Profiling the Nuclear Spatial Conformation of Livestock Genomes in Cell Lines and Liver Cells

The genome conformation within the nucleus is tightly organized, yet little is known about the underlying regulatory mechanisms of this architecture. Reportedly involved factors include the linear sequence of genes, epigenetic modifications on DNA or histones, protein-genome interactions and long distance interactions between co-regulated genes. However, how and to which extent the genome conformation regulates its function remains to be explained.

As part of the FAANG consortium (Functional Annotation of Animal Genomes), the French pilot projet FR-AgENCODE aims at improving the characterization of livestock genomes by assessing gene expression and genome conformation in different animal tissues from 4 species: cattle, pig, chicken and goat. Transcriptome profiling involves sequencing of polyA+ and small (<200nt) RNAs, while genome topology is inferred from High-Throughput Chromosome Conformation Capture (Hi-C) experiments. Here we report the adaptation of the in situ Hi-C original protocol on samples from the FR-AgENCODE tissue collection, in mouse fibroblasts and pig liver cells. We also present the bioinformatics pipeline that has been used to process the data and drive the optimization of the experimental part of the protocol. Specific metrics have been proposed to be used as Quality Control references in the context of the FAANG Bioinformatics and Data Analysis sub-committee.

Preliminary results shed some light on the spatial organization of the genome in animal cells and enable the exploration of the regulatory mechanisms between chromatin structure modification and gene expression.