Heritable transcriptional defects from aberrations of nuclear architecture

Abstract

Transcriptional heterogeneity due to plasticity of the epigenetic state of chromatin contributes to tumour evolution, metastasis and drug resistance1–3. However, the mechanisms that cause this epigenetic variation are incompletely understood. Here we identify micronuclei and chromosome bridges, aberrations in the nucleus common in cancer4,5, as sources of heritable transcriptional suppression. Using a combination of approaches, including long-term live-cell imaging and same-cell single-cell RNA sequencing (Look-Seq2), we identified reductions in gene expression in chromosomes from micronuclei. With heterogeneous penetrance, these changes in gene expression can be heritable even after the chromosome from the micronucleus has been re-incorporated into a normal daughter cell nucleus. Concomitantly, micronuclear chromosomes acquire aberrant epigenetic chromatin marks. These defects may persist as variably reduced chromatin accessibility and reduced gene expression after clonal expansion from single cells. Persistent transcriptional repression is strongly associated with, and may be explained by, markedly long-lived DNA damage. Epigenetic alterations in transcription may therefore be inherently coupled to chromosomal instability and aberrations in nuclear architecture.

Repair of DNA double-strand breaks leaves heritable impairment to genome function

“…This post-repair chromatin fatigue potentially affects numerous genes within the topologically defined chromatin neighbourhood that encountered, and recovered from, a single DNA breakage. This phenomenon is distinct from the recently described micronuclei-associated transcriptional repression of genes after re-integration into the nuclear genome ( 61 , 62 ). As reported in these studies, chromosome fragments being ejected from the nucleus in the form of micronuclei are brought into contact with cytoplasmic factors and seem to inherit persistent DNA damage accompanied by heterochromatinization and transcriptional repression ( 61 ).…”

“…This phenomenon is distinct from the recently described micronuclei-associated transcriptional repression of genes after re-integration into the nuclear genome ( 61 , 62 ). As reported in these studies, chromosome fragments being ejected from the nucleus in the form of micronuclei are brought into contact with cytoplasmic factors and seem to inherit persistent DNA damage accompanied by heterochromatinization and transcriptional repression ( 61 ). In our work, we applied Cas9 to understand consequences of single DSBs that could be fully repaired in otherwise intact interphase nuclei.…”

Genetic determinants of micronucleus formation in vivo

“…MN are chromosome fragments that are formed due to mitotic segregation errors 9 or unrepaired DNA breaks 10 leading to mitotic chromosome bridges and breakage–fusion–bridge events 11 , 12 . Protected by an atypical nuclear envelope 13 , MN can exist for several cellular generations, acquire aberrant epigenetic chromatin marks that may persist for future cellular generations 14 , 15 and can replicate their DNA, albeit asynchronously and more slowly than nuclear DNA 16 . Furthermore, the MN nuclear envelope can rupture, leading to the accumulation of MN DNA damage and subsequent chromosomal recombination (chromothripsis) 2 , 17 – 19 , as well as a potent proinflammatory response through cGAS (cyclic GMP-AMP synthase) 4 , 5 which can result in cellular senescence 7 , 8 .…”

A high-content screen reveals new regulators of nuclear membrane stability

“…However, they can cause DNA damage, gene expression changes, and activation of cell invasion and inflammation pathways, especially under conditions of mechanical stress 2,4–9 . In addition, persistent rupture of micronuclear membranes can lead to catastrophic changes in chromosome structure, ongoing chromatin defects, and altered gene expression patterns that are proposed to be initiating events in some tumors and drivers of metastasis 10–15 .…”

“…However, they can cause DNA damage, gene expression changes, and activation of cell invasion and inflammation pathways, especially under conditions of mechanical stress 2,4-9 . In addition, persistent rupture of micronuclear membranes can lead to catastrophic changes in chromosome structure, ongoing chromatin defects, and altered gene expression patterns that are proposed to be initiating events in some tumors and drivers of metastasis [10][11][12][13][14][15] . Nuclear membrane rupture occurs in a range of mechanically challenging conditions in vivo, including migration through dense extracellular matrices, at the leading edge of tumors, and during nuclear migration in fission yeast, C. elegans, and mouse models of laminopathies 4,5,8,[16][17][18][19][20][21][22] .…”