scholarly journals Using Telomeric Length Measurements and Methylation to Understand The Karyotype Diversification of Ctenomys Minutus (A Small Fossorial Mammals)

2021 ◽  
Author(s):  
Cristina A. Matzenbacher ◽  
Juliana Silva ◽  
Ana Leticia H. Garcia ◽  
Rafael Kretschmer ◽  
Mónica Cappetta ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Genomic Instability ◽  
Chromosomal Instability ◽  
Diploid Number ◽  
Karyotype Evolution ◽  
Chromosomal Rearrangements ◽  
Global Dna Methylation ◽  
Methylated Dna ◽  
Significant Difference ◽  
Length Measurements

Abstract The genus Ctenomys has been widely used in karyotype evolution studies due to the variation in their diploid numbers (2n), which range from 2n = 10 to 2n = 70. Ctenomys minutus is characterized by intraspecific variation in diploid number (2n = 42, 46, 48, and 50), which makes it an interesting model to investigate the genomic instability mechanisms that have led to different cytotypes in this species. We aimed to contribute to the knowledge about telomeres’ role in chromosomal instability and global DNA methylation in the genome evolution of C. minutus. This study found that telomere length differs between cytotypes, but only for females (50a<46a,48a,42), although methylation was also higher, no significant difference was shown. It was also shown that young individuals, regardless of cytotype, had the longest telomere and the most methylated DNA, although only the last was statistically significant. Despite this, there is still much to be answered, although new cytotypes seem to have emerged within the distribution of parental cytotypes by the accumulation of different chromosomal rearrangements.

scholarly journals Paternal arbuscular mycorrhizal fungal status affects DNA methylation in seeds

2017 ◽  
Vol 13 (9) ◽  
pp. 20170407 ◽  
Author(s):  
Sandra Varga ◽  
Carl D. Soulsbury
Keyword(s):  
Dna Methylation ◽  
Mycorrhizal Fungi ◽  
Seed Mass ◽  
Arbuscular Mycorrhizal ◽  
Similar Proportion ◽  
Global Dna Methylation ◽  
Transgenerational Effects ◽  
Methylated Dna ◽  
Arbuscular Mycorrhizal Fungal ◽  
First Time

Most land plants grow in association with arbuscular mycorrhizal fungi (AMF) in their roots and these fungi can cause transgenerational effects on plants' offspring. These may be caused by changes in DNA methylation of the offspring. In this study, we compared the amount of global DNA methylation in seeds of the gynodioecious plant Geranium sylvaticum in relation to the gender and the AMF status of the parents producing the seeds. The amount of DNA methylated was positively related to seed mass. Seeds produced by females had a similar proportion of methylated DNA regardless of the AMF status of the father siring the seed. By contrast, seeds from hermaphrodites had higher DNA methylation when sired by AMF fathers. We show to the best of our knowledge for the first time, that the AMF status of fathers can affect DNA methylation in seeds and that these changes in DNA methylation are further dependent on the gender of the mother producing the seeds.

scholarly journals Mitotic systemic genomic instability in yeast

2017 ◽  
Author(s):  
Nadia M. V. Sampaio ◽  
Aline Rodrigues-Prause ◽  
V. P. Ajith ◽  
Theodore M. Gurol ◽  
Mary J. Chapman ◽  
...  
Keyword(s):  
Genomic Instability ◽  
Loss Of Heterozygosity ◽  
Chromosomal Instability ◽  
Experimental Approach ◽  
Human Cancer ◽  
Chromosomal Rearrangements ◽  
Point Mutations ◽  
Genomic Variation ◽  
Genomic Disorder ◽  
Structural Genomic

