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6 results on '"Camilo Villaman"'

1. Benefiting from the intrinsic role of epigenetics to predict patterns of CTCF binding

Author

Camilo Villaman, Gianluca Pollastri, Mauricio Saez, and Alberto J.M. Martin

Subjects
CTCF, Binding Prediction, Histone Marks, Random Forests, Biotechnology, TP248.13-248.65
Abstract

Motivation: One of the most relevant mechanisms involved in the determination of chromatin structure is the formation of structural loops that are also related with the conservation of chromatin states. Many of these loops are stabilized by CCCTC-binding factor (CTCF) proteins at their base. Despite the relevance of chromatin structure and the key role of CTCF, the role of the epigenetic factors that are involved in the regulation of CTCF binding, and thus, in the formation of structural loops in the chromatin, is not thoroughly understood. Results: Here we describe a CTCF binding predictor based on Random Forest that employs different epigenetic data and genomic features. Importantly, given the ability of Random Forests to determine the relevance of features for the prediction, our approach also shows how the different types of descriptors impact the binding of CTCF, confirming previous knowledge on the relevance of chromatin accessibility and DNA methylation, but demonstrating the effect of epigenetic modifications on the activity of CTCF. We compared our approach against other predictors and found improved performance in terms of areas under PR and ROC curves (PRAUC-ROCAUC), outperforming current state-of-the-art methods.

Published
2023
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2. Early Transcriptional Changes Induced by Wnt/β-Catenin Signaling in Hippocampal Neurons

Author

Eduardo Pérez-Palma, Víctor Andrade, Mario O. Caracci, Bernabé I. Bustos, Camilo Villaman, Matías A. Medina, Miguel E. Ávila, Giorgia D. Ugarte, and Giancarlo V. De Ferrari

Subjects
Neurosciences. Biological psychiatry. Neuropsychiatry, RC321-571
Abstract

Wnt/β-catenin signaling modulates brain development and function and its deregulation underlies pathological changes occurring in neurodegenerative and neurodevelopmental disorders. Since one of the main effects of Wnt/β-catenin signaling is the modulation of target genes, in the present work we examined global transcriptional changes induced by short-term Wnt3a treatment (4 h) in primary cultures of rat hippocampal neurons. RNAseq experiments allowed the identification of 170 differentially expressed genes, including known Wnt/β-catenin target genes such as Notum, Axin2, and Lef1, as well as novel potential candidates Fam84a, Stk32a, and Itga9. Main biological processes enriched with differentially expressed genes included neural precursor (GO:0061364, p-adjusted = 2.5 × 10−7), forebrain development (GO:0030900, p-adjusted = 7.3 × 10−7), and stem cell differentiation (GO:0048863 p-adjusted = 7.3 × 10−7). Likewise, following activation of the signaling cascade, the expression of a significant number of genes with transcription factor activity (GO:0043565, p-adjusted = 4.1 × 10−6) was induced. We also studied molecular networks enriched upon Wnt3a activation and detected three highly significant expression modules involved in glycerolipid metabolic process (GO:0046486, p-adjusted = 4.5 × 10−19), learning or memory (GO:0007611, p-adjusted = 4.0 × 10−5), and neurotransmitter secretion (GO:0007269, p-adjusted = 5.3 × 10−12). Our results indicate that Wnt/β-catenin mediated transcription controls multiple biological processes related to neuronal structure and activity that are affected in synaptic dysfunction disorders.

Published
2016
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4. Automated generation of context-specific gene regulatory networks with a weighted approach in

Author

Leandro, Murgas, Sebastian, Contreras-Riquelme, J Eduardo, Martínez-Hernandez, Camilo, Villaman, Rodrigo, Santibáñez, and Alberto J M, Martin

Subjects
condition-specific networks, fungi, Cytoscape, systems biology, Articles, gene regulation, data integration, Research Articles
Abstract

The regulation of gene expression is a key factor in the development and maintenance of life in all organisms. Even so, little is known at whole genome scale for most genes and contexts. We propose a method, Tool for Weighted Epigenomic Networks in Drosophila melanogaster (Fly T-WEoN), to generate context-specific gene regulatory networks starting from a reference network that contains all known gene regulations in the fly. Unlikely regulations are removed by applying a series of knowledge-based filters. Each of these filters is implemented as an independent module that considers a type of experimental evidence, including DNA methylation, chromatin accessibility, histone modifications and gene expression. Fly T-WEoN is based on heuristic rules that reflect current knowledge on gene regulation in D. melanogaster obtained from the literature. Experimental data files can be generated with several standard procedures and used solely when and if available. Fly T-WEoN is available as a Cytoscape application that permits integration with other tools and facilitates downstream network analysis. In this work, we first demonstrate the reliability of our method to then provide a relevant application case of our tool: early development of D. melanogaster. Fly T-WEoN together with its step-by-step guide is available at https://weon.readthedocs.io.

