Chromosomes take fate into their own hands during micronucleus rupture

From the Hatch Lab, Basic Sciences Division

Within the hallowed walls of the cell, conflict simmers; a tenuous peace, and perhaps its very survival, rest on the slimmest of margins. Housed within the cell’s inner sanctum – the nucleus – is its most prized possession, the code which guides its every action: DNA. Safeguarding the fidelity of this code is paramount, as even small disturbances can wreak havoc on critical functions or, worse, birth a spreading pestilence that threatens not only the cell but the entire body within which it resides. But in its struggle for survival, the cell confronts a cruel irony – to support its vital functions, it must foster within its walls chemical agents that would pervert its genetic material at any opportunity. The role of protecting the DNA falls largely on the nuclear membrane, a gated wall that carefully controls those to whom it grants access. Even so, disaster’s specter is ever present; the nuclear membrane can rupture, causing the DNA to spill out, the toxic agents to flood in, and a desperate rush to repair the breach and stem the damage.

A nucleus, fortunately, ruptures relatively rarely and can usually be rapidly repaired. A micronucleus, on the other hand, isn’t so lucky. Micronuclei (MN) form when a chromosome gets separated from the pack during mitosis, resulting in the construction of a secondary nuclear membrane around this isolated DNA. MN are prone to  unrepairable rupture, leaving their DNA particularly at risk for major mutagenic events. “Despite the high frequency of MN rupture and its potential to drastically change gene expression, the molecular mechanisms of membrane rupture in MN and its full consequences are unclear”, writes the group led by Dr. Emily Hatch, assistant professor in Fred Hutch’s Basic Sciences Division and member of the Fred Hutch/UW Cancer Consortium. In a new article in Life Science Alliance led by Hatch lab postdoc Dr. Anna Mammel, the group identifies new characteristics that influence membrane stability in the MN.

Rupture is partly caused by defects in the nuclear lamina, a cytoskeletal network that lines the inner surface of the nuclear membrane, the group writes: “MN frequently have large gaps in the nuclear lamina meshwork, leaving areas of weak membrane that become the site of membrane rupture.” But rupture can be highly variable, with some MN more prone to it than others. In contemplating this fact, the authors reasoned that one major feature that distinguishes different micronuclei is which chromosome they contain. Thus, the group used a Fluorescent In Situ Hybridization (FISH) approach to identify the chromosomes within specific micronuclei and determine whether there was any correspondence between micronucleus rupture and chromosome identity. While most micronuclei ruptured eventually, they found chromosome identity to be a reliable predictor of how rapidly rupture occurs – micronuclei containing chromosome 18, for instance, ruptured very rapidly, whereas those containing chromosome 19 exhibited significantly delayed rupture, indicative of a more stable state.

The authors next examined several properties that differ between chromosomes – length, gene density, presence of ribosomal DNA, and centromere size and position – to determine which properties promote MN stability. They found two such traits: chromosome length and gene density. Why might these two traits confer stability? Regarding chromosome length, the authors posit that larger micronuclei may be inherently more stable, perhaps due to an increased ability to recruit nuclear proteins. Indeed, they found that micronuclei containing multiple chromosomes were also more stable, and that larger micronuclei contained more of the nuclear lamina protein Lamin B1 and the nuclear pore complex protein Nup133 and had fewer gaps in the nuclear lamina. The influence of gene density on MN stability was less clear – it did not appear to be due to increased MN size, nor did these MNs exhibit an enhanced ability to recruit nuclear proteins. However, while small MNs containing gene-dense chromosomes had very little Lamin B1, they seemed to make very good use of what they had - the architecture of the lamina, as assessed by superresolution microscopy, appeared well organized with few gaps. Thus, the authors concluded that gene-dense chromosomes can, via an as-yet-unknown mechanism, promote a more stable nuclear lamina organization in micronuclei than can gene-poor chromosomes.

mechanisms of micronucleus stability
Relationship between chromosome properties and micronucleus stability. Top: Micronuclei containing large chromosomes exhibit more Lamin B1 protein (blue) and delayed rupture. Middle: Micronuclei containing small, gene dense chromosomes exhibit delayed lamina disorganization and rupture. Bottom: Micronuclei containing small, gene poor chromosomes exhibit early lamina disorganization and rapid rupture. Image provided by Dr. Emily Hatch

Dr. Hatch expressed her surprise at the group’s findings: “Previous results in the field suggest that the presence of a lot of genes should impair nuclear lamina assembly, yet we find the opposite result.”  While the reason for this stability is unclear, Dr. Hatch has a hunch: “We are testing the hypothesis that high gene density inhibits nucleus growth, which is frequently misregulated in micronuclei.” Perhaps, then, this really is a unified story about micronuclear size – perhaps a larger micronucleus is great, so long as you’ve got enough DNA to fill it (and to recruit extra nuclear proteins), but if not, better to make it as small as possible (so as to make the most of what nuclear proteins you’ve got).

Dr. Hatch is excited about the new directions in which her team’s findings will take the field: “This work…means that previous work on the mechanism of nuclear membrane rupture has to be re-evaluated to take into account the identity of DNA associated with the rupture site. Our findings also indicate that knowing which chromosomes are biased towards micronucleation in different conditions will allow us to predict the fate of the cell, and the likelihood that it acquires genetic changes associated with disease…these results made us really curious about what chromosomes are in micronuclei and whether different conditions that cause micronucleation, including loss of tumor suppressors, activation of oncogenes, or just being an early embryo, cause different chromosomes to end up there, leading to different cell fates.”

This work was supported by the National Institutes of Health, the Rita Allen Foundation, and the Cellular Imaging, Bioinformatics, and Flow Cytometry Shared Resources of the Fred Hutch/University of Washington Cancer Consortium.

Fred Hutch/UW Cancer Consortium member Emily Hatch contributed to this work

Mammel AE, Huang HZ, Gunn AL, Choo E, Hatch EM. Chromosome length and gene density contribute to micronuclear membrane stability. Life Sci Alliance. 2021 Nov 17;5(2):e202101210. doi: 10.26508/lsa.202101210. PMID: 34789512; PMCID: PMC8605325.