Dynamic chromosomal interactions and control of heterochromatin positioning by Ki-67

Abstract

Ki67 forms a protective layer around mitotic chromosomes and is involved in genome positioning around nucleoli during interphase. However, a lack of genomic interaction maps has hampered a detailed understanding of the role of Ki67 in chromatin organization. We used pA-DamID to map genome-Ki67 interactions in three human cell lines and throughout the cell cycle. In mitosis, Ki67 shows a surprising preference for the distal 15-30 Mb of each chromosome. Early in interphase, when Ki67 is present in pre-nucleolar bodies, this is replaced by a pattern of large domains that overlaps with late-replicating DNA, which gradually shifts towards small chromosomes. Nucleolar perturbations indicate that these cell cycle dynamics correspond to nucleolar maturation during interphase. Furthermore, Ki67 competes with the nuclear lamina for interaction with late-replicating DNA, and controls replication timing at (peri)centromeric regions. Together, these results reveal a highly dynamic choreography of genome interactions and roles for Ki67 in genome organization.

Evidence for low nanocompaction of heterochromatin in living embryonic stem cells

“…It remains to be determined whether it interacts with components of heterochromatin, including HP1α, and whether its depletion affects the abundance of these proteins within heterochromatin and, consequently, its nanoscale organisation. However, our data are consistent with a recent genome‐wide mapping study which found that Ki‐67 binds centromere‐proximal regions marked with H3K9me3 in interphase (preprint: van Schaik et al , 2021 ). Also, the ability of Ki‐67 to adapt to different chromatin environments remains to be explored.…”

Single-molecule simultaneous profiling of DNA methylation and DNA-protein interactions with Nanopore-DamID

“…To compare Nanopore and Illumina-based approaches we sequenced conventional LaminB1-DamID libraries from N2A cells. LaminB1-occupancy profiles were comparable between technologies and similar to those obtained previously from mouse embryonic stem cells (mESCs) 26 ( Fig. 1f ).…”

“…LaminB1-occupancy profiles were comparable between technologies and similar to those obtained previously from mouse embryonic stem cells (mESCs) 26 (Fig. 1f).…”

“…e , The yield of sequencing from wild type cells is reduced compared to Dam expressing cells. f , Nanopore-DamID of LaminB1-Dam-expressing N2A cells shows enrichment in large lamin-associated domains similar to Illumina DamID and published mESC Illumina-DamID 26 . In contrast, untethered Dam occupancy is enriched in inter-LAD regions.…”

“…LADs were identified with a previously developed hidden markov model by comparing LaminB1-Dam signal to Dam-alone 27 . Nanopore-DamID LADs overlapped extensively with Illumina-DamID LADs (Jaccard metric=0.89, p<0.001 Genome Association Test 28 ) and LADs identified from a published mESC LaminB1 DamID dataset 26 (Jaccard metric=0.75, p<0.001 Genome Association Test), although some LADs were cell-type-specific ( Supplementary figure 6 ). These results confirm that selective sequencing of adenine methylated DNA, without amplification or purification, is methodologically simple, accurate, and cheaper than approaches where whole genome sequencing is required 22 .…”