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The Srs2 helicase prevents recombination by disrupting Rad51 nucleoprotein filaments.

Homologous recombination is a ubiquitous process with key functions in meiotic and vegetative cells for the repair of DNA breaks. It is initiated by the formation of single-stranded DNA on which recombination proteins bind to form a nucleoprotein filament that is active in searching for homology, in the formation of joint molecules and in the exchange of DNA strands. This process contributes to genome stability but it is also potentially dangerous to cells if intermediates are formed that cannot be processed normally and thus are toxic or generate genomic rearrangements. Cells must therefore have developed strategies to survey recombination and to prevent the occurrence of such deleterious events. In Saccharomyces cerevisiae, genetic data have shown that the Srs2 helicase negatively modulates recombination, and later experiments suggested that it reverses intermediate recombination structures. Here we show that DNA strand exchange mediated in vitro by Rad51 is inhibited by Srs2, and that Srs2 disrupts Rad51 filaments formed on single-stranded DNA. These data provide an explanation for the anti-recombinogenic role of Srs2 in vivo and highlight a previously unknown mechanism for recombination control.

Adenosine Triphosphatases↗

Recombination at mammalian telomeres: an alternative mechanism for telomere protection and elongation.

In human cells, homologous recombination (HR) provides an accurate mechanism for the repair of DNA double-strand breaks caused by replication fork breakdown or DNA damaging agents. HR also plays a role in the maintenance of eukaryotic telomeres; cells defective in the recombinational repair proteins RAD51D or RAD54 exhibit telomere shortening and end-to-end chromosome fusions. Here we discuss the way in which HR contributes to telomere protection and elongation in mammalian cells. Understanding the mechanisms by which HR promotes telomere maintenance has important implications for genomic stability and tumorigenesis.

Animals↗

Maintaining integrity.

Research on genome stability and integrity now extends far beyond the biochemistry of DNA repair to encompass signal transduction pathways that span numerous aspects of cellular life. Derailed genomic integrity pathways can result in debilitating genetic disorders, premature ageing, predisposition to cancer and degenerative conditions. Current progress in this rapidly expanding field was the subject of an EMBO workshop, Maintenance of Genomic Integrity, that took place in June 2004 in Galway, Ireland. Top

Animals↗

A subgroup of microsatellite stable colorectal cancers has elevated mutation rates and different responses to alkylating and oxidising agents.

An early step in the carcinogenesis of hereditary non-polyposis colorectal cancer (HNPCC) and some sporadic colorectal cancers (CRCs) is the acquisition of a 'mutator phenotype' resulting from defects in DNA mismatch repair (MMR) genes, which normally maintain genomic stability. This mutator phenotype causes an approximately 100-1000-fold increase in base substitutions and small insertion/deletion mutations thereby driving carcinogenesis. It also causes genome-wide microsatellite instability (MSI) due to the inability to repair mutations within these small, hard to replicate, repetitive DNA elements. In contrast, less is known about the role of mutator phenotypes in microsatellite stable (MSS) CRC. In this report, we have measured the mutation rates in 11 MSS CRC cell lines to obtain an estimate of the prevalence of mutator phenotypes in MSS carcinogenesis. Of the 11 cell lines, three of them (27%) possess spontaneous hypoxanthine phosphoribosyltransferase mutation rates approximately 10-100-fold above background. When challenged with alkylating and oxidising agents, the degree of survival and apoptotic responses are different, indicating that these cell lines may represent more than one mutator phenotype. These data demonstrate that a significant portion of MSS CRC cell lines has increased mutation rates and that this may play a role in MSS CRC carcinogenesis.

Alkylating Agents↗

Twisting the End Game: How Telomere Chromatin Modifications Shape Telomere Maintenance.

Cell division inevitably shortens telomeric DNA owing to the end-replication problem. Eukaryotic chromosomes possess specialized telomere structures to maintain genomic stability. In most proliferative cells, telomerase adds telomeric repeats during S-phase. In differentiated cells where telomerase is silenced, telomeres shorten progressively, thereby compromising genomic integrity. Consequently, cancer cells universally activate alternative telomere maintenance mechanisms during malignant transformation: ~80% reactivate telomerase, while a portion of the rest rely on BIR (break-induced replication)-mediated homologous recombination-based ALT (alternative lengthening of telomeres). Although these mechanisms are stable once established, the initial determinants influencing a cancer cell's choice remain poorly understood. This review discusses recent molecular insights into how telomeric chromatin properties profoundly impact this choice. After briefly introducing telomere chromatin characteristics and key players in its maintenance and dynamics, we discuss the mechanisms by which cancer cells acquire distinct telomere replication capabilities. In particular, we present an in-depth analysis linking telomere heterochromatin status to ALT. Furthermore, based on recent advances, we propose a coupled feedforward loop model explaining how the ALT state becomes "locked in" once initiated. Finally, we offer novel perspectives on rational, telomere-centric therapeutic interventions for ALT-positive cancers, focusing on strategies designed to disrupt such feedforward loops by manipulating telomeric chromatin structure.

