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201 results for “Genome stability”
Data from "Stability of genome-wide methylation patterns and parental environmental effects in the widespread, long-lived Lombardy poplar"
<p><strong>Data from : 'Stability of genome-wide methylation patterns and parental environmental effects in the widespread, long-lived Lombardy poplar'</strong></p> <p>An Vanden Broeck*, Tim Meese*, Pieter Verschelde, Karen Cox, Berthold Heinze, Dieter Deforce, Ellen De Meester and Filip Van Nieuwerburgh</p> <p> </p> <p>Related publication: Vanden Broeck, A.*, Meese, T.*, Verschelde, P. <em>et al.<strong> Genome-wide methylome stability and parental effects in the worldwide distributed Lombardy poplar</strong></em>. <em>BMC Biol</em> <strong>22</strong>, 30 (2024). https://doi.org/10.1186/s12915-024-01816-1</p> <ul> <li>* These authors contributed equally.</li> </ul> <p>--------------------------------------------------</p> <p><strong>Background: </strong>Despite the increasing number of epigenomic studies in plants, little is known about the forces that shape the methylome in long-lived woody perennials. The Lombardy poplar (<em>Populus nigra</em> cv. 'Italica' Duroi) offers an ideal opportunity to investigate the impact of the individual environmental history of trees on the methylome.</p> <p><strong>Results: </strong>We present the results of three interconnected experiments on Lombardy poplar. In the first experiment, we investigated methylome variability during a growing season and across vegetatively reproduced generations. We found that ramets collected over Europe and raised in common conditions have stable methylomes in symmetrical CG-contexts. In contrast, seasonal dynamics occurred in methylation patterns in CHH-context. In the second experiment, we investigated whether methylome patterns of plants grown in a non-parental environment correlate with the parental climate. We did not observe any biological relevant pattern that significantly correlates with the parental climate. Finally, we investigated whether the parental environment has persistent carry-over effects on the vegetative offspring's' phenotype. We combined new bud set observations of three consecutive growing seasons with former published bud set data. Using a linear mixed effects analysis, we found a statistically significant but weak short-term, parental carry-over effect on the timing of bud set. However, this effect was negligible compared to the direct effects of the offspring environment.</p> <p><strong>Conclusions: </strong>Genome-wide cytosine methylation patterns in symmetrical GC-context are stable in Lombardy poplar and appear to be mainly the result of random processes. In this widespread poplar clone, methylation patterns in GC-context can be used as bio-markers to infer a common ancestor and thus to investigate the environmental history of a specific Lombardy poplar on short time-scales. The Lombardy poplar shows high phenotypic plasticity in a novel environment which enabled this clonal tree to adapt and survive all over the temperate regions of the world.</p> <p> </p> <p><strong>ADDITIONAL FILES</strong></p> <p><strong>Additional file 1.</strong> CSV-file with information on the Lombardy poplar trees samples used for whole genome bisulfite sequencing (WGBS) in the two methylome experiments (<em>metadata</em>). The raw fastq datafiles obtained by whole genome bisulfite sequencing (WGBS) are available at the <a href="https://www.ncbi.nlm.nih.gov/geo/">Gene Expression Omnibus (GEO) database</a> (submission GSE225596).</p> <p><strong>Additional file 2.</strong> CSV-file with mapping statistics, bisulfite conversion rates and percentages of cytosine methylation for each DNA-sample analyzed by whole genome bisulfite sequencing (WGBS). (<em>processed data</em>).</p> <p><strong>Additional file 3</strong>. CSV-file with the total list of GO terms that were enriched in DMRs. DMRs were identified between groups by grouping the WGBS data from 16 individual Lombardy poplar ramets by their corresponding parent-of-origin (ortet ‘HUN4’ located in Hungary, ‘ITS3’ in Italy, ‘SPC1’ in Spain and ‘UKD2’ in the UK, respectively) (<em>processed data</em>).