Ki-67 is a chromatin-associated protein with a dynamic distribution pattern throughout the cell cycle and is thought to be involved in chromatin organization. The lack of genomic interaction maps has hampered a detailed understanding of its roles, particularly during interphase. By pA-DamID mapping in human cell lines, we find that Ki-67 associates with large genomic domains that overlap mostly with late-replicating regions. Early in interphase, when Ki-67 is present in pre-nucleolar bodies, it interacts with these domains on all chromosomes. However, later in interphase, when Ki-67 is confined to nucleoli, it shows a striking shift toward small chromosomes. Nucleolar perturbations indicate that these cell cycle dynamics correspond to nucleolar maturation during interphase, and suggest that nucleolar sequestration of Ki-67 limits its interactions with larger chromosomes. Furthermore, we demonstrate that Ki-67 does not detectably control chromatin-chromatin interactions during interphase, but it competes with the nuclear lamina for interaction with late-replicating DNA, and it controls replication timing of (peri)centromeric regions. Together, these results reveal a highly dynamic choreography of genome interactions and roles for Ki-67 in heterochromatin organization.
Bibliographical noteFunding Information:
We thank Masatoshi Takagi for the HCT116 Ki‐67‐AID cell line, and the NKI Digital Microscopy, Flow Cytometry, Genomics, Protein Production, and RHPC core facilities for technical assistance. We thank members of the BvS lab; Andrew Belmont and other members of the 4D Nucleome Center for Nuclear Cytomics for helpful suggestions. Supported by NIH Common Fund “4D Nucleome” Program grant U54 DK107965 (BvS, DMG), ERC Advanced Grant 694466 (BvS), MSCA/AIRC iCARE2.0 fellowship 800924 (SGM), and Marie Curie Fellowship 838555 (SGM). The Oncode Institute is partly supported by KWF Dutch Cancer Society.
© 2022 The Authors. Published under the terms of the CC BY NC ND 4.0 license.