Humans↗

Nutritional genomics.

The integration of genomics into nutritional sciences has illuminated the complexity of genome responses to nutritional exposures while offering opportunities to increase the effectiveness of nutritional interventions, both clinical and population based. Nutrients elicit multiple physiological responses that affect genome stability, imprinting, expression, and viability. These effects confer both health benefits and risks, some of which may not become apparent until later in life. Nutritional genomics challenges us to understand the reciprocal and complex interactions among the human genome and dietary components in normal physiology and pathophysiology. Understanding these interactions will refine current definitions of benefit and risk and lead to the establishment of dietary recommendations that have a high predictive value, minimize the risk of unintended consequences, and account for the modifying effects of human genetic variation. Furthermore, nutritional genomics will enable the design of effective dietary regimens for the prevention and management of complex chronic disease. This review focuses on new perspectives that have been presented to the nutritional sciences by the advent of genomics, and new challenges that demand attention because of their potential impact on, and immediate translation into, current public health nutrition recommendations and interventions.

Animals↗

[Chromatid exchanges as parameters of the chronon].

In chronogenetic theory different genes have a different stability ("ergon") which determines the duration ("chronon") of their action. The ergon/chronon of each gene is considered to be inherited. In order to verify whether genomic stability is a heritable trait, the frequency of sister chromatid exchanges (SCE) was observed in a sample of 12 MZ twin pairs distributed as follows: (formula; see text) The minimum intrapair variability as against the high interpair variability as to mean S.C.E. counts supports the hypothesis of genetic control on S.C.E. frequency. The increase in S.C.E. frequency in older pairs indicates the age-dependence of the phenomenon. The study will be extended to both DZ pairs and older twin pairs.

Adolescent↗

Proline residues within spacer peptide p1 are important for human immunodeficiency virus type 1 infectivity, protein processing, and genomic RNA dimer stability.

The full-length human immunodeficiency virus type 1 (HIV-1) mRNA encodes two precursor polyproteins, Gag and GagProPol. An infrequent ribosomal frameshifting event allows these proteins to be synthesized from the same mRNA in a predetermined ratio of 20 Gag proteins for each GagProPol. The RNA frameshift signal consists of a slippery sequence and a hairpin stem-loop whose thermodynamic stability has been shown in in vitro translation systems to be critical to frameshifting efficiency. In this study we examined the frameshift region of HIV-1, investigating the effects of altering stem-loop stability in the context of the complete viral genome and assessing the role of the Gag spacer peptide p1 and the GagProPol transframe (TF) protein that are encoded in this region. By creating a series of frameshift region mutants that systematically altered the stability of the frameshift stem-loop and the protein sequences of the p1 spacer peptide and TF protein, we have demonstrated the importance of stem-loop thermodynamic stability in frameshifting efficiency and viral infectivity. Multiple changes to the amino acid sequence of p1 resulted in altered protein processing, reduced genomic RNA dimer stability, and abolished viral infectivity. The role of the two highly conserved proline residues in p1 (position 7 and 13) was also investigated. Replacement of the two proline residues by leucines resulted in mutants with altered protein processing and reduced genomic RNA dimer stability that were also noninfectious. The unique ability of proline to confer conformational constraints on a peptide suggests that the correct folding of p1 may be important for viral function.

Amino Acid Sequence↗

Regulation of the DNA replication fork: a way to fight genomic instability.

DNA replication is a complex mechanism that functions due to the coordinated interplay of many factors. In the last few years, numerous studies have suggested that DNA replication factors are closely implicated in several DNA transaction events that maintain the integrity of the genome. Therefore, DNA replication fork factors have to be considered as part of a general process that aims to protect and replicate the genome in order to allow correct functioning of a cell and its eventual daughter cells. This is illustrated by the numerous factors that have a well-defined function at the DNA replication fork, but also play crucial roles in different DNA repair pathways such as base excision repair, nucleotide excision repair, double-strand break repair, and mismatch repair. Moreover, several of the replisome proteins have also been shown to be essential in sensing and transducing DNA damages through the checkpoint cascade pathways, including the recently characterised alternative clamps and clamp-loaders. In this review we present DNA replication factors that are involved in different DNA transaction and checkpoint regulation pathways, with emphasis on the link between DNA replication and maintenance of genomic stability.

Cell Cycle Proteins↗

Positive selection of yeast nonhomologous end-joining genes and a retrotransposon conflict hypothesis.