</p> <p><strong>Additional file 4. </strong>POWERPOINT-file. Heatmaps with GO terms over-represented in promoters containing DMRs in CpG-context per between-group pairwise comparison. DMRs were identified between groups by grouping the WGBS data from 16 individual Lombardy poplar ramets by their corresponding parent-of-origin (ortet ‘HUN4’ located in Hungary, ‘ITS3’ in Italy, ‘SPC1’ in Spain and ‘UKD2’ in the UK, respectively). A. HUN4 versus ITS3; B. HUN4 versus UKD2, C; ITS3 versus SPC1; D. HUN4 versus SCP1, E. SPC1 versus UKD2</p> <p><strong>Additional file 5. </strong>CSV-file with the raw data of the bud set observations in the common garden experiment (<em>raw data</em>).</p> <p><strong>Additional file 6. </strong>HTML-file with the R source codes to reproduce the results of the bud set analysis (<em>code,</em> <em>R script</em>).</p> <p><strong>Additional file 7. </strong>A text-file representing the Snakefile (i.e. a readable Python-based workflow) including the different steps and rules of the bioinformatics of the WGBS data analyses (<em>code, Snakefile</em>).</p> <p><strong>Additional file 8. </strong>RMD-file<strong> </strong>with the code to reproduce the analyses to identify differential methylated predefined regions (<em>code,</em> <em>R script</em>).</p> <p><strong>Additional file 9. </strong>R-script with the code to reproduce the clustering and visualizing of the GO enrichment results (<em>code,</em> <em>R script</em>).</p> <p><strong>Supporting files 1</strong>. Zip-folder with: i) excel-files listing the genes in DMRs, and ii) PNG-files with the ‘Biological Coefficient of Variation (BCV)’-plots between any of the six pairwise comparisons of Lombardy poplars grouped per ortet and identified with Bioconductor package edgeR. DMRs were identified between groups by grouping the WGBS data from 16 individual Lombardy poplar ramets by their corresponding parent-of-origin (‘HUN4’ located in Hungary, ‘ITS3’ in Italy, ‘SPC1’ in Spain and ‘UKD2’ in the UK, respectively) (<em>processed data</em>).</p> <p><strong>Supporting files 2</strong>. Zip-folder with PNG-files representing heatmaps and excel-files with clustered GO terms significant over-represented in promoters and gene regions located in DMRs. DMRs were identified between groups by grouping the WGBS data from 16 individual Lombardy poplar ramets by their corresponding parent-of-origin (ortet ‘HUN4’ located in Hungary, ‘ITS3’ in Italy, ‘SPC1’ in Spain and ‘UKD2’ in the UK, respectively. The files were obtained with the Bioconductor package simplifyEnrichment (<em>processed data</em>).</p> <p>---------------------------------------------------------</p> <p>Version 3:</p> <ul> <li>Renaming of file names according to the publisher's guidelines</li> <li>Additional file 2 includes also bisulfite conversion rates per sample</li> </ul>
Data from: Clonal evolution and genome stability in a 2,500-year-old fungal individual
Individuals of the basidiomycete fungus Armillaria are well-known for their ability to spread from woody substrate to substrate on the forest floor through the growth of rhizomoprhs. Here we made 248 collections of A. gallica in one locality in Michigan's Upper Peninsula. To identify individuals, we genotyped collections with molecular markers and somatic compatibility testing. We found several different individuals in proximity to one another, but one genetic individual stood out as exceptionally large, covering hundreds of tree root systems over approximate 75 hectares of forest floor. Based on observed growth rates of the fungus, we estimate the minimum age of the large individual as 2,500 years. With whole-genome sequencing and variant discovery, we also found that mutation had occurred within the somatic cells of the individual, reflecting its historical pattern of growth from a single point. The overall rate of mutation over the 90 mb genome, however, was extremely low. This same individual was first discovered in the late 1980s, but its full spatial extent and internal mutation dynamic was unkown at that time. The large individual of A. gallica has been remarkably resistant to genomic change as it has persisted in place.
