With better knowledge about the 3D structural organization of the genome comes the challenge of elucidating which factors determine these structures, what is their functional implications, and how are these structures modulated during cell processes such as cell differentiation or disease progression. Proteins and their complexes play critical roles in orchestrating chromatin interactions and chromosome folding. It is therefore important to link the discovery of endogenous protein complexes with their roles in the formation of specific chromatin interactions. Our goal in this component is to develop a new technology for elucidating the role of protein complexes in chromatin folding. Specifically we combine DNA-DNA proximity mapping with the discovery of the underlying causal protein complexes. We will develop the ?Genome Conformation Capture-Proteome? method (GCCP) for simultaneous detection of chromatin interactions and associated endogenous protein complexes. We will employ a proven pipeline for the isolation of native protein complexes, but extensively optimized for the purpose of reading out the chromatin interactome surrounding the detected specific protein complexes.
| 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 |
| 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 |
| Zhu, Yina; Gong, Ke; Denholtz, Matthew et al. (2017) Comprehensive characterization of neutrophil genome topology. Genes Dev 31:141-153 |
| 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 |
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