Loss of CBX2 induces genome instability and senescence-associated chromosomal rearrangements

The polycomb group protein CBX2 is an important epigenetic reader involved in cell proliferation and differentiation. While CBX2 overexpression occurs in a wide range of human tumors, targeted deletion results in homeotic transformation, proliferative defects, and premature senescence. However, its cellular function(s) and whether it plays a role in maintenance of genome stability remain to be determined. Here, we demonstrate that loss of CBX2 in mouse fibroblasts induces abnormal large-scale chromatin structure and chromosome instability. Integrative transcriptome analysis and ATAC-seq revealed a significant dysregulation of transcripts involved in DNA repair, chromocenter formation, and tumorigenesis in addition to changes in chromatin accessibility of genes involved in lateral sclerosis, basal transcription factors, and folate metabolism. Notably, Cbx2−/− cells exhibit prominent decondensation of satellite DNA sequences at metaphase and increased sister chromatid recombination events leading to rampant chromosome instability. The presence of extensive centromere and telomere defects suggests a prominent role for CBX2 in heterochromatin homeostasis and the regulation of nuclear architecture.

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Nuclear Envelope Integrity in Health and Disease: Consequences on Genome Instability and Inflammation

International Journal of Molecular Sciences ◽

10.3390/ijms22147281 ◽

2021 ◽

Vol 22 (14) ◽

pp. 7281

Author(s):

Benoit R. Gauthier ◽

Valentine Comaills

Keyword(s):

Nuclear Envelope ◽

Clinical Symptoms ◽

Genome Instability ◽

Chromosomal Rearrangements ◽

Wide Range ◽

Complex Chromosomal Rearrangements ◽

Health And Disease ◽

Dna Release ◽

Sting Pathway ◽

Eukaryote Genome

The dynamic nature of the nuclear envelope (NE) is often underestimated. The NE protects, regulates, and organizes the eukaryote genome and adapts to epigenetic changes and to its environment. The NE morphology is characterized by a wide range of diversity and abnormality such as invagination and blebbing, and it is a diagnostic factor for pathologies such as cancer. Recently, the micronuclei, a small nucleus that contains a full chromosome or a fragment thereof, has gained much attention. The NE of micronuclei is prone to collapse, leading to DNA release into the cytoplasm with consequences ranging from the activation of the cGAS/STING pathway, an innate immune response, to the creation of chromosomal instability. The discovery of those mechanisms has revolutionized the understanding of some inflammation-related diseases and the origin of complex chromosomal rearrangements, as observed during the initiation of tumorigenesis. Herein, we will highlight the complexity of the NE biology and discuss the clinical symptoms observed in NE-related diseases. The interplay between innate immunity, genomic instability, and nuclear envelope leakage could be a major focus in future years to explain a wide range of diseases and could lead to new classes of therapeutics.

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Refined detection and phasing of structural aberrations in pediatric acute lymphoblastic leukemia by linked-read whole-genome sequencing

Scientific Reports ◽

10.1038/s41598-020-59214-w ◽

2020 ◽

Vol 10 (1) ◽

Cited By ~ 1

Author(s):

Jessica Nordlund ◽

Yanara Marincevic-Zuniga ◽

Lucia Cavelier ◽

Amanda Raine ◽

Tom Martin ◽

...

Keyword(s):

Acute Lymphoblastic Leukemia ◽

Large Scale ◽

Fusion Gene ◽

Lymphoblastic Leukemia ◽

Chromosomal Rearrangements ◽

Block Size ◽

Compound Heterozygous ◽

Structural Variants ◽

Pediatric Acute Lymphoblastic Leukemia ◽

Wide Range

AbstractStructural chromosomal rearrangements that can lead to in-frame gene-fusions are a leading source of information for diagnosis, risk stratification, and prognosis in pediatric acute lymphoblastic leukemia (ALL). Traditional methods such as karyotyping and FISH struggle to accurately identify and phase such large-scale chromosomal aberrations in ALL genomes. We therefore evaluated linked-read WGS for detecting chromosomal rearrangements in primary samples of from 12 patients diagnosed with ALL. We assessed the effect of input DNA quality on phased haplotype block size and the detectability of copy number aberrations and structural variants in the ALL genomes. We found that biobanked DNA isolated by standard column-based extraction methods was sufficient to detect chromosomal rearrangements even at low 10x sequencing coverage. Linked-read WGS enabled precise, allele-specific, digital karyotyping at a base-pair resolution for a wide range of structural variants including complex rearrangements and aneuploidy assessment. With use of haplotype information from the linked-reads, we also identified previously unknown structural variants, such as a compound heterozygous deletion of ERG in a patient with the DUX4-IGH fusion gene. We conclude that linked-read WGS allows detection of important pathogenic variants in ALL genomes at a resolution beyond that of traditional karyotyping and FISH.

