Genome architectures revealed by tethered chromosome conformation capture and population-based modeling

Abstract

We developed Tethered Conformation Capture (TCC), a method for genome-wide mapping of chromatin interactions. By implementing solid-phase ligation, TCC substantially enhanced the signal-to-noise ratio and thus, enabled a detailed analysis of inter-chromosomal interactions. We identified a group of regions in each chromosome that predominantly mediate inter-chromosomal interactions. These regions are marked by high transcriptional activity, suggesting that their interactions are mediated by transcription factories. Each of these regions interacts with numerous other such regions throughout the genome in an indiscriminate fashion, partly driven by the accessibility of the partners. Therefore, it is likely that a different combination of interactions is present in different cells. Accommodating this variability, we developed a computational method to translate the TCC data into physical chromatin contacts in a population of three-dimensional genome structures. Statistical analysis of the resulting population demonstrates that the indiscriminate properties of inter-chromosomal interactions is consistent with the well-known architectural features of the human genome.

Two independent modes of chromatin organization revealed by cohesin removal

“…Roughly 100 mio fixed hepatocytes per sample were processed according to Kalhor et al 26 using HindIII. Libraries were PCR-amplified (12 cycles) and size selected with E-Gel® SizeSelect™ (Thermo Fisher).…”

“…To assess the consequence of Nipbl depletion and cohesin loss on chromosome organization , we performed tethered chromatin conformation capture 26 (referred below as Hi-C) on purified hepatocytes from wildtype (WT), tamoxifen control (TAM) and ΔNipbl animals (Fig. 1f).…”

Developing bioimaging and quantitative methods to study 3D genome

“…Radial positioning: Accumulating evidence from fluorescence in situ hybridization (FISH) and Hi-C suggests that, in many cell types, the spatial organization of chromosomes is related to gene density, with genedense chromosomal regions or whole chromosomes closer to the center of the nucleus, gene-poor chromosome more frequently at the periphery, and with the clustering of the rDNA-containing chromosomes close to nucleoli [10,[24][25][26]. This model of radial positioning not only is specific to human chromosome 18 and 19 [13,27] and all other human chromosomes [25], but also has been observed in other species such as rodents, birds, primates, suggesting that radial positioning is probably a general feature of the organization in eukaryotic cells [28].…”

“…3C-based molecular methods employ crosslinking and intramolecular DNA ligation to investigate the spatial interactions and relationship of different loci and even whole genomes. Among these approaches, Hi-C interrogates all possible cross-linked contacts at acceptable resolution within the whole genome [9][10][11][12].…”

Spatio-Temporal Organization of Replication in Bacteria and Eukaryotes (Nucleoids and Nuclei)

“…Importantly, recent developments in chromosome conformation capture (3C) techniques have confirmed the basic features of chromosome architecture by demonstrating the existence of steady-state, higher-order chromatin entities in cell populations. Two recent studies used unbiased, genome-wide 3C-called Hi-C-to elaborate chromosome architecture (Lieberman-Aiden et al 2009;Kalhor et al 2012). This analysis makes three key points.…”