Mapa global de la regulación de factores de transcripción tipo MADS-BOX en frutilla silvestre (Fragaria vesca).

90 p.Las interacciones entre proteínas y DNA son particularmente conservadas a lo largo de la evolución. El estudio de estas redes de interacción pueden dar pie al entendimiento de cómo se regulan los principales procesos celulares. Los factores de transcripción tipo MADS-BOX han sido descritos como reguladores maestros del desarrollo de flores y su arquitectura en angiospermas. Algunos de sus miembros como: APETALLA, AGAMOUS, FLOWERING LOCUS y, los pertenecientes a la subfamilia SEPALLATA entre otros, presentes en tomate, manzana y frutilla comercial; juegan un rol clave en los procesos de maduración del fruto.Fragaria vesca, cuyo genoma ha sido recientemente secuenciado y a diferencia de otras especies de este género, como la mencionada frutilla comercial (Fragaria x ananassa) y la frutilla chilena (Fragaria chiloensis), las cuales son altamente complejas a nivel genético, es una especie diploide lo que facilita su uso como modelo de estudio a nivel genético y fisiológico. El objetivo de esta investigación, es determinar los posibles genes regulados transcripcionalmente por los factores tipo MADS-BOX en Fragaria vesca, estableciendo la presencia y densidad de su correspondiente sitio de unión (CArG-BOX) dentro de las secuencias de 2Kb río arriba de cada uno de los 24.000 genes anotados en este genoma. Esto se realizó mediante la utilización de la suite para el descubrimiento y búsqueda de patrones MEME. Los resultados basados en los nueve miembros de la familia MADS-Box analizados, muestran un total de 5.828 regiones promotoras con presencia de sitios de respuesta afines, que se distribuyen de manera uniforme a lo largo de la región promotora a través de 64 secuencias de unión no siempre específicas para cada factor de transcripción. Dicha inespecificidad concuerda con el mecanismo de unión al DNA a través de multímeros, propio de esta familia. Los genes putativamente regulados por MADS-Box determinados en la presente investigación participan principalmente en procesos metabólicos con actividad catalítica o de unión, aunque se destacan 90 genes clasificados funcionalmente relacionados a desarrollo y 22 con rol de factores de transcripción. Se encontraron tres enzimas que regulan el inicio de las cascadas metabólicas en la síntesis de antocianinas y fenilpropanoides. Así como otras que participan en la degradación de aminoácidos esenciales como valina, leucina e isoleucina. Dado los presentes resultados, se revela la importancia de la regulación de los factores de transcripción en dichos procesos metabólicos, los cuales tienen un rol directo en el cómo los frutos ejecutan los procesos que determinan su color (o la falta de este) durante su periodo de maduración. Se proyecta, la validación experimental de los elementos de unión predichos a través de modelos estructurales e interacción DNA-Proteína in silico. Esta validación sería el punto de partida para comprobar que dichos elementos en regulatorios, son funcionales y responsables de que factores de transcripción de la familia MADS-box regulen efectivamente dichos genes blancos. /ABSTYRACT: Interactions between proteins and DNA are particularly conserved throughout evolution. The study of these interaction networks can unravel the key cellular processesThe MADS-box transcription factors have been described as master regulators of flower development in angiosperms and in its architecture, in which some of its members as APETALLA, AGAMOUS, FLOWERING LOCUS and, according to the results found in tomato, apple and commercial strawberry, those belonging to the subfamily SEPALLATA, among others, play a key role in the process of fruit ripening. Fragaria vesca, whose genome has recently been sequenced and, unlike other species of this genus as the mentioned commercial strawberry (Fragaria ananassa) and the Chilean strawberry (Fragaria chiloensis), it is a diploid species which facilitates its use as a model organism in genetics and at a physiological level.The objective of this research is to identify potential genes transcriptionally regulated by MADS-box transcription factors in Fragaria vesca, establishing the presence and density of its corresponding binding site, called CArG-box within 2Kb upstream sequences of each one of the 24,000 annotated genes in this genome. This was done using the suite for search and discovery of patterns MEME.The results based on the nine types of MADS-Box analyzed, which were defined based on information present in the current literature, shows a total of 5828 promoter regions with presence of at least one related response site, which are distributed uniformly along promoter regions through 64 specific sequences that are not always specific (shared) for each transcription factor, which matches with the DNA binding mechanism through self-multimers, common on this family.The genes putatively regulated by MADS-Box identified in this research are mainly involved in metabolic processes as binding or catalytic activity, although we also found 90 genes functionally related to development and 22 as transcription factors. Interestingly three enzymes which regulate the start of the metabolic cascade in anthocyanin and phenylpropanoid synthesis has been also found, as well as part of the breakdown of essential amino acids such as valine, leucine and isoleucine. Given these results, it’s clear the importance of regulation of transcription factors in these metabolic processes, which have a direct role in how fruits acquire its color during the ripening period.As further work, it will be necessary to structurally model the binding sites candidates in order to measure the affinity of DNA-protein interaction to determine their viability and establish a starting point for the experimental validation of the best candidates here described