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Loss of Cdc13 causes genome instability by a deficiency in replication-dependent telomere capping

10.1101/757864 ◽

2019 ◽

Author(s):

Rachel E Langston ◽

Dominic Palazzola ◽

Erin Bonnell ◽

Raymund J. Wellinger ◽

Ted Weinert

Keyword(s):

Homologous Recombination ◽

Genome Stability ◽

Genome Instability ◽

Chromosome Instability ◽

S Phase ◽

Temperature Sensitive ◽

End Joining ◽

Telomere Capping ◽

Non Homologous End Joining

AbstractIn budding yeast, Cdc13, Stn1, and Ten1 form a telomere binding heterotrimer dubbed CST. Here we investigate the role of Cdc13/CST in maintaining genome stability, using a Chr VII disome system that can generate recombinants, loss, and enigmatic unstable chromosomes. In cells expressing a temperature sensitive CDC13 allele, cdc13F684S, unstable chromosomes frequently arise due to problems in or near a telomere. Hence, when Cdc13 is defective, passage through S phase causes Exo1-dependent ssDNA and unstable chromosomes, which then are the source for whole chromosome instability events (e.g. recombinants, chromosome truncations, dicentrics, and/or loss). Specifically, genome instability arises from a defect in Cdc13’s replication-dependent telomere capping function, not Cdc13s putative post-replication telomere capping function. Furthermore, the unstable chromosomes form without involvement of homologous recombination nor non-homologous end joining. Our data suggest that a Cdc13/CST defect in semi-conservative replication near the telomere leads to ssDNA and unstable chromosomes, which then are lost or subject to complex rearrangements. This system defines a links between replication-dependent chromosome capping and genome stability in the form of unstable chromosomes.

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Impact of G-Quadruplexes and Chronic Inflammation on Genome Instability: Additive Effects during Carcinogenesis

Genes ◽

10.3390/genes12111779 ◽

2021 ◽

Vol 12 (11) ◽

pp. 1779

Author(s):

MaryElizabeth Stein ◽

Kristin A. Eckert

Keyword(s):

Chronic Inflammation ◽

Genome Stability ◽

Large Scale ◽

Oxidative Dna Damage ◽

Genome Instability ◽

Physiological State ◽

Dna Polymerases ◽

Small Scale ◽

Gene Promoters ◽

Maintain Genome Stability

Genome instability is an enabling characteristic of cancer, essential for cancer cell evolution. Hotspots of genome instability, from small-scale point mutations to large-scale structural variants, are associated with sequences that potentially form non-B DNA structures. G-quadruplex (G4) forming motifs are enriched at structural variant endpoints in cancer genomes. Chronic inflammation is a physiological state underlying cancer development, and oxidative DNA damage is commonly invoked to explain how inflammation promotes genome instability. We summarize where G4s and oxidative stress overlap, with a focus on DNA replication. Guanine has low ionization potential, making G4s vulnerable to oxidative damage. Impacts to G4 structure are dependent upon lesion type, location, and G4 conformation. Occasionally, G4s pose a challenge to replicative DNA polymerases, requiring specialized DNA polymerases to maintain genome stability. Therefore, chronic inflammation creates a dual challenge for DNA polymerases to maintain genome stability: faithful G4 synthesis and bypassing unrepaired oxidative lesions. Inflammation is also accompanied by global transcriptome changes that may impact mutagenesis. Several studies suggest a regulatory role for G4s within cancer- and inflammatory-related gene promoters. We discuss the extent to which inflammation could influence gene regulation by G4s, thereby impacting genome instability, and highlight key areas for new investigation.

