Análisis in silico de genes diana de miRNAs posiblemente inducidos por la infección con tuberculosis  <span class="so-article-trans-title" dir="auto"> Translated title: In silico analysis of miRNA target genes possibly induced by tuberculosis infection </span>

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Abstract

Resumen El objetivo fue identificar mediante análisis in silico los genes a los cuales se unen los miR-146a, miR-146b y miR-155 y, analizar las rutas metabólicas en las que intervienen durante la infección con tuberculosis. Para el análisis se utilizó: miRBase, UniProtKB, TargetScan Human, miRDB y miRTarBase. El miR-146a interacciona o se une a genes importantes en la adhesión celular y el proceso de fagocitosis (CLDN16 y ATP6V1C2, respectivamente) (P, 0.05), esta interacción podría tener implicaciones importantes en la patogénesis de la tuberculosis o enfermedades relacionadas. Los resultados de este trabajo sugieren que la activación de mecanismos moleculares específicos en respuesta a la tuberculosis está regulada por los miR-146a, miR-146b y miR-155. Los genes con los cuales los miR-146a y miR-155 interaccionan o se unen, están involucrados en la respuesta inmune y en procesos celulares imprescindibles durante una infección por tuberculosis.

Translated abstract

Abstract The objective was to identify, through in silico analysis, the genes to which miR-146a, miR-146b, and miR-155 bind and to analyze the metabolic pathways in which they participate during tuberculosis infection. For the analysis, it was used: miRBase, UniProtKB, TargetScan Human, miRDB, and miRTarBase. miR-146a interacts with or binds to genes important in cell adhesion and the process of phagocytosis (CLDN16 and ATP6V1C2, respectively) (P< 0.05); this interaction could have important implications in the pathogenesis of tuberculosis or related diseases. The results of this work suggest that the activation of specific molecular mechanisms in response to tuberculosis is regulated by miR-146a, miR-146b, and miR-155. The genes with which miR-146a and miR-155 interact or bind are involved in the immune response and cellular processes essential during tuberculosis infection.

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Predicting effective microRNA target sites in mammalian mRNAs

Vikram Agarwal, George Bell, Jin-Wu Nam … (2015)

MicroRNA targets are often recognized through pairing between the miRNA seed region and complementary sites within target mRNAs, but not all of these canonical sites are equally effective, and both computational and in vivo UV-crosslinking approaches suggest that many mRNAs are targeted through non-canonical interactions. Here, we show that recently reported non-canonical sites do not mediate repression despite binding the miRNA, which indicates that the vast majority of functional sites are canonical. Accordingly, we developed an improved quantitative model of canonical targeting, using a compendium of experimental datasets that we pre-processed to minimize confounding biases. This model, which considers site type and another 14 features to predict the most effectively targeted mRNAs, performed significantly better than existing models and was as informative as the best high-throughput in vivo crosslinking approaches. It drives the latest version of TargetScan (v7.0; targetscan.org), thereby providing a valuable resource for placing miRNAs into gene-regulatory networks. DOI: http://dx.doi.org/10.7554/eLife.05005.001

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Database resources of the national center for biotechnology information

Eric Sayers, Evan E Bolton, J. Rodney Brister … (2022)

The National Center for Biotechnology Information (NCBI) produces a variety of online information resources for biology, including the GenBank® nucleic acid sequence database and the PubMed® database of citations and abstracts published in life science journals. NCBI provides search and retrieval operations for most of these data from 35 distinct databases. The E-utilities serve as the programming interface for the most of these databases. Resources receiving significant updates in the past year include PubMed, PMC, Bookshelf, RefSeq, SRA, Virus, dbSNP, dbVar, ClinicalTrials.gov, MMDB, iCn3D and PubChem. These resources can be accessed through the NCBI home page at https://www.ncbi.nlm.nih.gov.

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miRDB: a microRNA target prediction and functional annotation database with a wiki interface.

Xiaowei Wang (2008)

MicroRNAs (miRNAs) are short noncoding RNAs that are involved in the regulation of thousands of gene targets. Recent studies indicate that miRNAs are likely to be master regulators of many important biological processes. Due to their functional importance, miRNAs are under intense study at present, and many studies have been published in recent years on miRNA functional characterization. The rapid accumulation of miRNA knowledge makes it challenging to properly organize and present miRNA function data. Although several miRNA functional databases have been developed recently, this remains a major bioinformatics challenge to miRNA research community. Here, we describe a new online database system, miRDB, on miRNA target prediction and functional annotation. Flexible web search interface was developed for the retrieval of target prediction results, which were generated with a new bioinformatics algorithm we developed recently. Unlike most other miRNA databases, miRNA functional annotations in miRDB are presented with a primary focus on mature miRNAs, which are the functional carriers of miRNA-mediated gene expression regulation. In addition, a wiki editing interface was established to allow anyone with Internet access to make contributions on miRNA functional annotation. This is a new attempt to develop an interactive community-annotated miRNA functional catalog. All data stored in miRDB are freely accessible at http://mirdb.org.

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Journal

Journal ID (publisher-id): rmcp

Title: Revista mexicana de ciencias pecuarias

Abbreviated Title: Rev. mex. de cienc. pecuarias

Publisher: Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias (Mérida, Yucatán, Mexico )

ISSN (Print): 2007-1124

ISSN (Electronic): 2448-6698

Publication date (Print and electronic): March 2024

Volume: 15

Issue: 1

Pages: 192-207

Affiliations

[3] orgnameUniversidad Autónoma de Querétaro Mexico

[2] orgnameUniversidad Autónoma de la Ciudad de México Mexico

[1] Querétaro orgnameInstituto Nacional de Investigaciones Forestales Agrícolas y Pecuarias orgdiv1Centro Nacional de Investigación Disciplinaria en Fisiología y Mejoramiento Animal México

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Publisher ID: S2007-11242024000100192 Publisher ID: S2007-1124(24)01500100192

DOI: 10.22319/rmcp.v15i1.6463

SO-VID: 0f50dee6-7b3f-4974-b412-d133ab716860

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This work is licensed under a Creative Commons Attribution-NonCommercial 4.0 International License.

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Date accepted : 19 October 2023

Date received : 14 May 2023

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Figures: 0, Tables: 0, Equations: 0, References: 47, Pages: 16

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Análisis in silico de genes diana de miRNAs posiblemente inducidos por la infección con tuberculosis Translated title: In silico analysis of miRNA target genes possibly induced by tuberculosis infection

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Most cited references 47

Predicting effective microRNA target sites in mammalian mRNAs

Database resources of the national center for biotechnology information

miRDB: a microRNA target prediction and functional annotation database with a wiki interface.

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