Transposable elements have clearly played a major role in shaping both the size and organization of eukaryotic genomes. However, the evolution of essential genes in core biological processes may also have been shaped by coevolution with these elements. This would be predicted to occur in instances where host proteins are either hijacked for use by mobile elements or recruited to defend against them. To detect such cases, we have used the Saccharomyces cerevisiae-Saccharomyces paradoxus sibling species pair to identify genes that have evolved under positive selection. We identify 72 such genes, which participate in a variety of biological processes but are enriched for genes involved in meiosis and DNA repair by nonhomologous end-joining (NHEJ). We confirm the signature of positive selection acting on NHEJ genes using orthologous sequences from all seven Saccharomyces sensu stricto species. Previous studies have found altered rates of Ty retrotransposition when these NHEJ genes are disrupted. We propose that the evolution of these repair proteins is likely to have been shaped by their interactions with Ty elements. Antagonistic pleiotropy, where critical genes like those involved in DNA repair are also subject to selective pressures imposed by mobile elements, could favor alleles that might be otherwise deleterious for their normal roles related to genome stability.

Base Sequence↗

Organization of chromosome ends in Ustilago maydis. RecQ-like helicase motifs at telomeric regions.

In this study we have established the structure of chromosome ends in the basidiomycete fungus Ustilago maydis. We isolated and characterized several clones containing telomeric regions and found that as in other organisms, they consist of middle repeated DNA sequences. Two principal types of sequence were found: UTASa was highly conserved in nucleotide sequence and located almost exclusively at the chromosome ends, and UTASb was less conserved in nucleotide sequence than UTASa and found not just at the ends but highly interspersed throughout the genome. Sequence analysis revealed that UTASa encodes an open reading frame containing helicase motifs with the strongest homology to RecQ helicases; these are DNA helicases whose function involves the maintenance of genome stability in Saccharomyces cerevisiae and in humans, and the suppression of illegitimate recombination in Escherichia coli. Both UTASa and UTASb contain a common region of about 300 bp located immediately adjacent to the telomere repeats that are also found interspersed in the genome. The analysis of the chromosome ends of U. maydis provides information on the general structure of chromosome ends in eukaryotes, and the putative RecQ helicase at UTASa may reveal a novel mechanism for the maintenance of chromosome stability.

Adenosine Triphosphatases↗

Nucleotide excision repair as a marker for susceptibility to tobacco-related cancers: a review of molecular epidemiological studies.

DNA repair is a complicated biological process consisting of several distinct pathways that play a central role in maintaining genomic stability. Research on DNA repair and cancer risk is a vital, emerging field that recently has seen rapid advances facilitated by the completion of the Human Genome Project. In this review, we described phenotypic and genotypic markers of nucleotide excision repair (NER) that have been used in molecular epidemiology studies. We summarized the population-based studies to date that have examined the association between DNA repair capacity phenotype and genetic polymorphisms of the NER genes and risk of tobacco-related cancers, including cancers of the lung, head and neck, prostate, bladder, breast, and esophagus. We also included studies of melanoma and nonmelanoma skin cancers because individuals with defective NER, such as patients with xeroderma pigmentosum (XP) are highly susceptible to ultraviolet light (UV)-induced melanoma and nonmelanoma skin cancers. The published data provide emerging evidence that DNA repair capacity may contribute to genetic susceptibility to cancers in the general population. However, many of the studies are limited in terms of the size of the study populations. Furthermore, all published findings are still considered preliminary, the assays used in the studies have yet to be validated, and the results need to be confirmed. Large and well-designed population-based studies are warranted to assess gene-gene and gene-environment interactions and to ultimately determine, which biomarkers of DNA repair capacity are useful for screening high-risk populations for primary prevention and early detection of tobacco-related cancers.

Biomarkers, Tumor↗

MCM proteins: DNA damage, mutagenesis and repair.

The MCM2-7 complex, which may act as a replicative helicase during DNA synthesis, plays a central role in S-phase genome stability. MCM proteins are required for processive DNA replication and are a target of S-phase checkpoints. Loss of MCM function causes DNA damage and genome instability. MCM expression is upregulated in proliferating cells, providing a diagnostic marker for both cancerous cells and cells with the potential to become malignant. The role of the MCM complex in genome integrity reflects its activity both at active replication forks and away from forks.

Cell Cycle Proteins↗

Characterization of the slow-growth phenotype of S. cerevisiae Whip/Mgs1 Sgs1 double deletion mutants.