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Genome stability is in the eye of the beholder: recent retrotransposon activity varies significantly across avian diversity

10.1101/2021.04.13.439746 ◽

2021 ◽

Author(s):

James D. Galbraith ◽

R. Daniel Kortschak ◽

Alexander Suh ◽

David L. Adelson

Keyword(s):

Transposable Elements ◽

Zebra Finch ◽

Dna Sequences ◽

Genome Stability ◽

Chromosomal Rearrangements ◽

Genome Structure ◽

Past Research ◽

Dominant Group ◽

Avian Genome ◽

Retrotransposon Activity

AbstractSince the sequencing of the zebra finch genome it has become clear the avian genome, while largely stable in terms of chromosome number and gene synteny, is more dynamic at an intrachromosomal level. A multitude of intrachromosomal rearrangements and significant variation in transposable element content have been noted across the avian tree. Transposable elements (TEs) are a source of genome plasticity, because their high similarity enables chromosomal rearrangements through non-allelic homologous recombination, and they have potential for exaptation as regulatory and coding sequences. Previous studies have investigated the activity of the dominant TE in birds, CR1 retrotransposons, either focusing on their expansion within single orders, or comparing passerines to non-passerines. Here we comprehensively investigate and compare the activity of CR1 expansion across orders of birds, finding levels of CR1 activity vary significantly both between and with orders. We describe high levels of TE expansion in genera which have speciated in the last 10 million years including kiwis, geese and Amazon parrots; low levels of TE expansion in songbirds across their diversification, and near inactivity of TEs in the cassowary and emu for millions of years. CR1s have remained active over long periods of time across most orders of neognaths, with activity at any one time dominated by one or two families of CR1s. Our findings of higher TE activity in species-rich clades and dominant families of TEs within lineages mirror past findings in mammals.Author SummaryTransposable elements (TEs) are mobile, self replicating DNA sequences within a species’ genome, and are ubiquitous sources of mutation. The dominant group of TEs within birds are chicken repeat 1 (CR1) retrotransposons, making up 7-10% of the typical avian genome. Because past research has examined the recent inactivity of CR1s within model birds such as the chicken and the zebra finch, this has fostered an erroneous view that all birds have low or no TE activity on recent timescales. Our analysis of numerous high quality avian genomes across multiple orders identified both similarities and significant differences in how CR1s expanded. Our results challenge the established view that TEs in birds are largely inactive and instead suggest that their variation in recent activity may contribute to lineage-specific changes in genome structure. Many of the patterns we identify in birds have previously been seen in mammals, highlighting parallels between the evolution of birds and mammals.

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AnnotationBustR: an R package to extract subsequences from GenBank annotations

PeerJ ◽

10.7717/peerj.5179 ◽

2018 ◽

Vol 6 ◽

pp. e5179 ◽

Cited By ~ 2

Author(s):

Samuel R. Borstein ◽

Brian C. O’Meara

Keyword(s):

Comparative Analysis ◽

Dna Sequences ◽

Large Scale ◽

Retrieval System ◽

Single Gene ◽

R Package ◽

Fasta File ◽

Search Terms ◽

Large Numbers ◽

Wide Range

BackgroundDNA sequences are pivotal for a wide array of research in biology. Large sequence databases, like GenBank, provide an amazing resource to utilize DNA sequences for large scale analyses. However, many sequence records on GenBank contain more than one gene or are portions of genomes. Inconsistencies in the way genes are annotated and the numerous synonyms a single gene may be listed under provide major challenges for extracting large numbers of subsequences for comparative analysis across taxa. At present, there is no easy way to extract portions from many GenBank accessions based on annotations where gene names may vary extensively.ResultsThe R packageAnnotationBustRallows users to extract sequences based on GenBank annotations through the ACNUC retrieval system given search terms of gene synonyms and accession numbers.AnnotationBustRextracts subsequences of interest and then writes them to a FASTA file for users to employ in their research endeavors.ConclusionFASTA files of extracted subsequences and accession tables generated byAnnotationBustRallow users to quickly find and extract subsequences from GenBank accessions. These sequences can then be incorporated in various analyses, like the construction of phylogenies to test a wide range of ecological and evolutionary hypotheses.

