Diversity of DNA methylation pattern and total DNA restriction pattern in symbiotic Nostoc

1996 ◽  
Vol 12 (1) ◽  
pp. 38-42 ◽  
Author(s):  
F. Lotti ◽  
L. Giovannetti ◽  
M. C. Margheri ◽  
S. Ventura ◽  
R. Materassi
Keyword(s):  
Dna Methylation ◽  
Methylation Pattern ◽  
Restriction Pattern ◽  
Dna Restriction ◽  
Total Dna ◽  
Dna Methylation Pattern

Impact of Global and Gene-Specific DNA Methylation Pattern in Relapsed Multiple Myeloma Patients Treated with Bortezomib

Blood ◽  
2011 ◽  
Vol 118 (21) ◽  
pp. 132-132
Author(s):  
Carlos Fernández de Larrea ◽  
Beatriz Martin-Antonio ◽  
María Teresa Cibeira ◽  
Alfons Navarro ◽  
Natalia Tovar ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Multiple Myeloma ◽  
Bone Marrow ◽  
Plasma Cells ◽  
Methylation Status ◽  
Methylation Pattern ◽  
Global Methylation ◽  
Bortezomib Treatment ◽  
Total Dna ◽  
Dna Methylation Pattern

Abstract Abstract 132 Background: There is increasing evidence on the importance of epigenetic mechanisms such as DNA methylation and acetylation in the pathogenesis of multiple myeloma (MM). A global DNA hypomethylation pattern with selective genes hypermethylated has been described in myeloma plasma cells when compared with normal plasma cells. This fact could constitute a potential target for the use of demethylating agents. The response to bortezomib, a widely used agent against myeloma cells through proteasome inhibition, is particularly variable in patients with relapsed or refractory disease. We examined both, the global DNA methylation pattern and methylation state in 30 genes, in DNA from bone marrow cells and correlated our findings with response, progression (PFS) and overall-survival (OS) to bortezomib in patients with relapsed myeloma. Methods: Seventy-five patients (37M/38F; median age 65 years, range 29 to 80) with relapsed MM were treated from December 2002 to March 2010 with bortezomib-based regimens at our institution. Median follow-up for patients alive was 31 months (range 6 to 45). Genomic DNA was isolated from bone marrow slides with plasma cell infiltration at the time of relapse using a commercial kit (Qiagen). Global methylation was determined in all patients by ELISA (Epigentek), obtaining the percentage of 5-methylcytosine (5-mC) present in total DNA. CpG island DNA methylation profile of 30 genes was determined in 42 patients by a DNA methylation PCR system based on methylation sensitive and/or dependent restriction enzymes digestion (Qiagen). These genes were selected based on either their potential impact on prognosis in previous reports, or on the pathogenesis of MM, involving several cellular pathways such as innate immune response (CD40, EP300, MIF, CBP, TGFB1, TGFBR2), cytokine receptors (CXCR4, CXCL12, IL6R, IL17RA), transcription factors (NFKB1, NFKBIB, IRF4), cytokine stimulus response (SOCS3), apoptosis (TNFRSF13C, TNFRSF21, TNFRSF25, BCL2L11), tumor suppression (TP53, BRCA1, DAPK1, CDH1, RASD1), cellular cycle control (CCNB1, CCND1, CCNA2, CCNE1, CDKN2A, CDKN1A) and efflux transporter (ABCG2). Results: Overall response (OR) was achieved in 62% of the patients (complete remission 6.7%, partial response 44% and minor response 10.7%), while 9 (12%) and 20 (26.7%) showed no response (NR) or progressive disease (PD), respectively. The median PFS and OS after bortezomib therapy were 6 and 19.6 months, respectively. A low global methylation status was observed (median 4.68% of 5-mC, range 0.02 to 13.6) and patients with more than 3.95% of total DNA methylated achieved better OS than patients with more unmethylated DNA (median 30 versus 15 months) (p=0.004; Figure 1). Concerning methylation on specific-genes, a methylation status lower than 3.97% in CXCR4 was correlated with a longer PFS after bortezomib treatment (p=0.009; Figure 2). Clustering analysis with methylation status for these genes, showed that NFkB presented a differential profile according to response to bortezomib (p=0.037). A relative low methylation percentage (lower than 6.7%) in this gene was also associated with longer OS after bortezomib treatment (p=0.015; Figure 3). A positive correlation was observed with high methylation status in NFkB and other genes involved in the same cellular pathway (NFKBIB, EP300, CBP, CCNA2, CCNB1) (p<0.025). Moreover, a combination of highly methylated global genome and low NFkB methylation status defined a specific subset of patients with better prognosis (p=0.005) in terms of OS. Finally, a multivariate analysis including number of previous treatment lines, autologous stem-cell transplantation, previous exposure to bortezomib as well as global and NFkB methylation status showed that only the last two variables retained significance (p=0.035, OR=0.43 and p=0.028, OR=3.4, respectively). Conclusion: In our study, a low methylation grade in the overall DNA was observed. A relative high methylation status in the global genome and low in NFkB were associated with longer OS after bortezomib therapy in patients with relapsed or refractory myeloma. These results could be explained through the potential cell effect mediated by bortezomib in the NFkb pathway. Finally, a subgroup of patients with an ominous prognosis associated with DNA methylation at relapse in spite of bortezomib treatment was identified. Disclosures: Fernández de Larrea: Novartis: Honoraria; Janssen: Honoraria; Celgene: Honoraria. Cibeira:Janssen: Honoraria; Celgene: Honoraria. Rosiñol:Janssen: Honoraria; Celgene: Honoraria. Blade:Janssen: Honoraria; Celgene: Honoraria.