WebCEMiTool: Co-expression modular analysis made easy

Co-expression analysis has been widely used to elucidate the functional architecture of genes under different biological processes. Such analysis, however, requires substantial knowledge about programming languages and/or bioinformatics skills. We present webCEMiTool,1 a unique online tool that performs comprehensive modular analyses in a fully automated manner. The webCEMiTool not only identifies co-expression gene modules but also performs several functional analyses on them. In addition, webCEMiTool integrates transcriptomic data with interactome information (i.e., protein-protein interactions) and identifies potential hubs on each network. The tool generates user-friendly html reports that allow users to search for specific genes in each module, as well as check if a module contains genes overrepresented in specific pathways or altered in a specific sample phenotype. We used webCEMiTool to perform a modular analysis of single-cell RNA-seq data of human cells infected with either Zika virus or dengue virus

Long non-coding RNAs responsive to salt and boron stress in the hyper-arid lluteño maize from atacama desert

© 2018 by the authors. Licensee MDPI, Basel, Switzerland. Long non-coding RNAs (lncRNAs) have been defined as transcripts longer than 200 nucleotides, which lack significant protein coding potential and possess critical roles in diverse cellular processes. Long non-coding RNAs have recently been functionally characterized in plant stress–response mechanisms. In the present study, we perform a comprehensive identification of lncRNAs in response to combined stress induced by salinity and excess of boron in the Lluteño maize, a tolerant maize landrace from Atacama Desert, Chile. We use deep RNA sequencing to identify a set of 48,345 different lncRNAs, of which 28,012 (58.1%) are conserved with other maize (B73, Mo17 or Palomero), with the remaining 41.9% belonging to potentially Lluteño exclusive lncRNA transcripts. According to B73 maize reference genome sequence, most Lluteño lncRNAs correspond to intergenic transcripts. Interestingly, Lluteño lncRNAs presents an unusual overall highe

ADAR1-mediated RNA-editing of 3'UTRs in breast cancer

RESULTS: We characterized A to G(I) mRNA editing in 81 breast cell lines, showing increased editing at 3'UTR and exonic regions in breast cancer cells compared to immortalized non-malignant cell lines. In addition, tumors from the BRCA TCGA cohort show a 24% increase in editing over normal breast samples when looking at 571 well-characterized UTRs targeted by ADAR1. Basal-like subtype breast cancer patients with high level of ADAR1 mRNA expression shows a worse clinical outcome and increased editing in their 3'UTRs. Interestingly, editing was particularly increased in the 3'UTRs of ATM, GINS4 and POLH transcripts in tumors, which correlated with their mRNA expression. We confirmed the role of ADAR1 in this regulation using a shRNA in a breast cancer cell line (ZR-75-1).CONCLUSIONS: Altogether, these results revealed a significant association between the mRNA editing in genes related to cancer-relevant pathways and clinical outcomes, suggesting an important role of ADAR1 expression an

High proportion of potential candidates for immunotherapy in a Chilean cohort of gastric cancer patients: results of the FORCE1 study

Gastric cancer (GC) is a heterogeneous disease. This heterogeneity applies not only to morphological and phenotypic features but also to geographical variations in incidence and mortality rates. As Chile has one of the highest mortality rates within South America, we sought to define a molecular profile of Chilean GCs (ClinicalTrials.gov identifier: NCT03158571/(FORCE1)). Solid tumor samples and clinical data were obtained from 224 patients, with subsets analyzed by tissue microarray (TMA; n = 90) and next generation sequencing (NGS; n = 101). Most demographic and clinical data were in line with previous reports. TMA data indicated that 60% of patients displayed potentially actionable alterations. Furthermore, 20.5% were categorized as having a high tumor mutational burden, and 13% possessed micro-satellite instability (MSI). Results also confirmed previous studies reporting high Epstein-Barr virus (EBV) positivity (13%) in Chilean-derived GC samples suggesting a high proportion of patients could benefit from immunotherapy. As expected, TP53 and PIK3CA were the most frequently altered genes. However, NGS demonstrated the presence of TP53, NRAS, and BRAF variants previously unreported in current GC databases. Finally, using the Kendall method, we report a significant correlation between EBV+ status and programmed death ligand-1 (PDL1)+ and an inverse correlation between p53 mutational status and MSI. Our results suggest that in this Chilean cohort, a high proportion of patients are potential candidates for immunotherapy treatment. To the best of our knowledge, this study is the first in South America to assess the prevalence of actionable targets and to examine a molecular profile of GC patients