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The role of epigenetics in maintaining genome stability

The Biochemist ◽

10.1042/bio03905012 ◽

2017 ◽

Vol 39 (5) ◽

pp. 12-15

Author(s):

Nicole C. Riddle

Keyword(s):

Cell Division ◽

Dna Sequences ◽

Genome Stability ◽

Daughter Cell ◽

Structural Integrity ◽

Genome Instability ◽

Epigenetic Mechanisms ◽

Lower Efficiency ◽

Segregation Of Chromosomes

Epigenetic mechanisms play important roles in maintaining our genomes, helping to ensure that after every cell division each daughter cell contains an intact copy of the genome without the structural integrity of the chromosomes being compromised. They are also important for the segregation of chromosomes during cell division and help protect the genome from transposable elements – DNA sequences that are able to move around the genome, generating new copies of themselves and potentially interfering with important genes. As we age, the frequency of errors during cell division increases, partly due to less effective epigenetic mechanisms tasked with maintaining genome stability. Whether the lower efficiency of epigenetic mechanisms is a by-product of ageing or if the increased genome instability drives ageing is currently the topic of on-going research.

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S. pombe DNA translocases Rrp1 and Rrp2 have distinct roles at centromeres and telomeres that ensure genome stability

10.1101/738435 ◽

2019 ◽

Author(s):

Anna Barg-Wojas ◽

Kamila Schirmeisen ◽

Jakub Muraszko ◽

Karol Kramarz ◽

Gabriela Baranowska ◽

...

Keyword(s):

Schizosaccharomyces Pombe ◽

Genome Stability ◽

Genome Instability ◽

Chromosome Instability ◽

Telomere Maintenance ◽

Nucleosome Dynamics ◽

Dna Translocases ◽

Telomere Function ◽

And Function ◽

Dna Translocase

ABSTRACTHomologous recombination (HR) is a DNA repair mechanism that ensures, together with heterochromatin machinery, the proper replication, structure and function of telomeres and centromeres that is essential for the maintenance of genome integrity. Schizosaccharomyces pombe Rrp1 and Rrp2 participate in HR and are orthologues of Saccharomyces cerevisiae Uls1, a SWI2/SNF2 DNA translocase and SUMO-Targeted Ubiquitin Ligase. We show that Rrp1 or Rrp2 upregulation leads to chromosome instability and growth defects. These phenotypes depend on putative DNA translocase activities of Rrp1 and Rrp2. Either Rrp1 or Rrp2 overproduction results in a reduction in global histone levels, suggesting that Rrp1 and Rrp2 may modulate nucleosome dynamics. In addition we show that Rrp2, but not Rrp1, acts at telomeres. We propose that this role depends on the previously described interaction between Rrp2 and Top2. We conclude that Rrp1 and Rrp2 have important roles for centromere and telomere function and maintenance, contributing to the preservation of genome stability during vegetative cell growth.SUMMARY STATEMENTSchizosaccharomyces pombe DNA translocases Rrp1 and Rrp2 modulate centromere and telomere maintenance pathways and dysregulation of their activity leads to genome instability.

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AnnotationBustR: An R package to extract subsequences from GenBank annotations

10.7287/peerj.preprints.2920 ◽

2017 ◽

Cited By ~ 1

Author(s):

Samuel R. Borstein ◽

Brian C. O'Meara

Keyword(s):

Comparative Analysis ◽

Dna Sequences ◽

Large Scale ◽

Retrieval System ◽

Single Gene ◽

R Package ◽

Fasta File ◽

Search Terms ◽

Large Numbers ◽

Wide Range

Background. DNA sequences are pivotal for a wide array of research in biology. Large sequence databases, like GenBank, provide an amazing resource to utilize DNA sequences for large scale analyses. However, many sequences on GenBank contain more than one gene or are portions of genomes, and inconsistencies in the way genes are annotated and the numerous synonyms a single gene may be listed under provide major challenges for extracting large numbers of subsequences for comparative analysis across taxa. At present, there is no easy way to extract portions from multiple GenBank accessions based on annotations where gene names may vary extensively. Results. The R package AnnotationBustR allows users to extract sequences based on GenBank annotations through the ACNUC retrieval system given search terms of gene synonyms and accession numbers. AnnotationBustR extracts portions of interest and then writes them to a FASTA file for users to employ in their research endeavors. Conclusion. FASTA files of extracted subsequences and accession tables generated by AnnotationBustR allow users to quickly find and extract subsequences from GenBank accessions. These sequences can then be incorporated in various analyses, like the construction of phylogenies to test a wide range of ecological and evolutionary hypotheses.

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