Jae Young Choi from New York University spoke at the Nanopore Community Meeting 2021 about “Unlocking the plant 3D genome architecture with Pore-C sequencing.” They spoke about how the genome is folded in a 3D conformation in the nucleus. There have also been many techniques to understand the folding. One such technique is Pore-C sequencing: a nanopore-based high-throughput 3D chromosome conformation capture technique. Pore-C uses the ligated products and provides amplification-free high resolution of repetitive regions. Choi’s group has been using Pore-C to assemble genomes of the plant Metrosideros from Hawaii. They used three flow cells on the GridION x5 to obtain a genome sequence. The were interested in Pore-C sequencing to better scaffold the genomes into 11 chromosomes of this genome. WIth four flow cells for Pore-C on the GridION they obtained this information. Next, they explored the 3D genome structure and transcription in rice (Oryza sativa) using three flow cells on the GridION X5 and a PromethION flow cell. Pore-C detects regions that are topologically associated: topologically associated domains (TADs). These regions are associated with enriched transcription, noted Choi, but they wanted to test this. They compared TADs from a Pore-C and a deep sequencing approach using short-read sequencing. The team was also interested in using Pore-C data to detect loops and enhancers. Choi and team used Pore-C to assemble genomes and learn about plant genome assembly and structure/function. It seems that Pore-C has several advantages: longer reads, less sequencing reads needed to determine contacts, and the opportunity to use DNA modification data to learn more about chromosome structure and function.