ABSTRACTConventional models of genome evolution generally include the assumption that mutations accumulate gradually and independently over time. We characterized the occurrence of sudden spikes in the accumulation of genome-wide loss-of-heterozygosity (LOH) inSaccharomyces cerevisiae, suggesting the existence of a mitotic systemic genomic instability process (mitSGI). We characterized the emergence of a rough colony morphology phenotype resulting from an LOH event spanning a specific locus (ACE2/ace2-A7). Surprisingly, half of the clones analyzed also carried unselected secondary LOH tracts elsewhere in their genomes. The number of secondary LOH tracts detected was 20-fold higher than expected assuming independence between mutational events. Secondary LOH tracts were not detected in control clones without a primary selected LOH event. We then measured the rates of single and double LOH at different chromosome pairs and found that coincident LOH accumulated at rates 30-100 fold higher than expected if the two underlying single LOH events occurred independently. These results were consistent between two different strain backgrounds, and in mutant strains incapable of entering meiosis. Our results indicate that a subset of mitotic cells within a population experience systemic genomic instability episodes, resulting in multiple chromosomal rearrangements over one or few generations. They are reminiscent of early reports from the classic yeast genetics literature, as well as recent studies in humans, both in the cancer and genomic disorder contexts, all of which challenge the idea of gradual accumulation of structural genomic variation. Our experimental approach provides a model to further dissect the fundamental mechanisms responsible for mitSGI.SIGNIFICANCE STATEMENTPoint mutations and alterations in chromosome structure are generally thought to accumulate gradually and independently over many generations. Here, we combined complementary genetic approaches in budding yeast to track the appearance of chromosomal changes resulting in loss-of-heterozygosity (LOH). Contrary to expectations, our results provided evidence for the occurrence of non-independent accumulation of multiple LOH events over one or a few cell generations. These results are analogous to recent reports of bursts of chromosomal instability in humans. Our experimental approach provides a framework to further dissect the fundamental mechanisms underlying systemic chromosomal instability processes, including in the human cancer and genomic disorder contexts.

306 ANALYSIS OF GLOBAL DNA METHYLATION IN BOVINE SPERMATOZOA

2006 ◽  
Vol 18 (2) ◽  
pp. 260
Author(s):  
H. Kato ◽  
M. Kishimoto ◽  
T. Mitani ◽  
K. Matsumoto ◽  
K. Saeki ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Species Difference ◽  
Restriction Enzymes ◽  
Area Measurement ◽  
Global Dna Methylation ◽  
Simple Method ◽  
Sperm Dna ◽  
Significant Difference ◽  
Bovine Spermatozoa ◽  
The Mean

Methylation of cytosine base in the CpG dinucleotide sequence (DNA methylation) is a major epigenetic modification of the genome and plays an important role in gene expression. Recently, global DNA methylation in genome was studied by using a restriction landmark genomic scanning (RLGS) method and/or a representational difference analysis (RDA) method. However, these methods are complicated and need to use restriction enzymes. Therefore, the information derived from those methods is restricted to the region of the DNA sequence which is able to be cleaved by restriction enzymes. In this study, to establish a simple method to estimate global DNA methylation level in bovine spermatozoa, we tried to develop the DNA methylation analyzing method by using immunostaining of 5-methylcytosine. The immunostaining method for 5-methylcytosine in this study was based on the method developed by Benchaib et al. (2003 Fertil. Steril. 80, 947-952) for human spermatozoa. Because of the species difference, we modified some treatments to apply to bovine spermatozoa. Frozen-thawed bovine spermatozoa were washed by using 30 and 45% Percoll gradient solutions. After washing, spermatozoa were treated with 0.25 dithicthreitol M (DTT) and 1% sodium dodecyl sulfate (SDS) at room temperature (RT). Then, treated spermatozoa were spread on a slide glass with Cytospin4 (30g, 5 � 104 cells/mL) and air-dried at RT. Air-dried bovine spermatozoa specimens were fixed in methanol: glacial acetic acid (3:1) solution at RT and treated with 1% Triton X and 1% SDS at RT; DNA was denatured with 6 N HCl at RT. After the denaturation, 5-methylcytosine in sperm DNA was analyzed by immunofluorescence technique with mouse anti 5-methylcytosine antibody and fluorescein isothiocyanate (FITC)-conjugated goat anti mouse IgG antibody. The total sperm DNA was counterstained with propidium iodide (PI). Stained samples were observed with a confocal laser scanning microscope and obtained images were analyzed with fluorescence image analysis software. The area that was clearly stained with PI in each sperm head was designated and measured as the area of total sperm DNA, and the number of the dots that showed FITC fluorescence within the total sperm DNA area was designated and measured as the area of 5-methylcytosine in total sperm DNA. The area measurement was performed with fixed light strength. Three bovine spermatozoa samples derived from different bulls, used daily for calf production by AI, were examined. The ratio of the mean total area of the 5-methylcytosine in sperm DNA to the mean total area of the sperm DNA was 34.1% in bull A (9.13 � 5.66 �m2, 26.75 � 5.29 �m2, n = 57), 45.2% in bull B (16.60 � 3.79 �m2, 36.74 � 5.95 �m2, n = 41) and 43.9% in bull C (14.66 � 4.27 �m2, 33.45 � 7.13 �m2, n = 22). There was significant difference in the ratio between bull A and bulls B and C (P < 0.01). More research is required to evaluate the meaning of this individual difference of DNA methylation between bulls. This work was supported by Wakayama Prefecture Collaboration of Regional Entities for the Advanced of Technological Excellence, Japan, and by a Grant-in-Aid for the 21st Century Center of Excellence Program of the MEXT, Japan.

