The 3D structure of genome has long been recognized as an important realm of cellular regulation. Molecular analysis of the 3D genome structure is becoming a reality due to new technology development. Preliminary studies suggest that direct physical models of the genome can be generated from genome-wide mapping of DNA-DNA proximities and population-based modeling, and that the resulting models can yield insights about genomic functions via statistical analyses. While these studies provide a glimpse of the potential of understanding cellular functions from the molecular structures of the genome, it remains a major challenge to develop an accurate physical model of the genome in space and time and relate the model structures to cellular functions. To meet this challenge, the proposed studies will focus on the three major technical barriers faced by all current mapping technologies: (i) inefficient and potentially biased data acquisition; (ii) lack of temporal resolution; and (iii) missing higher-order contact information. The proposed studies have two specific aims. One is to adapt current mapping technologies to a new structure capturing technique, namely flash freezing and cryomilling, for instant capturing and efficient processing of the nucleus thereby enabling extensive and unbiased mapping of maximum amount of chromatin contacts from fewer cells including single cells.
The second aim i s to develop new chemical approaches for DNA end joining, a critical and universal step in current mapping technologies. The new chemical approaches will not only improve data acquisition efficiency but also enable analyses and mapping of higher-order DNA-DNA contacts in single cells as well as ensemble of cells. These studies have the potential to shift the current focus of genome conformation analysis from 2D maps to 3D structures, thereby enhancing our ability to study the link between structure and function in the genome.
| Kim, Seung Joong; Fernandez-Martinez, Javier; Nudelman, Ilona et al. (2018) Integrative structure and functional anatomy of a nuclear pore complex. Nature 555:475-482 |
| Caridi, Christopher P; Delabaere, Laetitia; Tjong, Harianto et al. (2018) Quantitative Methods to Investigate the 4D Dynamics of Heterochromatic Repair Sites in Drosophila Cells. Methods Enzymol 601:359-389 |
| Hua, Nan; Tjong, Harianto; Shin, Hanjun et al. (2018) Producing genome structure populations with the dynamic and automated PGS software. Nat Protoc 13:915-926 |
| Dultz, Elisa; Mancini, Roberta; Polles, Guido et al. (2018) Quantitative imaging of chromatin decompaction in living cells. Mol Biol Cell 29:1763-1777 |
| Zhu, Yina; Gong, Ke; Denholtz, Matthew et al. (2017) Comprehensive characterization of neutrophil genome topology. Genes Dev 31:141-153 |
| Joseph, Agnel Praveen; Polles, Guido; Alber, Frank et al. (2017) Integrative modelling of cellular assemblies. Curr Opin Struct Biol 46:102-109 |
| Li, Qingjiao; Tjong, Harianto; Li, Xiao et al. (2017) The three-dimensional genome organization of Drosophila melanogaster through data integration. Genome Biol 18:145 |
| Dai, Chao; Li, Wenyuan; Tjong, Harianto et al. (2016) Mining 3D genome structure populations identifies major factors governing the stability of regulatory communities. Nat Commun 7:11549 |
| Tjong, Harianto; Li, Wenyuan; Kalhor, Reza et al. (2016) Population-based 3D genome structure analysis reveals driving forces in spatial genome organization. Proc Natl Acad Sci U S A 113:E1663-72 |
| Shin, Hanjun; Shi, Yi; Dai, Chao et al. (2016) TopDom: an efficient and deterministic method for identifying topological domains in genomes. Nucleic Acids Res 44:e70 |
Showing the most recent 10 out of 11 publications
