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Investigating Chromosome Conformation With Pore-C

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Nanopore sequencing can now be used for investigating chromatin contacts, to identify genome-wide contacts directly, without amplification.

Weill Cornell Medicine and Oxford Nanopore have published a pre-print describing this new technique, and a protocol and analysis tools are now available online.

Investigating genome architecture

Chromatin structure relies on the physical interaction of many genomic loci and investigating the architecture of the genome is relevant and important for understanding how genomic elements interact, and therefore how gene expression is regulated.

Most traditional methods of chromatin conformation capture and sequencing can only find pairwise interactions between two genomic loci. Coupling chromatin conformation capture with nanopore long reads means multiple contacts can be spanned in a single read, giving multi-way, higher order information.

More in-depth interrogation

This technique — Pore-C — is consistent with gold-standard pairwise contact maps at the compartment, topologically-associated domain, and loop levels, and more efficient than existing multi-way methods. The long-range information encoded in Pore-C reads can be used to scaffold and correct genome assemblies and aid the reconstruction of complex rearrangements spanning multiple megabases and chromosomes.

As well as aiming to provide a more in-depth interrogation of the 3D genome and its impact on regulation of gene expression, it is possible to access interactions among repeat regions, and across structural variants. By omitting PCR, the technique is also designed to minimize sequencing bias, enabling further insights in those regions with high or low GC-content.

Finally, as each nanopore long read contains more interactions compared to a short read, fewer sequencing reads are needed to build a complete picture.