RAD54L2 counters TOP2-DNA adducts to promote genome stability (Etoposide treated RPE1 CRISPR screens in TP53 and RAD53L2 knock outs)
<p>The catalytic cycle of topoisomerase 2 (TOP2) enzymes proceeds via a transient DNA double-strand break (DSB) intermediate termed the TOP2 cleavage complex (TOP2cc), in which the TOP2 protein is covalently bound to DNA. Anti-cancer agents such as etoposide operate by stabilising TOP2ccs, ultimately generating genotoxic TOP2-DNA protein crosslinks that require processing and repair. Here, we identify RAD54-like 2 (RAD54L2) as a factor promoting TOP2cc resolution. We demonstrate that RAD54L2 acts through a novel mechanism together with zinc finger protein associated with TDP2 and TOP2 (ZATT/ZNF451) and independent of tyrosyl-DNA phosphodiesterase 2 (TDP2). Our work suggests a model wherein RAD54L2 recognises sumoylated-TOP2 and, using its ATPase activity, promotes TOP2cc resolution and prevents DSB exposure. These findings suggest RAD54L2-mediated TOP2cc resolution as a potential mechanism for cancer-therapy resistance and highlight RAD54L2 as an attractive candidate for drug discovery.</p>
Data from: Genome-wide CRISPR synthetic lethality screen identifies a role for the ADP-ribosyltransferase PARP14 in replication fork stability controlled by ATR
<p>The DNA damage response is essential to maintain genomic stability, suppress replication stress, and protect against carcinogenesis. The ATR-CHK1 pathway is an essential component of this response, which regulates cell cycle progression in the face of replication stress. PARP14 is an ADP-ribosyltransferase with multiple roles in transcription, signaling, and DNA repair. To understand the biological functions of PARP14, we catalogued the genetic components that impact cellular viability upon loss of PARP14 by performing an unbiased, comprehensive, genome-wide CRISPR knockout genetic screen in PARP14-deficient cells. We uncovered the ATR-CHK1 pathway as essential for viability of PARP14-deficient cells, and identified regulation of DNA replication dynamics as an important mechanistic contributor to the synthetic lethality observed. Our work shows that PARP14 is an important modulator of the response to ATR-CHK1 pathway inhibitors.</p>
Endogenous p21 levels protect genomic stability by suppressing both excess and restrained nascent DNA synthesis
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Data from: Clonal evolution and genome stability in a 2,500-year-old fungal individual
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RAD54L2 counters TOP2-DNA adducts to promote genome stability (Etoposide treated RPE1 CRISPR screens in TP53 and RAD53L2 knock outs)
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Data from: Genome-wide CRISPR synthetic lethality screen identifies a role for the ADP-ribosyltransferase PARP14 in replication fork stability controlled by ATR
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Data from: Patterns of cyto-nuclear linkage disequilibrium in Silene latifolia: genomic heterogeneity and temporal stability
Non-random association of alleles in the nucleus and cytoplasmic organelles, or cyto-nuclear linkage disequilibrium (LD), is both an important component of a number of evolutionary processes and a statistical indicator of others. The evolutionary significance of cyto-nuclear LD will depend on both its magnitude and how stable those associations are through time. Here, we use a longitudinal population genetic data set to explore the magnitude and temporal dynamics of cyto-nuclear disequilibria through time. We genotyped 135 and 170 individuals from 16 and 17 patches of the plant species Silene latifolia in Southwestern VA, sampled in 1993 and 2008, respectively. Individuals were genotyped at 14 highly polymorphic microsatellite markers and a single-nucleotide polymorphism (SNP) in the mitochondrial gene, atp1. Normalized LD (D′) between nuclear and cytoplasmic loci varied considerably depending on which nuclear locus was considered (ranging from 0.005–0.632). Four of the 14 cyto-nuclear associations showed a statistically significant shift over approximately seven generations. However, the overall magnitude of this disequilibrium was largely stable over time. The observed origin and stability of cyto-nuclear LD is most likely caused by the slow admixture between anciently diverged lineages within the species' newly invaded range, and the local spatial structure and metapopulation dynamics that are known to structure genetic variation in this system.
