NCM 2021: Unlocking the plant 3D genome architecture with Pore-C sequencing

Jae Young discussed how Pore-C could be used to understand the 3D architecture of plant genomes; the 3D structure of chromosomes is important in enabling many fundamental biological processes to be performed (from molecular processes such as transcription and replication, to large-scale processes including development and disease progression). Pore-C is a nanopore-based technique for high-throughput, genome-wide chromosome conformation capture. For plant geneticists, Jae Young pointed out that a particular advantage of this method is its high resolution in repetitive regions, as well as its ability to detect higher-order multi-way interactions due to the long reads produced, and the read out of DNA modification information alongside. Jae Young discussed how Pore-C could be used, firstly, for plant genome assembly, presenting the example of generating a high-quality ‘chromosome-level genome assembly’ for the Hawaiian Metrosideros plant, using Pore-C data for assembly scaffolding (Choi et al. PNAS. 118:37. 2021). Secondly, he described how Pore-C data could be used to explore 3D chromosome structure, and its association with transcription regulation, providing the example of Oryza sativa (rice) genome analysis. Jae Young emphasised that, despite obtaining only ~1/5 of the contacts than that obtained in a very high-throughput Hi-C experiment on this plant (Dong et al. 2018), ‘it only really required 1/20th of the reads’ to achieve. This is due to the Pore-C advantage of providing multi-contact information in long reads. Jae Young also discussed how Pore-C could detect topologically associating domains (TADs) within the genome; TAD boundaries were found to be enriched for active transcription. Therefore, Pore-C was detecting ‘biologically relevant chromosome contacts’. The team could also use Pore-C to detect loops and candidate enhancers, with ‘high confidence’.