Overview

This project investigates the spatial conformation of the chromatin in the nucleus of pig muscle cells during late development.

Using High-throughput Chromosome Conformation Capture (in situ Hi-C), we identified, characterized and compared genomic interaction matrices from muscle samples at two different stages (90 and 110 days post gestation, with 3 biological replicates per stage).

Resources

Animals and samples

Information about the biological material that was used in this study is available:

  • at the EMBL-EBI BioSamples repository under the accession SAMEA7390788
  • at the FAANG data center using the accession PRJEB40576

Raw sequencing reads

Sequencing data generated by in situ Hi-C experiments are available:

  • at the EMBL-EBI European Nucleotide Archive under the accession PRJEB27455
  • at the FAANG data center using the accession PRJEB40576

Analysis results

Results from the computational data analysis are available at the INRAE Data Portail under the doi doi:10.15454/DOMEHB. This includes:

  • Hi-C interaction matrices generated by HiC-Pro from the sequencing reads for each of the 6 samples.
  • Detected TADs for each of the 6 interaction matrices using the juicer tool's arrowhead method.
  • Detected A/B genomic compartments for each of the 6 interaction matrices using the HiTC R package.

Computational tools

A code repository with documented scripts for data visualization and analysis has been made available at the INRAE Forge: pig3Dgenome. This includes:

  • list and description of the input files
  • differential analysis of the Hi-C interaction matrices
  • analysis of BODIs (Blocks Of Differential Interactions)
  • correlation analyses between number of interactions and number of either TADs or A/B compartments
  • statistical test about telomere clustering (DNA FISH 3D results)
  • visualization of Hi-C matrices

Reference

If you use this resource, please cite the following article

Marti-Marimon M, Vialaneix N, Lahbib-Mansais Y, Zytnicki M, Camut S, Robelin D, Yerle-Bouissou M and Foissac S (2021) Major Reorganization of Chromosome Conformation During Muscle Development in Pig. Front. Genet. 12:748239. doi: 10.3389/fgene.2021.748239

INRAE
French National Institute for Agricultural Research

FAANG
Functional Annotation of Animal Genomes