Protocol to identify higher order architectures across multiple species using HiArch

STAR Protocols, vol. 7, pp. 104912

Abstract

Three-dimensional genome organization plays a crucial regulatory role, but its evolutionary development across the tree of life remains unclear. Here, we present a protocol for identifying higher order genome architectures using HiArch. We describe steps for preprocessing Hi-C maps, applying NormDis normalization, and identifying global folding and checkerboard patterns. We then detail procedures for cross-sample comparison and statistical analysis. This protocol enables systematic and reproducible analysis of 3D genome organization across diverse species. For complete information on the use and execution of this protocol, please refer to Che et al. 1 1. Che, Y. ∙ Bush, S.J. ∙ Lin, H. ... The evolution of high-order genome architecture revealed from 1,000 species Cell. 2026; 189 :3760-3772.e19 Full Text Full Text (PDF) Scopus (2) PubMed Google Scholar

Authors 2

1. Mingxuan Li corresponding

   Xi'an Jiaotong University

   Affiliation as printed

   School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, China; MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, China. Electronic address: 3123154029@stu.xjtu.edu.cn

2. Kai Ye corresponding Aachen

   Leiden University · Xi'an Jiaotong University · First Affiliated Hospital of Xi'an Jiaotong University

   Affiliation as printed

   School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, China; MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an, China; Department of Gynecology and Obstetrics, Center for Mathematical Medical, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China; Genome Institute, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China; Faculty of Science, Leiden University, Leiden, the Netherlands. Electronic address: kaiye@xjtu.edu.cn