title: Multi-scale structural community organisation of the human genome.
abstract: BACKGROUND
  Structural interaction frequency matrices between all genome loci are now experimentally achievable thanks to high-throughput chromosome conformation capture technologies. This ensues a new methodological challenge for computational biology which consists in objectively extracting from these data the structural motifs characteristic of genome organisation.
  
  
  RESULTS
  We deployed the fast multi-scale community mining algorithm based on spectral graph wavelets to characterise the networks of intra-chromosomal interactions in human cell lines. We observed that there exist structural domains of all sizes up to chromosome length and demonstrated that the set of structural communities forms a hierarchy of chromosome segments. Hence, at all scales, chromosome folding predominantly involves interactions between neighbouring sites rather than the formation of links between distant loci.
  
  
  CONCLUSIONS
  Multi-scale structural decomposition of human chromosomes provides an original framework to question structural organisation and its relationship to functional regulation across the scales. By construction the proposed methodology is independent of the precise assembly of the reference genome and is thus directly applicable to genomes whose assembly is not fully determined.
authors.affiliation: Univ Lyon, Ens de Lyon, Univ Claude Bernard Lyon 1, CNRS, Laboratoire de Physique, F-69342, Lyon, France.|Present address: Montpellier Cancer Institute (ICM), Montpellier Cancer Research Institute (IRCM) Inserm U1194, University of Montpellier, Montpellier, France.
authors.forename: Rasha E
authors.initials: RE
authors.lastname: Boulos
authors.affiliation: Univ Lyon, Ens de Lyon, Univ Claude Bernard Lyon 1, CNRS, Laboratoire de Physique, F-69342, Lyon, France.|Present address: CNRS, GIPSA-lab, Grenoble, France.
authors.forename: Nicolas
authors.initials: N
authors.lastname: Tremblay
authors.affiliation: Univ Lyon, Ens de Lyon, Univ Claude Bernard Lyon 1, CNRS, Laboratoire de Physique, F-69342, Lyon, France.|Present address: LOMA, Université de Bordeaux, CNRS, UMR 5798, 51 Cours de le Libération, Talence, 33405, France.
authors.forename: Alain
authors.initials: A
authors.lastname: Arneodo
authors.affiliation: Univ Lyon, Ens de Lyon, Univ Claude Bernard Lyon 1, CNRS, Laboratoire de Physique, F-69342, Lyon, France.
authors.forename: Pierre
authors.initials: P
authors.lastname: Borgnat
authors.affiliation: Univ Lyon, Ens de Lyon, Univ Claude Bernard Lyon 1, CNRS, Laboratoire de Physique, F-69342, Lyon, France. benjamin.audit@ens-lyon.fr.
authors.forename: Benjamin
authors.initials: B
authors.lastname: Audit
mesh_terms: D000465:Algorithms; D002843:Chromatin / Q000648:ultrastructure*; D002877:Chromosomes, Human / Q000648:ultrastructure*; D019295:Computational Biology / Q000379:methods*; D015894:Genome, Human; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D017422:Sequence Analysis, DNA
chemical_list: D002843:Chromatin
keywords: Chromosome interaction network; Human genome; Multi-scale community mining; Spectral graph wavelets; Structural domain hierarchical organisation