Protocol for mapping the three-dimensional organization of dinoflagellate genomes

Georgi K Marinov; Anshul Kundaje; William J Greenleaf; Arthur R Grossman

doi:10.1016/j.xpro.2024.102941

Protocol for mapping the three-dimensional organization of dinoflagellate genomes

STAR Protoc. 2024 Mar 12;5(2):102941. doi: 10.1016/j.xpro.2024.102941. Online ahead of print.

Authors

Georgi K Marinov¹, Anshul Kundaje², William J Greenleaf³, Arthur R Grossman⁴

Affiliations

¹ Department of Genetics, Stanford University, Stanford, CA 94305, USA. Electronic address: marinovg@stanford.edu.
² Department of Genetics, Stanford University, Stanford, CA 94305, USA; Department of Computer Science, Stanford University, Stanford, CA 94305, USA.
³ Department of Genetics, Stanford University, Stanford, CA 94305, USA; Department of Applied Physics, Stanford University, Stanford, CA 94305, USA; Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA, USA.
⁴ Carnegie Institution for Science, Division of Biosphere Sciences and Engineering, Stanford, CA 94305, USA.

Abstract

Dinoflagellate genomes often are very large and difficult to assemble, which has until recently precluded their analysis with modern functional genomic tools. Here, we present a protocol for mapping three-dimensional (3D) genome organization in dinoflagellates and using it for scaffolding their genome assemblies. We describe steps for crosslinking, nuclear lysis, denaturation, restriction digest, ligation, and DNA shearing and purification. We then detail procedures sequencing library generation and computational analysis, including initial Hi-C read mapping and 3D-DNA scaffolding/assembly correction. For complete details on the use and execution of this protocol, please refer to Marinov et al.¹.

Keywords: Evolutionary biology; Genomics; Sequencing.