Exploring three-dimensional organization of the genome by mapping chromatin contacts and population modeling

We present a method for assaying the structure of the entire genome. This method measures the relative spatial proximity of all loci by combining the 3C and massively-parallel sequencing technologies. We call this method "Tethered Conformation Capture'' (TCC). The output of TCC is a catalogue of several million contacts that involve all regions of the genome and are not biased to any particular locus or loci. Furthermore, TCC catalogues feature a significantly improved signal-to-noise ratio compared to other 3C-based methods. This improvement is a direct result of replacing the diluted liquid phase ligation strategy, which is a staple of all 3C-based methods, with a novel solid-phase ligation strategy that is drastically more effective in preventing the unwanted spurious ligation events.;We also applied TCC to human lymphoblastoid cells, generating a catalogue of more than one hundred million contacts. This catalogues enabled a systematic study of the genome architecture. As the lymphoblastoid cells that were are also a subject of the studies by the Encyclopedia of DNA Elements (ENCODE) Consortium, we were able to interpret the genome-wide architectural features in the context of the available one dimensional functional data across the genome, such as gene expression levels, binding of various transcription factors, and histone modifications.;These analyses revealed new insights into the three-dimensional organization of the human genome. We found that genomic distance is an important determining factor in determining the contact frequency between loci on the same chromosome: contact probability decreases rapidly with increasing distance between loci. However, genomic distance is not the only determining factor in intrachromosomal contact frequency; the other important factor is functional activity. Functionally active and inactive loci---defined by transcriptional activity, gene density, activating histone modifications, and etc.---show distinct patterns of intrachromosomal contact behavior. Inactive regions prefer to interact with their neighboring loci while active regions are more likely to form long-range interactions. Furthermore, active loci are more likely to localize at the border of their chromosome's territory while inactive loci are prefer to localize internally. Moreover, the centromere affects the spatial organization of the active and inactive loci differently: active loci on the two chromosome arms frequently interact with each other; however, contact between inactive loci on different chromosome arms is effectively blocked by the centromere.;We also extracted a detailed profile of interactions between chromosomes. This profile revealed that interactions between chromosomes are abundant overall but distributed among a very large number of low-frequency locus-locus contacts. The loci that mediate these contact belong to a specific subgroup of the active regions. Surprisingly, the members of this subgroup not only form interchromosomal interactions with numerous loci across the genome, they do so with seemingly little dependence on their interaction partners' identities. Moreover, only a subset of these numerous interactions are present in each cell in the population. The exact subset that exists in each cell is likely determined by the accessibility of loci to each other in that cell, but each contact exists in only a small fraction of the cell population.;We referred to this pattern of contact between different chromosomes as indiscriminate interactions and further investigated their underlying mechanisms. The organization of these interactions together with their association with the highest levels of functional activity suggested that they are mediated by the functional machineries of the nucleus, such as transcription factories. We also found that the improved signal-to-noise ratio in TCC is fundamentally important for observing these low-frequency interactions between chromosomes. Without using the solid-phase ligation strategy, true contacts between chromosomes cannot be separated from the background noise. (Abstract shortened by UMI.).