R-loops and regulatory changes in chronologically ageing fission yeast cells drive non-random patterns of genome rearrangements

TY - JOUR

T1 - R-loops and regulatory changes in chronologically ageing fission yeast cells drive non-random patterns of genome rearrangements

AU - Ellis, David A.

AU - Reyes-Martín, Félix

AU - Rodríguez-López, María

AU - Cotobal, Cristina

AU - Sun, Xi Ming

AU - Saintain, Quentin

AU - Jeffares, Daniel C.

AU - Marguerat, Samuel

AU - Tallada, Víctor A.

AU - Bähler, Jürg

N1 - Funding Information: This research was funded by a BBSRCDTP studentship to DAE (London Interdisciplinary Doctoral Programme) [grant number BB/ M009513/1] funded by the Biotechnology and Biological Sciences Research Council (https:// bbsrc.ukri.org/); a Wellcome Senior Investigator Award to JB [grant number 095598/Z/11/Z] funded by the Wellcome Trust (https://wellcome.org/); and Medical Research Council funding to SM (https:// mrc.ukri.org/). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. © 2021 Ellis et al.

PY - 2021/8/31

Y1 - 2021/8/31

N2 - Aberrant repair of DNA double-strand breaks can recombine distant chromosomal breakpoints. Chromosomal rearrangements compromise genome function and are a hallmark of ageing. Rearrangements are challenging to detect in non-dividing cell populations, because they reflect individually rare, heterogeneous events. The genomic distribution of de novo rearrangements in non-dividing cells, and their dynamics during ageing, remain therefore poorly characterized. Studies of genomic instability during ageing have focussed on mitochondrial DNA, small genetic variants, or proliferating cells. To characterize genome rearrangements during cellular ageing in non-dividing cells, we interrogated a single diagnostic measure, DNA breakpoint junctions, using Schizosaccharomyces pombe as a model system. Aberrant DNA junctions that accumulated with age were associated with microhomology sequences and R-loops. Global hotspots for age-associated breakpoint formation were evident near telomeric genes and linked to remote breakpoints elsewhere in the genome, including the mitochondrial chromosome. Formation of breakpoint junctions at global hotspots was inhibited by the Sir2 histone deacetylase and might be triggered by an age-dependent de-repression of chromatin silencing. An unexpected mechanism of genomic instability may cause more local hotspots: age-associated reduction in an RNA-binding protein triggering R-loops at target loci. This result suggests that biological processes other than transcription or replication can drive genome rearrangements. Notably, we detected similar signatures of genome rearrangements that accumulated in old brain cells of humans. These findings provide insights into the unique patterns and possible mechanisms of genome rearrangements in non-dividing cells, which can be promoted by ageing-related changes in gene-regulatory proteins.

AB - Aberrant repair of DNA double-strand breaks can recombine distant chromosomal breakpoints. Chromosomal rearrangements compromise genome function and are a hallmark of ageing. Rearrangements are challenging to detect in non-dividing cell populations, because they reflect individually rare, heterogeneous events. The genomic distribution of de novo rearrangements in non-dividing cells, and their dynamics during ageing, remain therefore poorly characterized. Studies of genomic instability during ageing have focussed on mitochondrial DNA, small genetic variants, or proliferating cells. To characterize genome rearrangements during cellular ageing in non-dividing cells, we interrogated a single diagnostic measure, DNA breakpoint junctions, using Schizosaccharomyces pombe as a model system. Aberrant DNA junctions that accumulated with age were associated with microhomology sequences and R-loops. Global hotspots for age-associated breakpoint formation were evident near telomeric genes and linked to remote breakpoints elsewhere in the genome, including the mitochondrial chromosome. Formation of breakpoint junctions at global hotspots was inhibited by the Sir2 histone deacetylase and might be triggered by an age-dependent de-repression of chromatin silencing. An unexpected mechanism of genomic instability may cause more local hotspots: age-associated reduction in an RNA-binding protein triggering R-loops at target loci. This result suggests that biological processes other than transcription or replication can drive genome rearrangements. Notably, we detected similar signatures of genome rearrangements that accumulated in old brain cells of humans. These findings provide insights into the unique patterns and possible mechanisms of genome rearrangements in non-dividing cells, which can be promoted by ageing-related changes in gene-regulatory proteins.

UR - http://www.scopus.com/inward/record.url?scp=85115754926&partnerID=8YFLogxK

U2 - 10.1371/journal.pgen.1009784

DO - 10.1371/journal.pgen.1009784

M3 - Article

C2 - 34464389

AN - SCOPUS:85115754926

SN - 1553-7390

VL - 17

JO - PLoS Genetics

JF - PLoS Genetics

IS - 8

M1 - 1009784

ER -