Nuclear chromosome locations dictate segregation error frequencies

Abstract

Chromosome segregation errors during cell divisions generate aneuploidies and micronuclei, which can undergo extensive chromosomal rearrangements such as chromothripsis1–5. Selective pressures then shape distinct aneuploidy and rearrangement patterns—for example, in cancer6,7—but it is unknown whether initial biases in segregation errors and micronucleation exist for particular chromosomes. Using single-cell DNA sequencing8 after an error-prone mitosis in untransformed, diploid cell lines and organoids, we show that chromosomes have different segregation error frequencies that result in non-random aneuploidy landscapes. Isolation and sequencing of single micronuclei from these cells showed that mis-segregating chromosomes frequently also preferentially become entrapped in micronuclei. A similar bias was found in naturally occurring micronuclei of two cancer cell lines. We find that segregation error frequencies of individual chromosomes correlate with their location in the interphase nucleus, and show that this is highest for peripheral chromosomes behind spindle poles. Randomization of chromosome positions, Cas9-mediated live tracking and forced repositioning of individual chromosomes showed that a greater distance from the nuclear centre directly increases the propensity to mis-segregate. Accordingly, chromothripsis in cancer genomes9 and aneuploidies in early development10 occur more frequently for larger chromosomes, which are preferentially located near the nuclear periphery. Our findings reveal a direct link between nuclear chromosome positions, segregation error frequencies and micronucleus content, with implications for our understanding of tumour genome evolution and the origins of specific aneuploidies during development.

Micronuclei from misaligned chromosomes that satisfy the spindle assembly checkpoint in cancer cells

“…This is consistent with recent high-resolution live-cell studies in both cancer and non-cancer human cells that showed that the vast majority of lagging chromosomes have a transient nature and are corrected during anaphase by an Aurora-B-dependent mechanism that prevents micronuclei formation, 46,60 and the relatively low frequency of micronuclei formation even after induction of massive chromosome segregation errors by experimental abrogation of the SAC. 61,62 Defects in chromosome alignment are normally avoided by increased Aurora B activity at centromeres of misaligned chromosomes. 27 However, the correction of erroneous attachments underlying some chromosome alignment defects (e.g., syntelic attachments) appears to be less robust in cancer cells that also show overly stabilized kinetochore-microtubule attachments.…”

“…This is consistent with recent high-resolution live-cell studies in both cancer and non-cancer human cells that showed that the vast majority of lagging chromosomes have a transient nature and are corrected during anaphase by an Aurora-B-dependent mechanism that prevents micronuclei formation, 46 , 60 and the relatively low frequency of micronuclei formation even after induction of massive chromosome segregation errors by experimental abrogation of the SAC. 61 , 62 …”

“… 50 , 51 Indeed, RPE-1 cells treated with microtubule-targeting drugs at concentrations that stabilize microtubules satisfy the SAC in the presence of misaligned chromosomes and do so faster under conditions that promote the formation of syntelic attachments. 62 , 63 , 64 In addition to direct missegregation from misaligned chromosomes, late-aligning chromosomes are also more prone to lag behind in anaphase and missegregate at higher frequencies in human cancer cells, or upon SAC inactivation or stabilization of incorrect kinetochore-microtubule attachments in normal cells. 62 , 65 Together with the fact that non-transformed human cells rely on a robust p53-dependent mechanism that limits the proliferation of aneuploid cells, 66 the present work helps to explain how spontaneous misaligned chromosomes in cancer cells eventually satisfy the SAC and may constitute a direct route to chromosomal instability.…”

Chromosome Inequality: Causes and Consequences of Non-Random Segregation Errors in Mitosis and Meiosis

“…A release from monastrol, an Eg5 kinesin inhibitor, enriched for anaphase lagging of chromosomes 1 and 2 in human cells, chromosome 4 in PtK1 cells, and chromosome 3 + X in Indian Muntjac cells [ 47 , 48 ]. Compromising attachment error correction and the spindle assembly checkpoint (SAC) by inhibiting the kinase Mps1 revealed a high missegregation frequency of larger chromosomes with a difference up to threefold in human cells and of chromosome 3 + X in Indian Muntjac cells [ 33 , 48 , 49 ]. Larger chromosomes were also found to missegregate more frequently in human cells when attachment error correction was compromised by inhibiting Aurora B kinase, when microtubules were stabilized by low concentrations of taxol, or when chromosome congression was compromised by inhibition of the mitotic kinesin CENP-E [ 49 , 50 ].…”

“…Compromising attachment error correction and the spindle assembly checkpoint (SAC) by inhibiting the kinase Mps1 revealed a high missegregation frequency of larger chromosomes with a difference up to threefold in human cells and of chromosome 3 + X in Indian Muntjac cells [ 33 , 48 , 49 ]. Larger chromosomes were also found to missegregate more frequently in human cells when attachment error correction was compromised by inhibiting Aurora B kinase, when microtubules were stabilized by low concentrations of taxol, or when chromosome congression was compromised by inhibition of the mitotic kinesin CENP-E [ 49 , 50 ]. Interestingly, generating DNA damage in human cells during the interphase, using ionizing radiation or by causing replication stress, specifically elevated structural rearrangements and micronuclear incorporation of larger chromosomes as well [ 33 , 51 , 52 ].…”