiation. Analysis of expression levels showed that imprinted genes expressed from the non-methylated chromosome were generally up-regulated, and those expressed from the methylated chromosome were down-regulated in mutant cells. However, expression levels of several imprinted genes acquiring biallelic expression were not affected, suggesting the existence of compensatory mechanisms that control their RNA level. Since neural differentiation was partially impaired in Zfp57-mutant cells, this study also indicates that imprinted genes and/or non-imprinted ZFP57-target genes are required for proper neurogenesis in cultured ESCs.

وصف الملف: electronic resource

العلاقة: https://doaj.org/toc/2045-2322Test

الوصول الحر: https://doaj.org/article/6c8c1651a3bf4c37b51d4600ee824ba6Test

المؤلفون: Dario Righelli, Claudia Angelini

المصدر: PLoS ONE, Vol 16, Iss 5, p e0244122 (2021)

مصطلحات موضوعية: Medicine, Science

الوصف: During last years "irreproducibility" became a general problem in omics data analysis due to the use of sophisticated and poorly described computational procedures. For avoiding misleading results, it is necessary to inspect and reproduce the entire data analysis as a unified product. Reproducible Research (RR) provides general guidelines for public access to the analytic data and related analysis code combined with natural language documentation, allowing third-parties to reproduce the findings. We developed easyreporting, a novel R/Bioconductor package, to facilitate the implementation of an RR layer inside reports/tools. We describe the main functionalities and illustrate the organization of an analysis report using a typical case study concerning the analysis of RNA-seq data. Then, we show how to use easyreporting in other projects to trace R functions automatically. This latter feature helps developers to implement procedures that automatically keep track of the analysis steps. Easyreporting can be useful in supporting the reproducibility of any data analysis project and shows great advantages for the implementation of R packages and GUIs. It turns out to be very helpful in bioinformatics, where the complexity of the analyses makes it extremely difficult to trace all the steps and parameters used in the study.

وصف الملف: electronic resource

العلاقة: https://doaj.org/toc/1932-6203Test

الوصول الحر: https://doaj.org/article/64b88bb12ed74a14836b49e972f18c49Test

المؤلفون: Nicola G Criscuolo, Claudia Angelini

المصدر: PLoS ONE, Vol 15, Iss 2, p e0229330 (2020)

مصطلحات موضوعية: Medicine, Science

الوصف: Population genetics focuses on the analysis of genetic differences within and between-group of individuals and the inference of the populations' structure. These analyses are usually carried out using Bayesian clustering or maximum likelihood estimation algorithms that assign individuals to a given population depending on specific genetic patterns. Although several tools were developed to perform population genetics analysis, their standard graphical outputs may not be sufficiently informative for users lacking interactivity and complete information. StructuRly aims to resolve this problem by offering a complete environment for population analysis. In particular, StructuRly combines the statistical power of the R language with the friendly interfaces implemented using the shiny libraries to provide a novel tool for performing population clustering, evaluating several genetic indexes, and comparing results. Moreover, graphical representations are interactive and can be easily personalized. StructuRly is available either as R package on GitHub, with detailed information for its installation and use and as shinyapps.io servers for those users who are not familiar with R and the RStudio IDE. The application has been tested on Linux, macOS and Windows operative systems and can be launched as a shiny app in every web browser.

وصف الملف: electronic resource

العلاقة: https://doaj.org/toc/1932-6203Test

الوصول الحر: https://doaj.org/article/ce12e07b98ca4ddf9b7afdf6904f4041Test

المؤلفون: Alessandro Fiorenzano, Emilia Pascale, Cristina D'Aniello, Dario Acampora, Cecilia Bassalert, Francesco Russo, Gennaro Andolfi, Mauro Biffoni, Federica Francescangeli, Ann Zeuner, Claudia Angelini, Claire Chazaud, Eduardo J. Patriarca, Annalisa Fico, Gabriella Minchiotti

المصدر: Nature Communications, Vol 7, Iss 1, Pp 1-16 (2016)

مصطلحات موضوعية: Science

الوصف: Stem cell plasticity is crucial for early embryo development and the differentiation of stem cells. Here, the authors show that the extracellular protein Cripto sustains mouse ESC self-renewal and maintains mouse EpiSC as well as human ESC pluripotency and controls the metabolic reprogramming in ESCs to EpiSC transition.

