The roughly two meters of DNA in the human genome is intricately packaged to form the chromatin and chromosomes in each cell nucleus. In addition to its structural role, this organization has critical regulatory functions. In particular, the formation of hubs in the human genome plays an essential role in regulating genes in different cell types. We recently demonstrated the ability to create reliable maps of loops, using an in situ Hi-C method for three-dimensional genome sequencing. Hi-C characterizes the three-dimensional configuration of the genome by determining the frequency of physical contact between all pairs of loci, genome-wide. The proposed project will develop more sophisticated technologies that can identify not only loops - which involve a pair of genomic positions - but hubs, which can involve many interacting DNA positions (often five or more such positions). We will examine the dynamics of these hubs in the setting of differentiating embryonic stem (ES) cells in humans and mice.
Aim 1 will develop COLA, a variant of the in situ Hi-C protocol that can identify contacts between large numbers of loci at once in intact nuclei.
Aim 2 will develop split-pool barcoding, which can identify contacts between unlimited numbers of loci, but which requires disruption of the nucleus. The results of both methods will be integrated and compared to one another and, in Aim 3, will be independently validated using microscopy. The proposed project will advance our understanding of the determinants and functions of chromatin hubs, and present a technological framework for comprehensive analysis of higher-order genome structure in any cell type. All methods and data will be freely and rapidly released to the scientific community.
The formation of hubs between sets of loci in the human genome plays an essential role in regulating genes and controlling how cells function. We recently demonstrated the ability to create reliable maps of looping, genome-wide, using the in situ Hi-C method for three-dimensional genome sequencing. This project will develop more sophisticated technologies capable of identifying not only loops - which involve two positions in the genome - but also hubs - which can involve an arbitrary number of positions. We will use these technologies to study stem cell differentiation. The project will help us understand how genome folding enables healthy cells to differentiate and respond to their environment, and how altered folding contributes to cancer, autoimmunity and a wide range of other diseases.
| Matthews, Benjamin J; Dudchenko, Olga; Kingan, Sarah B et al. (2018) Improved reference genome of Aedes aegypti informs arbovirus vector control. Nature 563:501-507 |
| Robinson, James T; Turner, Douglass; Durand, Neva C et al. (2018) Juicebox.js Provides a Cloud-Based Visualization System for Hi-C Data. Cell Syst 6:256-258.e1 |
| Di Pierro, Michele; Cheng, Ryan R; Lieberman Aiden, Erez et al. (2017) De novo prediction of human chromosome structures: Epigenetic marking patterns encode genome architecture. Proc Natl Acad Sci U S A 114:12126-12131 |
| Rao, Suhas S P; Huang, Su-Chen; Glenn St Hilaire, Brian et al. (2017) Cohesin Loss Eliminates All Loop Domains. Cell 171:305-320.e24 |
| Eagen, Kyle P; Aiden, Erez Lieberman; Kornberg, Roger D (2017) Polycomb-mediated chromatin loops revealed by a subkilobase-resolution chromatin interaction map. Proc Natl Acad Sci U S A 114:8764-8769 |
| Kieffer-Kwon, Kyong-Rim; Nimura, Keisuke; Rao, Suhas S P et al. (2017) Myc Regulates Chromatin Decompaction and Nuclear Architecture during B Cell Activation. Mol Cell 67:566-578.e10 |
| Dudchenko, Olga; Batra, Sanjit S; Omer, Arina D et al. (2017) De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds. Science 356:92-95 |
| Phanstiel, Douglas H; Van Bortle, Kevin; Spacek, Damek et al. (2017) Static and Dynamic DNA Loops form AP-1-Bound Activation Hubs during Macrophage Development. Mol Cell 67:1037-1048.e6 |
| Di Pierro, Michele; Zhang, Bin; Aiden, Erez Lieberman et al. (2016) Transferable model for chromosome architecture. Proc Natl Acad Sci U S A 113:12168-12173 |
| Durand, Neva C; Shamim, Muhammad S; Machol, Ido et al. (2016) Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments. Cell Syst 3:95-8 |
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