scholarly journals Hypo-methylation mediates chromosomal instability in pancreatic NET

2017 ◽  
Vol 24 (3) ◽  
pp. 137-146 ◽  
Author(s):  
I Marinoni ◽  
A Wiederkeher ◽  
T Wiedmer ◽  
S Pantasis ◽  
A Di Domenico ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Chromosomal Instability ◽  
Global Dna Methylation ◽  
Epigenetic Changes ◽  
Knock Down ◽  
Alternative Lengthening ◽  
Increased Risk ◽  
Pancreatic Net ◽  
G0 Phase

DAXX and or ATRX loss occur in 40% of pancreatic neuroendocrine tumors (PanNETs). PanNETs negative for DAXX or ATRX show an increased risk of relapse. The tumor-associated pathways activated upon DAXX or ATRX loss and how this event may induce chromosomal instability (CIN) and alternative lengthening telomeres (ALT) are still unknown. Both DAXX and ATRX are involved in DNA methylation regulation. DNA methylation of heterochromatin and of non-coding sequences is extremely important for the maintenance of genomic stability. We analyzed the association of DAXX and/or ATRX loss and CIN with global DNA methylation in human PanNET samples and the effect of DAXX knock-down on methylation and cell proliferation. We assessedLINE1as well as global DNA methylation in 167 PanNETs, and we found that DAXX and or ATRX-negative tumors and tumors with CIN were hypomethylated. DAXX knock-down in PanNET cell lines blocked cells in G1/G0 phase and seemed to increase CIN in QGP-1 cells. However, no direct changes in DNA methylation were observed after DAXX knock-downin vitro. In conclusion, our data indicate that epigenetic changes are crucial steps in the progression of PanNETs loss and suggest that DNA methylation is the mechanism via which CIN is induced, allowing clonal expansion and selection.

Maternal intermittent fasting before mating alters hepatic DNA methylation in offspring

Epigenomics ◽  
2021 ◽  
Author(s):  
Wenzhen Yin ◽  
Yuan Liang ◽  
Lijun Sun ◽  
Yue Yin ◽  
Weizhen Zhang
Keyword(s):  
Dna Methylation ◽  
Bisulfite Sequencing ◽  
Intermittent Fasting ◽  
Global Dna Methylation ◽  
Impaired Glucose Metabolism ◽  
Methylated Dna ◽  
Glucose Levels ◽  
Blood Glucose Levels ◽  
Genome Wide ◽  
Genome Bisulfite Sequencing

Aim: Our aim was to explore how maternal intermittent fasting (IF) influences offspring metabolism. Materials & methods: A model of female C57BL/6J mice alternate-day feeding before mating was established and alteration of hepatic DNA methylation in offspring analyzed by whole genome bisulfite sequencing. Results: IF dams weighed less (p = 0.03) and had lower random blood glucose levels (p = 0.04). Lower birth weight (p = 0.0031) and impaired glucose metabolism were also observed in the offspring of the IF mice. The hepatic genome-wide DNA methylation maps showed a correlation between maternal IF and decreased hepatic global DNA methylation of adult offspring. In the offspring liver, 2869 differentially methylated DNA regions were altered. Conclusions: Our finding suggests that maternal IF before mating significantly alters hepatic DNA methylation in offspring.

Methylation of global DNA repeat LINE-1 and subtelomeric DNA repeats D4Z4 in leukocytes is associated with biochemical recurrence in African American prostate cancer patients

2019 ◽  
Vol 40 (9) ◽  
pp. 1055-1060
Author(s):  
Junfeng Xu ◽  
Chia-Wen Tsai ◽  
Wen-Shin Chang ◽  
Yuyan Han ◽  
Da-Tian Bau ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Dna Methylation ◽  
African American ◽  
Confidence Interval ◽  
Biochemical Recurrence ◽  
Survival Function ◽  
Global Dna Methylation ◽  
Dna Repeats ◽  
Significant Difference ◽  
Epidemiological Characteristics