وصف الملف: electronic resource

العلاقة: https://doaj.org/toc/2041-1723Test

الوصول الحر: https://doaj.org/article/2bb01357f66344a6adf138525180fdf0Test

المؤلفون: Filomena Gabriella Fulcoli, Monica Franzese, Xiangyang Liu, Zhen Zhang, Claudia Angelini, Antonio Baldini

المصدر: Nature Communications, Vol 7, Iss 1, Pp 1-11 (2016)

مصطلحات موضوعية: Science

الوصف: Deficit in transcription factor Tbx1 causes heart defects in humans and mice. Here the authors show that Tbx1 regulates gene expression by recruiting histone methyltransferases that affect chromatin marks, and that a drug inhibiting histone demethylation ameliorates the cardiovascular phenotype in Tbx1 haploinsufficient or hypomorphic mice.

وصف الملف: electronic resource

العلاقة: https://doaj.org/toc/2041-1723Test

الوصول الحر: https://doaj.org/article/c605fbaffcc6411d82a4fb0d53111f97Test

المؤلفون: Ezio Di Costanzo, Vincenzo Ingangi, Claudia Angelini, Maria Francesca Carfora, Maria Vincenza Carriero, Roberto Natalini

المصدر: PLoS ONE, Vol 11, Iss 9, p e0162553 (2016)

مصطلحات موضوعية: Medicine, Science

الوصف: Experiments of cell migration and chemotaxis assays have been classically performed in the so-called Boyden Chambers. A recent technology, xCELLigence Real Time Cell Analysis, is now allowing to monitor the cell migration in real time. This technology measures impedance changes caused by the gradual increase of electrode surface occupation by cells during the course of time and provide a Cell Index which is proportional to cellular morphology, spreading, ruffling and adhesion quality as well as cell number. In this paper we propose a macroscopic mathematical model, based on advection-reaction-diffusion partial differential equations, describing the cell migration assay using the real-time technology. We carried out numerical simulations to compare simulated model dynamics with data of observed biological experiments on three different cell lines and in two experimental settings: absence of chemotactic signals (basal migration) and presence of a chemoattractant. Overall we conclude that our minimal mathematical model is able to describe the phenomenon in the real time scale and numerical results show a good agreement with the experimental evidences.

وصف الملف: electronic resource

العلاقة: http://europepmc.org/articles/PMC5040252?pdf=renderTest; https://doaj.org/toc/1932-6203Test

الوصول الحر: https://doaj.org/article/732ba4033f014624b17fdb08f9325a4dTest

المؤلفون: Pietro Liò, Claudia Angelini, Italia De Feis, Viet-Anh Nguyen

المصدر: PLoS ONE, Vol 7, Iss 9, p e42489 (2012)

مصطلحات موضوعية: Medicine, Science

الوصف: A major goal of bioinformatics is the characterization of transcription factors and the transcriptional programs they regulate. Given the speed of genome sequencing, we would like to quickly annotate regulatory sequences in newly-sequenced genomes. In such cases, it would be helpful to predict sequence motifs by using experimental data from closely related model organism. Here we present a general algorithm that allow to identify transcription factor binding sites in one newly sequenced species by performing Bayesian regression on the annotated species. First we set the rationale of our method by applying it within the same species, then we extend it to use data available in closely related species. Finally, we generalise the method to handle the case when a certain number of experiments, from several species close to the species on which to make inference, are available. In order to show the performance of the method, we analyse three functionally related networks in the Ascomycota. Two gene network case studies are related to the G2/M phase of the Ascomycota cell cycle; the third is related to morphogenesis. We also compared the method with MatrixReduce and discuss other types of validation and tests. The first network is well known and provides a biological validation test of the method. The two cell cycle case studies, where the gene network size is conserved, demonstrate an effective utility in annotating new species sequences using all the available replicas from model species. The third case, where the gene network size varies among species, shows that the combination of information is less powerful but is still informative. Our methodology is quite general and could be extended to integrate other high-throughput data from model organisms.

