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Structural features of the fly chromatin colors revealed by automatic three-dimensional modeling

François Serra, Davide Baù, View ORCID ProfileGuillaume Filion, View ORCID ProfileMarc A. Marti-Renom
doi: https://doi.org/10.1101/036764
François Serra
1CNAG-CRG, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003 Barcelona, Spain.
2Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003 Barcelona, Spain
3Universitat Pompeu Fabra (UPF), Barcelona, Spain.
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Davide Baù
1CNAG-CRG, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003 Barcelona, Spain.
2Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003 Barcelona, Spain
3Universitat Pompeu Fabra (UPF), Barcelona, Spain.
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Guillaume Filion
2Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003 Barcelona, Spain
3Universitat Pompeu Fabra (UPF), Barcelona, Spain.
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  • ORCID record for Guillaume Filion
  • For correspondence: martirenom@cnag.crg.eu guillaume.filion@crg.eu
Marc A. Marti-Renom
1CNAG-CRG, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003 Barcelona, Spain.
2Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003 Barcelona, Spain
3Universitat Pompeu Fabra (UPF), Barcelona, Spain.
4Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona. Spain
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  • ORCID record for Marc A. Marti-Renom
  • For correspondence: martirenom@cnag.crg.eu guillaume.filion@crg.eu
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Abstract

Background The sequence of a genome is insufficient to understand all genomic processes carried out in the cell nucleus. To achieve this, the knowledge of its threedimensional architecture is necessary. Advances in genomic technologies and the development of new analytical methods, such as Chromosome Conformation Capture (3C) and its derivatives, provide unprecedented insights on the spatial organization of genomes. However, inferring structures from raw contact data is a tedious process for shortage of available tools.

Results Here we present TADbit, a computational framework to analyze and model the chromatin fiber in three dimensions. To illustrate the use of TADbit, we automatically modeled 50 genomic domains from the fly genome revealing differential structural features of the previously defined chromatin colors, establishing a link between the conformation of the genome and the local chromatin composition.

Conclusions TADbit provides three-dimensional built from 3C-based experiments, which are ready for visualization and for characterizing their relation to gene expression and epigenetic states. TADbit is open-source and available for download from http://www.3DGenomes.org.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
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Posted January 15, 2016.
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Structural features of the fly chromatin colors revealed by automatic three-dimensional modeling
François Serra, Davide Baù, Guillaume Filion, Marc A. Marti-Renom
bioRxiv 036764; doi: https://doi.org/10.1101/036764
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Structural features of the fly chromatin colors revealed by automatic three-dimensional modeling
François Serra, Davide Baù, Guillaume Filion, Marc A. Marti-Renom
bioRxiv 036764; doi: https://doi.org/10.1101/036764

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