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

<div><p>Motivation</p><p>miRNAs 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.</p><p>Results</p><p>In the present study we describe the development of a fast and user-friendly software, named <i>infinity</i>, 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 <i>in vivo</i> by performing chromatin immunoprecipitation assays on a subset of new <i>in silico</i> 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.</p><p>Conclusions</p><p>The <i>infinity</i> software that we have developed is a powerful tool to underscore new TF/miRNA regulatory networks.</p><p>Availability and Implementation</p><p><i>Infinity</i> 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 <a href="https://github.com/bio-devel/infinity" target="_blank">https://github.com/bio-devel/infinity</a>. The website is implemented in JavaScript, PHP and HTML with all major browsers supported.</p></div

Results of the <i>in silico</i> analysis of 1 kb of promoter (-0,5kb,+ 0,5kb from TSS) of the 4 miRNA clusters validated by <i>in vivo</i> experiments.

<p>Results of the <i>in silico</i> analysis of 1 kb of promoter (-0,5kb,+ 0,5kb from TSS) of the 4 miRNA clusters validated by <i>in vivo</i> experiments.</p

Frequency of CCAAT matrices among miRNA loci.

<p>Frequency of CCAAT matrices, found by <i>infinity</i>, (A) on 939 miRNA loci between -60kb to 5kb respect pre-miRNA; (B) on 740 miRNA loci between -6kb to 2kb respect TSS. Distribution of CCAAT matrices position, found by <i>infinity</i>, (C) on 740 miRNA loci between -6kb to 2kb respect TSS; (D) on 463 miRNA loci between -0,5kb to 0,5kb respect TSS; (E) on 936 miRNA loci between -3kb to 5kb respect pre-miRNA. (F) Frequency of CCAAT matrices, found by <i>infinity</i> on 936 miRNA loci between -3kb to 5kb respect pre-miRNA.</p

Results of the <i>in silico</i> analysis of 5 kb downstream the 3’of the 6 pre-miRNA validated by <i>in vivo</i> experiments.

<p>Results of the <i>in silico</i> analysis of 5 kb downstream the 3’of the 6 pre-miRNA validated by <i>in vivo</i> experiments.</p

NF-Y binds <i>in vivo</i> the CCAAT-matrices on miRNAs loci.

<p>ChIPs performed on SW480 cells using the indicated antibodies. PCR were performed using specific primers for the immunoprecipitated DNA fragments (on promoter regions and downstream of 3’UTR regions) containing the indicated CCAAT-matrices found with <i>infinity</i>. Only CCAAT visualized by ChIP are indicated.</p

Comparison of used string matching algorithms shows the difference of elaboration time.

<p>A stream text of 65kb with 4 symbol alphabet has been processed by searching algorithm: Boyer-Moore, Brute Force, Matlab and the two algorithms provided by java, JVMfind and JVMindexOf. The pattern matrix is a 8-length characters of the same alphabet but has no match purposely. This test has been elaborated by a Sony Vaio (CPU Intel Pentium 1.10 GHz, RAM 1GB) 10,000 times to obtain the average elapsed time.</p

118 miRNA up-regulated on colorectal cancer patients.

<p>Representation of a meta-analysis on PubMed database to collect articles that investigated the aberrant miRNA gene expression patterns in colorectal samples from colorectal cancer patients. This search retrieved 118 up-regulated miRNAs in colon cancer.</p