High-order three-dimensional (3D) interactions between more than two genomic loci are common in human chromatin, but their role in gene regulation is unclear. Previous high-order 3D chromatin assays either measure distant interactions across the genome or proximal interactions at selected targets. To address this gap, we developed Pore-C, which combines chromatin conformation capture with nanopore sequencing of concatemers to profile proximal high-order chromatin contacts at the genome scale. We also developed the statistical method Chromunity to identify sets of genomic loci with frequencies of high-order contacts significantly higher than background (‘synergies’). Applying these methods to human cell lines, we found that synergies were enriched in enhancers and promoters in active chromatin and in highly transcribed and lineage-defining genes. In prostate cancer cells, these included binding sites of androgen-driven transcription factors and the promoters of androgen-regulated genes. Concatemers of high-order contacts in highly expressed genes were demethylated relative to pairwise contacts at the same loci. Synergies in breast cancer cells were associated with tyfonas, a class of complex DNA amplicons. These results rigorously link genome-wide high-order 3D interactions to lineage-defining transcriptional programs and establish Pore-C and Chromunity as scalable approaches to assess high-order genome structure.
PMID: 35637420 DOI: 10.1038/s41587-022-01289-z
Aditya S Deshpande 1 2 3, Netha Ulahannan 1 2, Matthew Pendleton 4, Xiaoguang Dai 4, Lynn Ly 5, Julie M Behr 1 2 3, Stefan Schwenk 6, Will Liao 2, Michael A Augello 7 8, Carly Tyer 4, Priyesh Rughani 4, Sarah Kudman 9, Huasong Tian 1 2, Hannah G Otis 2 10, Emily Adney 1 2, David Wilkes 9, Juan Miguel Mosquera 1 9, Christopher E Barbieri 7 8 9, Ari Melnick 9 11, David Stoddart 6, Daniel J Turner 4 5 6, Sissel Juul 4 5 6, Eoghan Harrington 4, Marcin Imieliński 12 13 14 15 16
Affiliations
1 Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA.
2 New York Genome Center, New York, NY, USA.
3 Tri-Institutional PhD Program in Computational Biology and Medicine, New York, NY, USA.
4 Oxford Nanopore Technologies, New York, NY, USA.
5 Oxford Nanopore Technologies, San Francisco, CA, USA.
6 Oxford Nanopore Technologies, Oxford, UK.
7 Department of Urology, Weill Cornell Medicine, New York, NY, USA.
8 Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA.
9 Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA.
10 Weill Cornell/Rockefeller/Sloan Kettering Tri-Institutional MD-PhD Program, New York, NY, USA.
11 Division of Hematology/Oncology, Weill Cornell Medicine, New York, NY, USA.
12 Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA.
13 New York Genome Center, New York, NY, USA. mski@mskilab.org.
14 Sandra and Edward Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA.
15 Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY, USA.
16 Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA.
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