Published
2021

5. Automated generation of context-specific Gene Regulatory Networks with a weighted approach in D. melanogaster

Author

J. Eduardo Martinez, Camilo Villaman, Sebastián Contreras-Riquelme, Alberto J. M. Martin, Rodrigo Santibáñez, and Leandro Murgas

Subjects
Regulation of gene expression, biology, Computer science, Process (engineering), Gene regulatory network, Context (language use), Computational biology, biology.organism_classification, Chromatin, Histone, Gene expression, DNA methylation, biology.protein, Melanogaster, Epigenetics, Drosophila melanogaster, Gene, Transcription factor, Epigenomics
Abstract

MotivationThe regulation of gene expression is a key factor in the development and maintenance of life in all organisms. This process is carried out mainly through the action of transcription factors (TFs), although other actors such as ncRNAs are involved. In this work, we propose a new method to construct Gene Regulatory Networks (GRNs) depicting regulatory events in a certain context for Drosophila melanogaster. Our approach is based on known relationships between epigenetics and the activity of transcription factors.ResultsWe developed method, Tool for Weighted Epigenomic Networks in D. melanogaster (Fly T-WEoN), which generates GRNs starting from a reference network that contains all known gene regulations in the fly. Regulations that are unlikely taking place are removed by applying a series of knowledge-based filters. Each of these filters is implemented as an independent module that considers a type of experimental evidence, including DNA methylation, chromatin accessibility, histone modifications, and gene expression. Fly T-WEoN is based on heuristic rules that reflect current knowledge on gene regulation in D. melanogaster obtained from literature. Experimental data files can be generated with several standard procedures and used solely when and if available.Fly T-WEoN is available as a Cytoscape application that permits integration with other tools, and facilitates downstream network analysis. In this work, we first demonstrate the reliability of our method to then provide a relevant application case of our tool: early development of D. melanogaster.AvailabilityFly T-WEoN, together with its step-by-step guide is available at https://weon.readthedocs.ioContactalberto.martin@umayor.cl

Published
2020

6. Automated generation of context-specific gene regulatory networks with a weighted approach in Drosophila melanogaster

Author

Sebastián Contreras-Riquelme, Alberto J. M. Martin, J. Eduardo Martinez-Hernandez, Camilo Villaman, Rodrigo Santibáñez, and Leandro Murgas

Subjects
Regulation of gene expression, 0303 health sciences, biology, Computer science, Systems biology, Biomedical Engineering, Biophysics, Gene regulatory network, Bioengineering, Computational biology, biology.organism_classification, Biochemistry, Chromatin, Biomaterials, 03 medical and health sciences, 0302 clinical medicine, Melanogaster, Drosophila melanogaster, Gene, 030217 neurology & neurosurgery, 030304 developmental biology, Biotechnology, Epigenomics
Abstract

The regulation of gene expression is a key factor in the development and maintenance of life in all organisms. Even so, little is known at whole genome scale for most genes and contexts. We propose a method, Tool for Weighted Epigenomic Networks in Drosophila melanogaster (Fly T-WEoN), to generate context-specific gene regulatory networks starting from a reference network that contains all known gene regulations in the fly. Unlikely regulations are removed by applying a series of knowledge-based filters. Each of these filters is implemented as an independent module that considers a type of experimental evidence, including DNA methylation, chromatin accessibility, histone modifications and gene expression. Fly T-WEoN is based on heuristic rules that reflect current knowledge on gene regulation in D. melanogaster obtained from the literature. Experimental data files can be generated with several standard procedures and used solely when and if available. Fly T-WEoN is available as a Cytoscape application that permits integration with other tools and facilitates downstream network analysis. In this work, we first demonstrate the reliability of our method to then provide a relevant application case of our tool: early development of D. melanogaster . Fly T-WEoN together with its step-by-step guide is available at https://weon.readthedocs.io .

Published
2021

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