Noam Kaplan, Introduction to Hi-C:
In this talk I will introduce the Chromatin Conformation Capture set of technologies, mainly focusing on Hi-C. We will discuss what types of interaction patterns have been found with Hi-C, how they are detected, and their biological interpretation.
Noam Kaplan, How the genome encodes 3D genome organization:
Topologically Associating Domains (TADs) constitute a new level of high-order chromatin organization. TAD-like interaction patterns have been found in a wide range of species, from bacteria to mammals. In mammals, TADs have been suggested to specify regulatory microenvironments in which promoters and enhancers interact. Thus, explaining TADs and how they are encoded in the genome is a major challenge in the field. I will propose a probabilistic model that can explain how TADs can be encoded by simple 1D information specified by independent local events. I will show this model both explains current data and correctly predicts how genome organization changes in genetic disease.
Noam Kaplan, Using Hi-C to solve outstanding problems in genome assembly:
Though Hi-C is now being used routinely to study the characteristic genome organizations of different cell types and species, the strongest signals in Hi-C experiments are ubiquitous in all species. While these interaction patterns are often uninteresting – and even detrimental – for studying the biology of genome organization, I will show how they can be used to solve a set of major challenges in the field of genome assembly, including scaffolding, haplotyping and microbiome assembly.
Dariusz Plewczyński, Three-dimensional genome architecture of human B-lymphoblastoid cells seen by ChIA-PET: lessons from CTCF and RNAPII-mediated chromatin interactions:
Chromosomal folding are important features of genome organization, which play critical roles in genome functions, including transcriptional regulation. Using 3C-based mapping technologies to render long-range chromatin interactions has started to reveal some basic principles of spatial genome organization. Among 3D genome mapping technologies, ChIA-PET is unique in its ability to generate multiple datasets (in a single experiment), including binding sites, enriched chromatin interactions (mediated by specific protein factors, like CTCF), as well as non-enriched interactions that reflect topological neighborhoods of higher-order associations. The multifarious nature of ChIA-PET data represents an important advantage in capturing multi-layer structural-functional information, but also imposes new challenges in multi-scale modeling of 3D genome. We applied an advanced ChIA-PET strategy combined with computational modelling to comprehensively map higher-order chromosome folding and specific chromatin interactions mediated by CTCF and RNAPII with haplotype specificity and nucleotide resolution in different human cell lineages. We find that CTCF/cohesin-mediated interaction anchors serve as structural foci for spatial organization of constitutive genes concordant with CTCF-motif orientation, whereas RNAPII interacts within these structures by selectively drawing cell-type- specific genes towards CTCF-foci for coordinated transcription. Furthermore, we show that haplotype-variants and allelic-interactions have differential effects on chromosome configuration influencing gene expression and may provide mechanistic insights into functions associated with disease susceptibility. 3D-genome simulation suggests a model of chromatin folding around chromosomal axes, where CTCF is involved in defining the interface between condensed and open compartments for structural regulation. Our 3D-genome strategy thus provides unique insights in the topological mechanism of human variations and diseases.
Dariusz Plewczyński, 3DGNOME: an integrated 3 Dimensional GeNOme Modeling Engine for data-driven simulation of spatial genome organization:
Recent advances in high-throughput chromosome conformation capture (3C) technology, such as Hi-C and ChIA-PET, have demonstrated the importance of 3D genome organization in development, cell differentiation and transcriptional regulation. There is now a widespread need for computational tools to generate and analyze 3D structural models from 3C data. Here, we present 3D GeNOme Modeling Engine (3D-GNOME) – a web service which generates 3D structures from 3C data and provides tools to visually inspect and annotate the resulting structures, in addition to a variety of statistical plots and heatmaps which characterize the selected genomic region. 3D-GNOME simulates the structure and provides a convenient user interface for further analysis. Alternatively, a user may generate structures using published ChIA-PET data for the GM12878 cell line by simply specifying a genomic region of interest. 3D-GNOME is freely available at http://3dgnome.cent.uw.edu.pl/ providing unique insights in the topological mechanism of human variations and diseases. Further refinement of 3gNOME and application to additional ChIA-PET and other types of 3D genome mapping data will help to advance our understanding of genome structures and functions.