title: Integrating multi-omic features exploiting Chromosome Conformation Capture data.
abstract: The representation, integration, and interpretation of omic data is a complex task, in particular considering the huge amount of information that is daily produced in molecular biology laboratories all around the world. The reason is that sequencing data regarding expression profiles, methylation patterns, and chromatin domains is difficult to harmonize in a systems biology view, since genome browsers only allow coordinate-based representations, discarding functional clusters created by the spatial conformation of the DNA in the nucleus. In this context, recent progresses in high throughput molecular biology techniques and bioinformatics have provided insights into chromatin interactions on a larger scale and offer a formidable support for the interpretation of multi-omic data. In particular, a novel sequencing technique called Chromosome Conformation Capture allows the analysis of the chromosome organization in the cell's natural state. While performed genome wide, this technique is usually called Hi-C. Inspired by service applications such as Google Maps, we developed NuChart, an R package that integrates Hi-C data to describe the chromosomal neighborhood starting from the information about gene positions, with the possibility of mapping on the achieved graphs genomic features such as methylation patterns and histone modifications, along with expression profiles. In this paper we show the importance of the NuChart application for the integration of multi-omic data in a systems biology fashion, with particular interest in cytogenetic applications of these techniques. Moreover, we demonstrate how the integration of multi-omic data can provide useful information in understanding why genes are in certain specific positions inside the nucleus and how epigenetic patterns correlate with their expression.
authors.affiliation: Bioinformatics Unit, Institute of Biomedical Technologies, Italian National Research Council Milan, Italy.
authors.forename: Ivan
authors.initials: I
authors.lastname: Merelli
authors.affiliation: Computer Science Department, University of Torino Torino, Italy.
authors.forename: Fabio
authors.initials: F
authors.lastname: Tordini
authors.affiliation: Computer Science Department, University of Torino Torino, Italy.
authors.forename: Maurizio
authors.initials: M
authors.lastname: Drocco
authors.affiliation: Computer Science Department, University of Torino Torino, Italy.
authors.forename: Marco
authors.initials: M
authors.lastname: Aldinucci
authors.affiliation: Computer Laboratory, University of Cambridge Cambridge, UK.
authors.forename: Pietro
authors.initials: P
authors.lastname: Liò
authors.affiliation: Bioinformatics Unit, Institute of Biomedical Technologies, Italian National Research Council Milan, Italy.
authors.forename: Luciano
authors.initials: L
authors.lastname: Milanesi
keywords: Chromosome Conformation Capture; chromatin spatial organization; gene neighborhood map; linking gene regulatory elements; multi-omic data integration