Genome stability of murine cytomegalovirus vectors with large deletions and insertions
<p>We investigated the basic characteristics of a new murine cytomegalovirus (MCMV) vector platform. Using BAC technology, we engineered replication-competent recombinant MCMVs with deletions of up to 26% of the wild type genome. To this end, we targeted five gene blocks (m01-m17, m106-m109, m129-m141, m144-m158, and m159-m170). BACs featuring deletions from 26-18% of the wild type genome exhibited delayed virus reconstitution, while smaller deletions (up to 16%) demonstrated reconstitution kinetics similar to the wild type. Utilizing an innovative methodology, we introduced large genomic DNA segments, up to 35 kbp, along with reporter genes into a newly designed vector with a potential cloning capacity of 46 kbp (Q4). Next, two independent stuffer DNAs were inserted into the Q4 BAC resulting in Q4-LAD and Q4-LRBAs BACs. LAD is an AT-rich DNA sequence based on inactivated human adenovirus genome (34 kbp) and a non-coding portion of human LRBA (LPS responsive beige-like anchor protein) gene a non-coding portion of human LRBA gene which is GC-rich (36 kbp). The Q4-LRBAs BAC was further modified by inserting two different transgene expression cassettes encoding for either Gaussian luciferase (GLuc) resulting in Q4-LRBAs-GLuc. First, we rescued replicating vectors after transfection of MEFs with the above described BACs. Each vector preparation was passaged up to 10 passage on MEFs. Then MEF cells (70% confluence) were infected with Q4, Q4-LAD, and Q4-LRBAs-GLuc at MOI 0.5. derived from passage 1, 5 and 10. As control we used lysates of wild type BAC derived MCMV infected MEFs after passages 1, 5, 10, 15, and 20. After 48 hpi, virus particles were harvested, purified, and DNA was extracted using the NucleoSpin Tissue kit (Macherey-Nagel, Germany). Illumina NGS was performed on 100 ng DNA template for each sample (paired end sequencing, 2×150 bp, 5 Mio reads/sample). This dataset contains the raw sequencing data (individually named .zip files) and a table (an .xlsx file packed into MCMV Vector Stability_VACCINES_2024.zip) with the detailed specifications of the dataset. The reference sequences, which we used for the analysis in our Vaccines paper (Riedl et al. Vaccines, 2024), are provided in a zipped folder in .gb format.</p>
ATM-ESCO2-SMC3 axis promotes 53BP1 recruitment in response to DNA damage and safeguards genome integrity by stabilizing cohesin complex
<p>53BP1 is primarily known as a key regulator in DNA double-strand break (DSB) repair. However, the mechanism of DSB-triggered cohesin modification-modulated chromatin structure on the recruitment of 53BP1 remains largely elusive. Here we identified acetyltransferase ESCO2 as a regulator for DSB-induced cohesin-dependent chromatin structure dynamics, which promotes 53BP1 recruitment. Mechanistically, in response to DNA damage, ATM phosphorylates ESCO2 S196 and T233. MDC1 recognizes phosphorylated ESCO2 and recruits ESCO2 to DSB sites. ESCO2-mediated acetylation of SMC3 stabilizes cohesin complex conformation and regulates the chromatin structure at DSB breaks, which is essential for the recruitment of 53BP1 and the formation of 53BP1 microdomains. Furthermore, depletion of ESCO2 in both colorectal cancer cells and xenografted nude mice sensitizes cancer cells to chemotherapeutic drugs. Collectively, our results reveal a molecular mechanism for the ATM-ESCO2-SMC3 axis in DSB repair and genome integrity maintenance with a vital role in chemotherapy response in colorectal cancer.</p>
ATM-ESCO2-SMC3 axis promotes 53BP1 recruitment in response to DNA damage and safeguards genome integrity by stabilizing cohesin complex
<p>53BP1 is primarily known as a key regulator in DNA double-strand break (DSB) repair. However, the mechanism of DSB-triggered cohesin modification-modulated chromatin structure on the recruitment of 53BP1 remains largely elusive. Here we identified acetyltransferase ESCO2 as a regulator for DSB-induced cohesin-dependent chromatin structure dynamics, which promotes 53BP1 recruitment. Mechanistically, in response to DNA damage, ATM phosphorylates ESCO2 S196 and T233. MDC1 recognizes phosphorylated ESCO2 and recruits ESCO2 to DSB sites. ESCO2-mediated acetylation of SMC3 stabilizes cohesin complex conformation and regulates the chromatin structure at DSB breaks, which is essential for the recruitment of 53BP1 and the formation of 53BP1 microdomains. Furthermore, depletion of ESCO2 in both colorectal cancer cells and xenografted nude mice sensitizes cancer cells to chemotherapeutic drugs. Collectively, our results reveal a molecular mechanism for the ATM-ESCO2-SMC3 axis in DSB repair and genome integrity maintenance with a vital role in chemotherapy response in colorectal cancer.</p>
