Filling annotation gaps in yeast genomes using genome-wide contact maps
| Autor: | Gilles Fischer, Martial Marbouty, Gianni Liti, Christophe Zimmer, Hervé Marie-Nelly, Axel Cournac, Romain Koszul |
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| Přispěvatelé: | Régulation spatiale des Génomes - Spatial Regulation of Genomes, Institut Pasteur [Paris] (IP)-Centre National de la Recherche Scientifique (CNRS), Imagerie et Modélisation, Institut de Recherche sur le Cancer et le Vieillissement (IRCAN), Université Nice Sophia Antipolis (1965 - 2019) (UNS), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université Côte d'Azur (UCA), Biologie Computationnelle et Quantitative = Laboratory of Computational and Quantitative Biology (LCQB), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Biologie Paris Seine (IBPS), Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), R.K. from the European Research Council under the 7th Framework Program (FP7/2007-2013)/ERC grant agreement (260822) and by Agence Nationale de la Recherche (ANR-09-PIRI-0024) to C.Z. and R.K. H.M-N. is supported by a fellowship from Fondation pour la Recherche Médicale (FRM). MM is the recipient of an Association pour la Recherche sur le Cancer fellowship (20100600373) and C.Z. is also supported by a FRM grant (DEQ20100318291)., ANR-09-PIRI-0024,Chromodyn(2009), European Project: 260822,EC:FP7:ERC,ERC-2010-StG_20091118,DICIG(2011), Institut Pasteur [Paris]-Centre National de la Recherche Scientifique (CNRS), Université Nice Sophia Antipolis (... - 2019) (UNS), Institut de Biologie Paris Seine (IBPS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Martin, Marie, Programme interdisciplinaire sur les systèmes biologiques et d'innovation biomédicale - - Chromodyn2009 - ANR-09-PIRI-0024 - PIRI - VALID, Dynamic Interplay between Eukaryotic Chromosomes: Impact on Genome Stability - DICIG - - EC:FP7:ERC2011-06-01 - 2017-05-31 - 260822 - VALID |
| Jazyk: | angličtina |
| Rok vydání: | 2014 |
| Předmět: |
Statistics and Probability
MESH: Molecular Sequence Annotation/methods [SDV]Life Sciences [q-bio] Centromere Computational biology Biology Origin of replication DNA Ribosomal Synteny Biochemistry Genome Chromosome conformation capture 03 medical and health sciences Annotation MESH: Genome Fungal/genetics 0302 clinical medicine Consensus Sequence Consensus sequence MESH: Consensus Sequence Molecular Biology Ribosomal DNA 030304 developmental biology MESH: DNA Ribosomal/genetics Genetics 0303 health sciences Chromosome Molecular Sequence Annotation MESH: Synteny Genomics Computer Science Applications [SDV] Life Sciences [q-bio] Computational Mathematics MESH: Genomics/methods Computational Theory and Mathematics MESH: Centromere/genetics Genetic Loci Saccharomycetales MESH: Saccharomycetales/genetics Genome Fungal 030217 neurology & neurosurgery MESH: Genetic Loci/genetics |
| Zdroj: | Bioinformatics Bioinformatics, 2014, 30 (15), pp.2105-13. ⟨10.1093/bioinformatics/btu162⟩ Bioinformatics, Oxford University Press (OUP), 2014, 30 (15), pp.2105-13. ⟨10.1093/bioinformatics/btu162⟩ |
| ISSN: | 1367-4803 1367-4811 |
| DOI: | 10.1093/bioinformatics/btu162 |
| Popis: | Motivations: De novo sequencing of genomes is followed by annotation analyses aiming at identifying functional genomic features such as genes, non-coding RNAs or regulatory sequences, taking advantage of diverse datasets. These steps sometimes fail at detecting non-coding functional sequences: for example, origins of replication, centromeres and rDNA positions have proven difficult to annotate with high confidence. Here, we demonstrate an unconventional application of Chromosome Conformation Capture (3C) technique, which typically aims at deciphering the average 3D organization of genomes, by showing how functional information about the sequence can be extracted solely from the chromosome contact map. Results: Specifically, we describe a combined experimental and bioinformatic procedure that determines the genomic positions of centromeres and ribosomal DNA clusters in yeasts, including species where classical computational approaches fail. For instance, we determined the centromere positions in Naumovozyma castellii , where these coordinates could not be obtained previously. Although computed centromere positions were characterized by conserved synteny with neighboring species, no consensus sequences could be found, suggesting that centromeric binding proteins or mechanisms have significantly diverged. We also used our approach to refine centromere positions in Kuraishia capsulata and to identify rDNA positions in Debaryomyces hansenii . Our study demonstrates how 3C data can be used to complete the functional annotation of eukaryotic genomes. Availability and implementation: The source code is provided in the Supplementary Material. This includes a zipped file with the Python code and a contact matrix of Saccharomyces cerevisiae . Contact: romain.koszul@pasteur.fr Supplementary information: Supplementary data are available at Bioinformatics online |
| Databáze: | OpenAIRE |
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