Identification of Gene Positioning Factors Using High-Throughput Imaging Mapping

Cell. 2015 Aug 13;162(4):911-23. doi: 10.1016/j.cell.2015.07.035.


Genomes are arranged non-randomly in the 3D space of the cell nucleus. Here, we have developed HIPMap, a high-precision, high-throughput, automated fluorescent in situ hybridization imaging pipeline, for mapping of the spatial location of genome regions at large scale. High-throughput imaging position mapping (HIPMap) enabled an unbiased siRNA screen for factors involved in genome organization in human cells. We identify 50 cellular factors required for proper positioning of a set of functionally diverse genomic loci. Positioning factors include chromatin remodelers, histone modifiers, and nuclear envelope and pore proteins. Components of the replication and post-replication chromatin re-assembly machinery are prominently represented among positioning factors, and timely progression of cells through replication, but not mitosis, is required for correct gene positioning. Our results establish a method for the large-scale mapping of genome locations and have led to the identification of a compendium of cellular factors involved in spatial genome organization.

Publication types

  • Research Support, N.I.H., Intramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Cell Line
  • Cell Nucleus / genetics*
  • DNA Replication
  • Genes*
  • Genetic Techniques*
  • Humans
  • Image Processing, Computer-Assisted / methods
  • In Situ Hybridization, Fluorescence / methods
  • Single-Cell Analysis / methods