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We describe tethered conformation capture (TCC), a method for genome-wide mapping of chromatin interactions. By performing ligations on solid substrates rather than in solution, TCC substantially enhances the signal-to-noise ratio, thereby facilitating a detailed analysis of interactions within and between chromosomes. We identified a group of regions in(More)
Conformation capture technologies (e.g., Hi-C) chart physical interactions between chromatin regions on a genome-wide scale. However, the structural variability of the genome between cells poses a great challenge to interpreting ensemble-averaged Hi-C data, particularly for long-range and interchromosomal interactions. Here, we present a probabilistic(More)
The host factor, nuclear factor of activated T-cells (NFAT), regulates the transcription and replication of HIV-1. Here, we have determined the crystal structure of the DNA binding domain of NFAT bound to the HIV-1 long terminal repeat (LTR) tandem kappaB enhancer element at 3.05 A resolution. NFAT binds as a dimer to the upstream kappaB site (Core II), but(More)
Darren L. Bates,1 Kristen K.B. Barthel,1 Yongqing Wu,2 Reza Kalhor,2 James C. Stroud,1 Michael J. Giffin,1 and Lin Chen2,* 1Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, CO 80309-0215, USA 2Molecular and Computational Biology, Department of Chemistry, Norris Cancer Center, University of Southern California, Los(More)
Forkhead Box (Fox) proteins share the Forkhead domain, a winged-helix DNA binding module, which is conserved among eukaryotes from yeast to humans. These sequence-specific DNA binding proteins have been primarily characterized as transcription factors regulating diverse cellular processes from cell cycle control to developmental fate, deregulation of which(More)
Population–based 3D genome structure analysis reveals driving forces in spatial genome organization Harianto Tjong, Wenyuan Li, Reza Kalhor, Chao Dai, Shengli Hao, Ke Gong, Yonggang Zhou, Haochen Li, Xianghong Jasmine Zhou, Mark A. Le Gros, Carolyn A. Larabell, Lin Chen, and Frank Alber Molecular and Computational Biology, Department of Biological Sciences,(More)
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