Transgenerational transcriptional heterogeneity from cytoplasmic chromatin

Abstract

Transcriptional heterogeneity from plasticity of the epigenetic state of chromatin is thought to contribute to tumor evolution, metastasis, and drug resistance. However, the mechanisms leading to nongenetic cell-to-cell variation in gene expression remain poorly understood. Here we demonstrate that heritable transcriptional changes can result from the formation of micronuclei, aberrations of the nucleus that are common in cancer. Micronuclei have fragile nuclear envelopes (NE) that are prone to spontaneous rupture, which exposes chromosomes to the cytoplasm and disrupts many nuclear activities. Using a combination of long-term live-cell imaging and same-cell, single-cell RNA sequencing (Look-Seq2), we identified significant reduction of gene expression in micronuclei, both before and after NE rupture. Furthermore, chromosomes in micronuclei fail to normally recover histone 3 lysine 27 acetylation, a critical step for the reestablishment of normal transcription after mitosis. These transcription and chromatin defects can persist into the next generation in a subset of cells, even after these chromosomes are incorporated into normal daughter nuclei. Moreover, persistent transcriptional repression is strongly associated with, and may be explained by, surprisingly long-lived DNA damage to these reincorporated chromosomes. Therefore, heritable alterations in transcription can originate from aberrations of nuclear architecture.

Mitotic tethering enables en masse inheritance of a shattered micronuclear chromosome

“…12 ). The nuclear foci resulting from inheritance of the clustered micronuclei fragments in the daughter nuclei may be similar to the recently described micronuclear body 42 . While the absence of rounded droplets in live cell imaging offers no support for chromosome fragment tethering through a mechanism involving TOPBP1 condensation 43 , chromosome fragment clustering throughout mitosis may be mediated by the multiple phosphate-binding BRCT domains of TOPBP1 44 and/or by CIP2A oligomerization through its proposed coiled-coil domain.…”

The fate of extra centrosomes in newly formed tetraploid cells: should I stay, or should I go?

“…As a result, chromosomes trapped in micronuclei are prone to incomplete replication, DNA breaks, and chromosomal shattering leading to complex rearrangements (i.e., chromothripsis) ( Crasta et al, 2012 ; Hatch et al, 2013 ; Zhang et al, 2015 ; Liu et al, 2018 ; Tang et al, 2022 ). There is evidence micronucleus instability can cause punctuated bursts of numerical and structural chromosomal alterations within a few cell divisions and promote inflammation, epithelial-to-mesenchymal transition, and metastasis ( Mackenzie et al, 2017 ; Bakhoum et al, 2018 ; Umbreit et al, 2020 ), but we are still learning about the cellular events leading to micronuclei rupture in normal and cancer cells ( Sepaniac et al, 2021 ; Agustinus et al, 2022 ; Mammel et al, 2022 ; Papathanasiou et al, 2022 ). Chromothripsis is more frequent in WGD+ than WGD− cancers ( Notta et al, 2016 ; Cortés-Ciriano et al, 2020 ), likely reflecting an increase in both the rates and tolerance of genomic alterations in tetraploid cells.…”

Mitotic clustering of pulverized chromosomes from micronuclei

“…How CIP2A-TOPBP1 functions to tether fragments remain to be determined, but could occur through higher-order molecular interactions mediated by an extensive coiled-coil domain on CIP2A 30 and/or the condensate-forming property of TOPBP1 49 . Mitotic clustering promotes the biased partitioning of most chromosome fragments en masse toward one daughter cell, which are then reincorporated into the interphase nucleus and persist as micronuclei bodies 28 in the next cell cycle. Finally, clustered fragments that are spatially positioned in close nuclear proximity may become reassembled with increased DNA repair kinetics 50 to generate a spectrum of genomic rearrangements 6 .…”

“…2a-c) with expanded fluorescence signal (Extended Data Fig. 2de) that resembled subnuclear territories termed micronuclei bodies 28 . The nuclear envelope of micronuclei undergoes efficient disassembly during mitosis 6 , suggesting that fragment clustering is not caused by failures in micronuclear envelope breakdown.…”