Human chromosome‐specific aneuploidy is influenced by DNA ‐dependent centromeric features

Abstract

Intrinsic genomic features of individual chromosomes can contribute to chromosome-specific aneuploidy. Centromeres are key elements for the maintenance of chromosome segregation fidelity via a specialized chromatin marked by CENP-A wrapped by repetitive DNA. These long stretches of repetitive DNA vary in length among human chromosomes. Using CENP-A genetic inactivation in human cells, we directly interrogate if differences in the centromere length reflect the heterogeneity of centromeric DNA-dependent features and whether this, in turn, affects the genesis of chromosome-specific aneuploidy. Using three distinct approaches, we show that mis-segregation rates vary among different chromosomes under conditions that compromise centromere function. Whole-genome sequencing and centromere mapping combined with cytogenetic analysis, small molecule inhibitors, and genetic manipulation revealed that inter-chromosomal heterogeneity of centromeric features, but not centromere length, influences chromosome segregation fidelity. We conclude that faithful chromosome segregation for most of human chromosomes is biased in favor of centromeres with high abundance of DNA-dependent centromeric components. These inter-chromosomal differences in centromere features can translate into non-random aneuploidy, a hallmark of cancer and genetic diseases.

A genetic memory initiates the epigenetic loop necessary to preserve centromere position

“…555349,BD). Immunofluorescence in combination with fluorescence in situ hybridization (FISH) was performed as described previously (Dumont et al, 2020). Images of DAPI counterstained and immuno-/FISH-stained cells were collected using a Deltavision Core system (Applied Precision).…”

“…Read mapping was performed as previously described (Dumont et al, 2020). Briefly, reads were mapped using the BWA-MEM algorithm of the BWA software package (Li & Durbin, 2009;preprint: Li, 2013) on the human reference genome GRCh38.p12 which includes centromere reference models (Miga et al, 2014;Nechemia-Arbely et al, 2017;Schneider et al, 2017).…”

CENP-A chromatin prevents replication stress at centromeres to avoid structural aneuploidy

“…Changes in centromere size may contribute to meiotic drive (2), but may also elicit genome instability (7) by increasing the rate of chromosome mis-segregation (8). While recombination at centromeres is suppressed in meiosis (9), it is present in somatic cells and enhanced in cancerous cells (10) where whole-arm chromosome translocations are prevalent (11,12).…”

“…Thymidine analog staining was completed as above with secondary antibodies being anti-mouse Alexa Fluor 647 (IdU) and antimouse AlexaFluor 405 (ssDNA). Slides were mounted and imaged using an Olympus IX-71 DeltaVision Image Restoration Microscope (Applied Precision) and replication tracks measured using FIJI software.mFISH karyotypingCells grown to ~ 75-80% confluency were treated with colcemid for 3 h and prepared as previously described(8) for the mFISH karyotyping. The Metafer imaging platform (MetaSystems) and the Isis software were used for automated acquisition of the chromosome spread and mFISH image analysis.…”

Aneuploidy-driven genome instability triggers resistance to chemotherapy

“…Chromosome mis-segregation has been proposed to be a non-random process (Worrall et al 2018;Dumont et al 2019). We therefore considered whether the specific karyotypic remodeling present in TRMP was the result of a biased chromosome mis-segregation pattern caused by Mps1i treatment.…”