DeTOKI identifies and characterizes the dynamics of chromatin TAD-like domains in a single cell
Xiao Li, Guangjie Zeng, Angsheng Li, Zhihua Zhang
Abstract
Topologically associating domains (TAD) are a key structure of the 3D mammalian genomes. However, the prevalence and dynamics of TAD-like domains in single cells remain elusive. Here we develop a new algorithm, named deTOKI, to decode TAD-like domains with single-cell Hi-C data. By non-negative matrix factorization, deTOKI seeks regions that insulate the genome into blocks with minimal chance of clustering. deTOKI outperforms competing tools and reliably identifies TAD-like domains in single cells. Finally, we find that TAD-like domains are not only prevalent, but also subject to tight regulation in single cells.
Topics & Concepts
BiologyChromatinGenomeComputational biologyNon-negative matrix factorizationCluster analysisEvolutionary biologyGeneticsComputer scienceMatrix decompositionArtificial intelligenceGenePhysicsQuantum mechanicsEigenvalues and eigenvectorsGenomics and Chromatin DynamicsSingle-cell and spatial transcriptomicsRNA Research and Splicing