Abstract Global DNA methylation may play important roles in cancer etiology and prognosis. The goal of this study is to investigate whether the methylation of long interspersed nucleotide elements (LINE-1) and subtelomeric DNA repeats D4Z4 in leukocyte DNA is associated with aggressive prostate cancer (PCa) in African Americans. We measured DNA methylation levels of LINE-1 and D4Z4 in 306 African American (AA) PCa patients using pyrosequencing and compared their methylation levels among clinical variables. We further applied multivariate Cox proportional hazards model and Kaplan–Meier survival function and log-rank tests to assess the association between DNA methylation and biochemical recurrence (BCR). Overall, there was no significant difference of the methylation levels of LINE-1 and D4Z4 among patients with different clinical and epidemiological characteristics. However, the methylation of LINE-1 and D4Z4 was associated with BCR. Patients with lower LINE-1 methylation and higher D4Z4 methylation exhibited markedly increased risks of BCR with adjusted hazard ratios of 3.34 (95% confidence interval, 1.32–8.45) and 4.12 (95% confidence interval, 1.32–12.86), respectively, and significantly shorter BCR-free survival times. Our results suggest that lower global DNA methylation and higher subtelomeric region methylation may predict worse prognosis in localized AA PCa patients.

scholarly journals A novel understanding of global DNA methylation in bobcat (Lynx rufus)

Genome ◽  
2020 ◽  
Vol 63 (2) ◽  
pp. 125-130
Author(s):  
Bonnie Cantrell ◽  
Sydney Friedman ◽  
Hannah Lachance ◽  
Chris Bernier ◽  
Brenda Murdoch ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Conservation Biology ◽  
Differential Methylation ◽  
Lynx Rufus ◽  
Global Dna Methylation ◽  
Epigenetic Mechanisms ◽  
Methylated Dna ◽  
Genome Wide ◽  
Weight Data ◽  
Insight Into

Epigenetic mechanisms may provide a novel prospective of bobcat (Lynx rufus) adaptation to habitat loss/fragmentation. Previous research has focused on bobcat behavior and genetics, but epigenetics has not been studied in bobcat. The aim of this study was to determine the quantity of global DNA methylation in the liver of 30 bobcats. DNA was extracted from liver samples obtained from the Vermont Fish and Wildlife Department. The percent of global DNA methylation was quantified and calculated using the MethylFlashTM Methylated DNA 5-mC Quantification Kit from Epigentek (Farmingdale, NY, USA). Age, sex, and carcass weight data were collected at sampling and analyzed with percent of global DNA methylation. Global DNA methylation was found to range from 0.46% to 2.76%. Age ranged from <1 to 12 years old and weight ranged from 3.18 to 13.61 kg. Further analysis of differential methylation may provide insight into novel means of bobcat conservation within different regions of Vermont. These results reinforce the need for genome-wide epigenetic studies in conservation biology.

scholarly journals Reproductive isolation in a nascent species pair is associated with aneuploidy in hybrid offspring

2015 ◽  
Vol 282 (1802) ◽  
pp. 20142862 ◽  
Author(s):  
Anne-Marie Dion-Côté ◽  
Radka Symonová ◽  
Petr Ráb ◽  
Louis Bernatchez
Keyword(s):  
Reproductive Isolation ◽  
Chromosome Numbers ◽  
Chromosomal Instability ◽  
Diploid Number ◽  
Chromosomal Rearrangements ◽  
Coregonus Clupeaformis ◽  
Lake Whitefish ◽  
Mitotic Instability ◽  
Two Populations

Speciation may occur when the genomes of two populations accumulate genetic incompatibilities and/or chromosomal rearrangements that prevent inter-breeding in nature. Chromosome stability is critical for survival and faithful transmission of the genome, and hybridization can compromise this. However, the role of chromosomal stability on hybrid incompatibilities has rarely been tested in recently diverged populations. Here, we test for chromosomal instability in hybrids between nascent species, the ‘dwarf’ and ‘normal’ lake whitefish ( Coregonus clupeaformis ). We examined chromosomes in pure embryos, and healthy and malformed backcross embryos. While pure individuals displayed chromosome numbers corresponding to the expected diploid number (2 n = 80), healthy backcrosses showed evidence of mitotic instability through an increased variance of chromosome numbers within an individual. In malformed backcrosses, extensive aneuploidy corresponding to multiples of the haploid number (1 n = 40, 2 n = 80, 3 n = 120) was found, suggesting meiotic breakdown in their F 1 parent. However, no detectable chromosome rearrangements between parental forms were identified. Genomic instability through aneuploidy thus appears to contribute to reproductive isolation between dwarf and normal lake whitefish, despite their very recent divergence (approx. 15–20 000 generations). Our data suggest that genetic incompatibilities may accumulate early during speciation and limit hybridization between nascent species.

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