Data from: Patterns of cyto-nuclear linkage disequilibrium in Silene latifolia: genomic heterogeneity and temporal stability
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Data from: White shark genome reveals ancient elasmobranch adaptations associated with wound healing and the maintenance of genome stability
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Genomic prediction with non-additive effects in beef cattle: Stability of variance component and genetic effect estimates against population size
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Data from: Resource stability and geographic isolation are associated with genome divergence in western Palearctic crossbills
While many conifers produce annually variable seed crops, serotinous species (which hold seeds in cones for multiple years) represent unusually stable food resources for seed predators. Such stability is conducive to residency and potentially population divergence of consumers as exemplified by the Cassia crossbill (Loxia sinesciuris) in North America. We used genotyping-by-sequencing to test whether three Mediterranean subspecies of common crossbills (L. curvirostra) associated with the serotinous Aleppo pine (Pinus halepensis) were more genetically distinct than European crossbills associated with non-serotinous conifers. We assembled a Cassia crossbill draft genome as a reference for mapping GBS reads, and as a first step towards a more contiguous genome assembly. We found clear patterns of genetic divergence for each of the P. halepensis-associated subspecies. Geographic isolation, as promoted by resource stability and residency, is associated with genetic divergence of two of these subspecies. However, geographic isolation cannot account for divergence of L. c. hispana. Instead, resource stability likely contributed to divergence by reducing dispersal and increasing resource competition that may limit breeding by immigrants. In contrast, we found no differentiation among common crossbills associated with less stable resources, and only slight differentiation between common crossbills and parrot crossbills (L. pytyopsittacus). The substantial morphological divergence between common and parrot crossbills has likely originated or been maintained by selection despite gene flow generated by spatiotemporal resource fluctuation. Our results indicate that phenological as well as morphological characteristics of conifers have influenced crossbill diversification, and suggest a possible link between resource stability and population divergence.
Data from: Ancient hybridization and genomic stabilization in a swordtail fish
A rapidly increasing body of work is revealing that the genomes of distinct species often exhibit hybrid ancestry, presumably due to postspeciation hybridization between closely related species. Despite the growing number of documented cases, we still know relatively little about how genomes evolve and stabilize following hybridization, and to what extent hybridization is functionally relevant. Here, we examine the case of Xiphophorus nezahualcoyotl, a teleost fish whose genome exhibits significant hybrid ancestry. We show that hybridization was relatively ancient and is unlikely to be ongoing. Strikingly, the genome of X. nezahualcoyotl has largely stabilized following hybridization, distinguishing it from examples such as human–Neanderthal hybridization. Hybridization-derived regions are remarkably distinct from other regions of the genome, tending to be enriched in genomic regions with reduced constraint. These results suggest that selection has played a role in removing hybrid ancestry from certain functionally important regions. Combined with findings in other systems, our results raise many questions about the process of genomic stabilization and the role of selection in shaping patterns of hybrid ancestry in the genome.
Data from: Resource stability and geographic isolation are associated with genome divergence in western Palearctic crossbills
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Data from: Ancient hybridization and genomic stabilization in a swordtail fish
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Setdb1 safeguards genome stability against stem cell necroptosis and bowel inflammation (RNA-seq)
GEO Series GSE129172. Mus musculus. 8 samples. Type: Expression profiling by high throughput sequencing.
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