وصف الملف: electronic resource

العلاقة: https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22984403/pdf/?tool=EBITest; https://doaj.org/toc/1932-6203Test

الوصول الحر: https://doaj.org/article/2801908567ec448c9d897ec7576a02f6Test

المؤلفون: Valerio Costa, Claudia Angelini, Luciana D'Apice, Margherita Mutarelli, Amelia Casamassimi, Linda Sommese, Maria Assunta Gallo, Marianna Aprile, Roberta Esposito, Luigi Leone, Aldo Donizetti, Stefania Crispi, Monica Rienzo, Berardo Sarubbi, Raffaele Calabrò, Marco Picardi, Paola Salvatore, Teresa Infante, Piergiuseppe De Berardinis, Claudio Napoli, Alfredo Ciccodicola

المصدر: PLoS ONE, Vol 6, Iss 4, p e18493 (2011)

مصطلحات موضوعية: Medicine, Science

الوصف: Hybridization- and tag-based technologies have been successfully used in Down syndrome to identify genes involved in various aspects of the pathogenesis. However, these technologies suffer from several limits and drawbacks and, to date, information about rare, even though relevant, RNA species such as long and small non-coding RNAs, is completely missing. Indeed, none of published works has still described the whole transcriptional landscape of Down syndrome. Although the recent advances in high-throughput RNA sequencing have revealed the complexity of transcriptomes, most of them rely on polyA enrichment protocols, able to detect only a small fraction of total RNA content. On the opposite end, massive-scale RNA sequencing on rRNA-depleted samples allows the survey of the complete set of coding and non-coding RNA species, now emerging as novel contributors to pathogenic mechanisms. Hence, in this work we analysed for the first time the complete transcriptome of human trisomic endothelial progenitor cells to an unprecedented level of resolution and sensitivity by RNA-sequencing. Our analysis allowed us to detect differential expression of even low expressed genes crucial for the pathogenesis, to disclose novel regions of active transcription outside yet annotated loci, and to investigate a plethora of non-polyadenylated long as well as short non coding RNAs. Novel splice isoforms for a large subset of crucial genes, and novel extended untranslated regions for known genes--possibly novel miRNA targets or regulatory sites for gene transcription--were also identified in this study. Coupling the rRNA depletion of samples, followed by high-throughput RNA-sequencing, to the easy availability of these cells renders this approach very feasible for transcriptome studies, offering the possibility of investigating in-depth blood-related pathological features of Down syndrome, as well as other genetic disorders.

وصف الملف: electronic resource

العلاقة: http://europepmc.org/articles/PMC3080369?pdf=renderTest; https://doaj.org/toc/1932-6203Test

الوصول الحر: https://doaj.org/article/e2883b5932bf4b86bfd7a945914c2955Test

المؤلفون: Claudia Angelini, Ankit Verma, Basilia Acurzio, Carlo Giaccari, Floriana Della Ragione, Francesco Cecere, Andrea Riccio, Robert Feil, Flavia Cerrato, Annalisa Fico, Alessia Polito, Salvatore Fioriniello

المساهمون: Acurzio, B., Verma, A., Polito, A., Giaccari, C., Cecere, F., Fioriniello, S., Della Ragione, F., Fico, A., Cerrato, F., Angelini, C., Feil, R., Riccio, A., Institut de Génétique Moléculaire de Montpellier (IGMM), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)

