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3D-GNOME 3.0 - 3D chromatin organization web service

3D genome organization plays a critical role in its functioning. Alterations of this organization caused by structural variants (SVs) may lead to changes in gene transcription or even to disease. The recent advent of Chromosome Conformation Capture (3C) based techniques such as ChIA-PET and Hi-C allows us to investigate genome spatial organization. The rising volume of sequencing data in turn enables highly accurate identification of structural variation. Combination of those two sources of information can reveal mechanisms of genome regulation.

The current available in-situ CTCF and RNAPII ChIA-PET chromatin contacts obtained from the GM12878 cell line mapped to the GRCh38 genome assembly and extended the 1000 Genomes SVs dataset (3202 samples on GRCh38). Also we need to analyze changes in spatial distances between genes and enhancers in chromatin 3D model ensembles.

This web service provides ensembles of 3D models of genomic structures for all 3,202 samples from the 1000 Genomes Project phase 3 SV release. Enter an ID of a sample and choose a genomic region of interest at the Run analysis page to obtain a 3D model of the region for this particular individual. The models are built at the resolution of individual chromatin loops and visualize alterations emerging in genomic structures after introduction of SVs.

To accommodate the new data and creating ensembles we moved the computation of the 3D-GNOME engine from CPU to GPU version, which gives a speed-up of 30x vs the previous versions.

You can also upload to the service your own interaction data in bedpe (paired-end BED) format together with bed or vcf file containing SVs to visualize structures formed by the submitted long-range contacts and altered by the provided SVs. The CTCF/RNAPII arcs are visualized using the IGV tool with additional genes and SVs annotations. For 3D model visualization, we use a viewer: NGL, where we provide colouring by gene and enhancer location. The models are downloadable in mmcif and xyz format.

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chromatin model