Infinity: An In-Silico Tool for Genome-Wide Prediction of Specific DNA Matrices in miRNA Genomic Loci

Abstract

MotivationmiRNAs are potent regulators of gene expression and modulate multiple cellular processes in physiology and pathology. Deregulation of miRNAs expression has been found in various cancer types, thus, miRNAs may be potential targets for cancer therapy. However, the mechanisms through which miRNAs are regulated in cancer remain unclear. Therefore, the identification of transcriptional factor–miRNA crosstalk is one of the most update aspects of the study of miRNAs regulation.ResultsIn the present study we describe the development of a fast and user-friendly software, named infinity, able to find the presence of DNA matrices, such as binding sequences for transcriptional factors, on ~65kb (kilobase) of 939 human miRNA genomic sequences, simultaneously. Of note, the power of this software has been validated in vivo by performing chromatin immunoprecipitation assays on a subset of new in silico identified target sequences (CCAAT) for the transcription factor NF-Y on colon cancer deregulated miRNA loci. Moreover, for the first time, we have demonstrated that NF-Y, through its CCAAT binding activity, regulates the expression of miRNA-181a, -181b, -21, -17, -130b, -301b in colon cancer cells.ConclusionsThe infinity software that we have developed is a powerful tool to underscore new TF/miRNA regulatory networks.Availability and ImplementationInfinity was implemented in pure Java using Eclipse framework, and runs on Linux and MS Windows machine, with MySQL database. The software is freely available on the web at https://github.com/bio-devel/infinity. The website is implemented in JavaScript, PHP and HTML with all major browsers supported.

Genome-Wide Association Study Reveals Genetic Architecture and Candidate Genes for Yield and Related Traits under Terminal Drought, Combined Heat and Drought in Tropical Maize Germplasm

“…With availability of reference genomes and user-friendly bioinformatics tools for in-silico prediction, further downstream analyses have become feasible in recent years [ 65 ]. Candidate genes are of relevance for functional validation to unearth the regulatory mechanisms underlying each trait of interest.…”

Designing and Expression of Recombinant Chimeric Spike Protein from SARS-CoV-2 in Escherichia coli and Its Immunogenicity Assessment

“…Chimer protein was further evaluated regarding antigenicity, allergenicity, toxicity, and solubility using bioinformatics tools in Table 1 . To facilitate the cloning and expression of the proposed candidate vaccine in a suitable expression vector, the amino acid sequence of the vaccine model was back-translated into nucleotide sequences using the Gene Infinity server based on the codon usage table of E. coli ( 27 ). The resulting DNA sequence was then optimized by assessing its GC content, codon adaptation index (CAI), and codon frequency distribution (CFD) using the GenScript Tool ( 20 ).…”

Methods of MicroRNA Promoter Prediction and Transcription Factor Mediated Regulatory Network

“…Thus, Falcone et al developed a software, named infinity, to reveal new regulatory networks of TFs and miRNAs [35]. They collected TSS positions from miRStart and extracted the promoter region sequences of miRNAs from UCSC Genome Browser.…”

“…The previous related studies just provided limited regulatory network of TFs on miRNAs, which restricted the identification of novel TF-miRNA networks. Thus, Falcone et al developed a software, named infinity, to reveal new regulatory networks of TFs and miRNAs [ 35 ]. They collected TSS positions from miRStart and extracted the promoter region sequences of miRNAs from UCSC Genome Browser.…”