المصدر: Scientific reports (Nature Publishing Group) 11 (2021). doi:10.1038/s41598-021-93297-3
info:cnr-pdr/source/autori:Acurzio B.; Verma A.; Polito A.; Giaccari C.; Cecere F.; Fioriniello S.; Della Ragione F.; Fico A.; Cerrato F.; Angelini C.; Feil R.; Riccio A./titolo:Zfp57 inactivation illustrates the role of ICR methylation in imprinted gene expression during neural differentiation of mouse ESCs/doi:10.1038%2Fs41598-021-93297-3/rivista:Scientific reports (Nature Publishing Group)/anno:2021/pagina_da:/pagina_a:/intervallo_pagine:/volume:11
Scientific Reports
Scientific Reports, Nature Publishing Group, 2021, 11 (1), ⟨10.1038/s41598-021-93297-3⟩
Scientific Reports, Vol 11, Iss 1, Pp 1-17 (2021)

مصطلحات موضوعية: nervous system development, wildtype, Mutant, Zfp57, Mice, 0302 clinical medicine, Neural Stem Cells, Neural Stem Cell, Imprinting (psychology), cell mutant, [SDV.BDD]Life Sciences [q-bio]/Development Biology, Regulation of gene expression, 0303 health sciences, Multidisciplinary, allele, article, Gene Expression Regulation, Developmental, Mouse Embryonic Stem Cells, Imprinting, Cell Differentiation, Methylation, protein function, ORIGIN-SPECIFIC EXPRESSIONDNA METHYLATIONDISTAL CHROMOSOME-7STEM-CELLSIDENTIFICATIONMULTIPLEMECHANISMSCHROMATINMAINTAINSTRANSIENT, Cell biology, DNA methylation, Medicine, Epigenetics, Science, Biology, Chromosome, Chromosomes, Genomic Imprinting, 03 medical and health sciences, hybrid mouse strain, Genetics, Animals, controlled study, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Gene, 030304 developmental biology, cell culture, [SDV.GEN]Life Sciences [q-bio]/Genetics, ES-derived neural progenitor cells, Animal, Mouse Embryonic Stem Cell, DNA Methylation, Repressor Proteins, JB1, methylation, Genomic imprinting, Zfp57, Genetics, Epigenetics, Imprinting, allele, article, cell culture, cell mutant, chromosome, controlled study, hybrid mouse strain, methylation, mouse embryonic stem cell, nervous system development, protein function, ES-derived neural progenitor cells, JB1, wildtype, Zfp57, 030217 neurology & neurosurgery

الوصف: ZFP57 is required to maintain the germline-marked differential methylation at imprinting control regions (ICRs) in mouse embryonic stem cells (ESCs). Although DNA methylation has a key role in genomic imprinting, several imprinted genes are controlled by different mechanisms, and a comprehensive study of the relationship between DMR methylation and imprinted gene expression is lacking. To address the latter issue, we differentiated wild-type and Zfp57-/- hybrid mouse ESCs into neural precursor cells (NPCs) and evaluated allelic expression of imprinted genes. In mutant NPCs, we observed a reduction of allelic bias of all the 32 genes that were imprinted in wild-type cells, demonstrating that ZFP57-dependent methylation is required for maintaining or acquiring imprinted gene expression during differentiation. Analysis of expression levels showed that imprinted genes expressed from the non-methylated chromosome were generally up-regulated, and those expressed from the methylated chromosome were down-regulated in mutant cells. However, expression levels of several imprinted genes acquiring biallelic expression were not affected, suggesting the existence of compensatory mechanisms that control their RNA level. Since neural differentiation was partially impaired in Zfp57-mutant cells, this study also indicates that imprinted genes and/or non-imprinted ZFP57-target genes are required for proper neurogenesis in cultured ESCs.

الوصول الحر: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::04bb9c4281c514697366597f30862f67Test
https://doi.org/10.1038/s41598-021-93297-3Test