Probing the principles of genome organization with single-cell technologies

Guy Nir ^1,2 Irene Farabella ³ Cynthia Perez Estrada ^4,5 Carl G. Ebeling ⁶ Brain J. Beliveau ^1,2,7,8 Hiroshi M. Sasaki ^1,2,7 S. Dean Lee ¹ Son C. Nguyen ¹ Ruth B. McCole ¹ Shyamtanu Chattoraj ¹ Jelena Erceg ¹ Jumana Alhaj Abed ¹ Nuno M. C. Martins ¹ Huy Q. Nguyen ¹ Mohammed A. Hannan ¹ Sheikh Russell ⁴ Neva C. Durand ^4,9 Suhas S. P. Rao ^4,5,10 Jocelyn Y. Kishi ^1,2,7 Paula Soler-Vila ³ Michele Di Pierro ⁵ Jose N. Onuchic ⁵ Steven P. Callahan ¹¹ John M. Schreiner ¹¹ Jeff A. Stuckey ¹² Peng Yin ^1,2,7 Erez Lieberman Aiden ^4,5,9,13 Marc A. Marti-Renom ^3,14 C.-ting Wu ^1,2

¹Department of Genetics, Harvard Medical School, USA
²Wyss Institute for Biologically Inspired Engineering, Harvard University, USA
³CNAG-CRG, Centre for Genomic Regulation (Crg), Barcelona Institute of Science and Technology (BIST), Spain
⁴Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, USA
⁵Center for Theoretical Biological Physics, Rice University, USA
⁶Department of Fluorescence, Bruker Nano Inc., USA
⁷Department of Systems Biology, Harvard Medical School, USA
⁸Department of Genome Sciences, University of Washington, USA
⁹Broad Institute, Massachusetts Institute of Technology and Harvard University, USA
¹⁰Department of Structural Biology, Stanford University School of Medicine, USA
¹¹Department of Computer Science, Zero Epsilon, LLC, USA
¹²Department of Fluorescence, Bruker Nano Inc., USA
¹³Departments of Computer Science and Computational and Applied Mathematics, Rice University, USA
¹⁴Gene Regulation, Stem Cells and Cancer Program, Centre for Genomic Regulation (CRG), Spain

Here, I introduce new technology for visualizing chromosomal DNA at super-resolution and its integration with Hi-C data to produce three-dimensional models of chromosome organization. Using the super-resolution microscopy methods of OligoSTORM and OligoDNA-PAINT, we traced eight megabases of human chromosome 19, which is the longest stretch of genomic DNA investigated thus far with super-resolution microscopy (Nir*, Farabella*, Perez-Estrada*, Ebeling*…, Stuckey, Yin, Liberman-Aiden, Marti-Renom, and C-ting Wu). Leveraging this technology, we discovered different levels of genomic packaging of genomic elements that ranged in size from a few kilobases to over a megabase. Interestingly, we also obtained evidence that maternal and paternal homologous regions are organized differently. Focusing on chromosomal regions that contribute to compartments, we discovered distinct structures that, despite considerable variability, can predict whether such regions correspond to active or inactive compartments. We then performed integrative modeling, which brings together our super-resolution images with Hi-C contact frequency maps and achieves 10 kb resolution. Finally, I will describe how we are starting to use our multiplexed genome imaging technology to study the principles that govern chromosome folding. We aim at visualizing genome reorganization that occurs through aging or as a result of genetic engineering of structural variations at critical genomic positions of developing mice.