Higher-Order Inter-chromosomal Hubs Shape 3D Genome Organization in the Nucleus

• Sofia A. Quinodoz ^[1] ; Noah Ollikainen ^[1] ; Barbara Tabak ^[2]
  1. [1] California Institute of Technology

     California Institute of Technology

     Estados Unidos

     
  2. [2] University of Massachusetts Medical School

     University of Massachusetts Medical School

     City of Worcester, Estados Unidos

     
• Localización: Cell, ISSN 0092-8674, Vol. 174, Nº. 3, 2018, págs. 744-757
• Idioma: inglés
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• Resumen

  • Eukaryotic genomes are packaged into a 3-dimensional structure in the nucleus. Current methods for studying genome-wide structure are based on proximity ligation. However, this approach can fail to detect known structures, such as interactions with nuclear bodies, because these DNA regions can be too far apart to directly ligate. Accordingly, our overall understanding of genome organization remains incomplete. Here, we develop split-pool recognition of interactions by tag extension (SPRITE), a method that enables genome-wide detection of higher-order interactions within the nucleus. Using SPRITE, we recapitulate known structures identified by proximity ligation and identify additional interactions occurring across larger distances, including two hubs of inter-chromosomal interactions that are arranged around the nucleolus and nuclear speckles. We show that a substantial fraction of the genome exhibits preferential organization relative to these nuclear bodies. Our results generate a global model whereby nuclear bodies act as inter-chromosomal hubs that shape the overall packaging of DNA in the nucleus.