RecQ DNA helicases from many organisms have been indicated to function in the maintenance of genomic stability. In human cells, mutation in the WRN helicase, a RecQ-like DNA helicase, results in the Werner syndrome (WS), a genetic disorder characterized by genomic instability and premature ageing. Similarly, mutation in SGS1, the RECQ homologue in budding yeast, results in genomic instability and accelerated ageing. We previously demonstrated that mouse WRN interacts physically with a novel, highly conserved protein that we named WHIP, and that in budding yeast cells, simultaneous deletion of WHIP/MGS1 and SGS1 results in slow growth and shortened life span. Here we show by using genetic analysis in Saccharomyces cerevisiae that mgs1Delta sgs1Delta cells have increased rates of terminal G2/M arrest, and show elevated rates of spontaneous sister chromatid recombination (SCR) and rDNA array recombination. Finally, we report that complementation of the synthetic relationship between SGS1 and WHIP/MGS1 requires both the helicase and Top3-binding activities of Sgs1, as well as the ATPase activity of Mgs1. Our results suggest that Whip/Mgs1 is implicated in DNA metabolism, and is required for normal growth and cell cycle progression in the absence of Sgs1.

Adenosine Triphosphatases↗

H3K9 methylation and RNA interference regulate nucleolar organization and repeated DNA stability.

Investigations aimed at identifying regulators of nuclear architecture in Drosophila demonstrated that cells lacking H3K9 methylation and RNA interference (RNAi) pathway components displayed disorganized nucleoli, ribosomal DNA (rDNA) and satellite DNAs. The levels of H3K9 dimethylation (H3K9me2) in chromatin associated with repeated DNAs decreased dramatically in Su(var)3-9 and dcr-2 (dicer-2) mutant tissues compared with wild type. We also observed a substantial increase in extrachromosomal circular (ecc) repeated DNAs in mutant tissues. The disorganized nucleolus phenotype depends on the presence of Ligase 4 and ecc DNA formation is not induced by removal of cohesin. We conclude that the structural integrity and organization of repeated DNAs and nucleoli are regulated by the H3K9 methylation and RNAi pathways, and other regulators of heterochromatin-mediated silencing. In addition, repeated DNA stability involves suppression of non-homologous end joining (NHEJ) or other recombination pathways. These results suggest a mechanism for how local chromatin structure can regulate genome stability, and the organization of chromosomal elements and nuclear organelles.

Animals↗

Telomeric length in individuals and cell lines with altered p53 status.

Telomeres play an important role in maintaining chromosomal stability and are often shortened in transformed cells. p53 is the most commonly mutated gene in cancers and its status is thought to reflect the level of genomic stability. We measured telomeric length by Southern blot analysis in cells from cancer-prone syndromes and in selected cancer cells with altered p53 status. Mean telomeric lengths in the cancer-prone syndromes Li-Fraumeni syndrome, Fanconi's anemia, and ataxia telangiectasia, were shorter in the affected individuals than in their unaffected parents. We also found that altered p53 expression in selected cancer cell model systems may be associated with shortened telomeric length, but did not appear to be associated with significant alterations in telomerase activity.

Ataxia Telangiectasia↗

ECHO: a nanopore sequencing-based workflow for (epi)genetic profiling of the human repeatome.

SUMMARY: The human genome is dominated by repetitive DNA, whose genetic and epigenetic variation plays a key role in gene regulation, genome stability, and disease. Recent advances in long-read sequencing now enable large-scale, haplotype-resolved, and DNA methylation-informative analysis of the human genome, including on previously inaccessible complex and repetitive regions. However, the comprehensive, simultaneous characterisation of the "human repeatome" remains challenging, largely due to the lack of comprehensive tools integrated in a single pipeline that can capture the full spectrum of variation across diverse types of DNA repeats. Here, we present ECHO, a user-friendly, Snakemake-based pipeline for the "(Epi)genomic Characterisation of Human Repetitive Elements using Oxford Nanopore Sequencing." ECHO provides a reproducible and scalable framework for end-to-end analysis of whole-genome nanopore sequencing data, enabling integrative but also tailored (epi)genetic analyses of the human repeatome. AVAILABILITY AND IMPLEMENTATION: ECHO is freely available at Github: https://github.com/leenput/ECHO-pipeline, with the archived version at Zenodo: https://zenodo.org/records/19068468.

Humans↗

Analysis of the cytogenetic stability of the human embryonal kidney cell line 293 by cytogenetic and STR profiling approaches.

We have characterized the cytogenetic alterations of the human embryonal cell line 293 by spectral karyotyping and G-banding analysis. To investigate its genomic stability, we compared the karyotypes of 293 and its daughter line EcR-293. Genotype profiling through short tandem repeats complemented the analysis. While displaying almost identical STR profiles and thus verifying their origin and their close relation, the two lines were remarkably different in their number of chromosomes and setup of aberrant chromosomes. However, the cell lines retained a stable karyotype in long term culture. The establishment of subclones from EcR-293, expressing inducible lacZ or MEN1 transgenes, only added minor changes to the karyotype. Our study shows that the cytogenetic constitution of a clonal cell line of the 293 origin appears to be sufficiently stable. However, care should be taken when comparing the properties of independent 293 lineages, since clonal variations might be substantial.

Cell Culture Techniques↗