A new approach of gene co-expression network inference reveals significant biological processes involved in porcine muscle development in late gestation.

TitleA new approach of gene co-expression network inference reveals significant biological processes involved in porcine muscle development in late gestation.
Publication TypeJournal Article
Year of Publication2018
AuthorsMarti-Marimon, M, Vialaneix, N, Voillet, V, Yerle-Bouissou, M, Lahbib-Mansais, Y, Liaubet, L
JournalSci Rep
Volume8
Issue1
Pagination10150
Date Published2018 Jul 05
ISSN2045-2322
Abstract

The integration of genetic information in the cellular and nuclear environments is crucial for deciphering the way in which the genome functions under different physiological conditions. Experimental techniques of 3D nuclear mapping, a high-flow approach such as transcriptomic data analyses, and statistical methods for the development of co-expressed gene networks, can be combined to develop an integrated approach for depicting the regulation of gene expression. Our work focused more specifically on the mechanisms involved in the transcriptional regulation of genes expressed in muscle during late foetal development in pig. The data generated by a transcriptomic analysis carried out on muscle of foetuses from two extreme genetic lines for birth mortality are used to construct networks of differentially expressed and co-regulated genes. We developed an innovative co-expression networking approach coupling, by means of an iterative process, a new statistical method for graph inference with data of gene spatial co-localization (3D DNA FISH) to construct a robust network grouping co-expressed genes. This enabled us to highlight relevant biological processes related to foetal muscle maturity and to discover unexpected gene associations between IGF2, MYH3 and DLK1/MEG3 in the nuclear space, genes that are up-regulated at this stage of muscle development.

DOI10.1038/s41598-018-28173-8
Alternate JournalSci Rep
PubMed ID29977047
PubMed Central IDPMC6033925
Grant ListANR-09-GENM005 / / Agence Nationale de la Recherche (French National Research Agency) /