Correlation between Ecological Plasticity of Elite Winter Wheat Varieties and DNA Methylation Pattern Polymorphism within Variety

2016 ◽  
Vol 12 (2) ◽  
pp. 50-59 ◽  
Author(s):  
O.P. Kravets ◽  
◽  
D.O. Sokolova ◽  
A.M. Berestyana ◽  
O.R. Shnurenko ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Winter Wheat ◽  
Methylation Pattern ◽  
Wheat Varieties ◽  
Ecological Plasticity ◽  
Dna Methylation Pattern ◽  
Pattern Polymorphism ◽  
Winter Wheat Varieties

Examination of the dynamics of global DNA methylation pattern establishment during spermatogenesiss

2007 ◽  
Vol 30 (4) ◽  
pp. 90
Author(s):  
Kirsten Niles ◽  
Sophie La Salle ◽  
Christopher Oakes ◽  
Jacquetta Trasler
Keyword(s):  
Dna Methylation ◽  
Germ Cell ◽  
Germ Cells ◽  
Epigenetic Modification ◽  
Methylation Pattern ◽  
Chromosome 9 ◽  
Specific Gene ◽  
Global Methylation ◽  
Dna Methylation Pattern ◽  
Methylation Patterns

Background: DNA methylation is an epigenetic modification involved in gene expression, genome stability, and genomic imprinting. In the male, methylation patterns are initially erased in primordial germ cells (PGCs) as they enter the gonadal ridge; methylation patterns are then acquired on CpG dinucleotides during gametogenesis. Correct pattern establishment is essential for normal spermatogenesis. To date, the characterization and timing of methylation pattern acquisition in PGCs has been described using a limited number of specific gene loci. This study aimed to describe DNA methylation pattern establishment dynamics during male gametogenesis through global methylation profiling techniques in a mouse model. Methods: Using a chromosome based approach, primers were designed for 24 regions spanning chromosome 9; intergenic, non-repeat, non-CpG island sequences were chosen for study based on previous evidence that these types of sequences are targets for testis-specific methylation events. The percent methylation was determined in each region by quantitative analysis of DNA methylation using real-time PCR (qAMP). The germ cell-specific pattern was determined by comparing methylation between spermatozoa and liver. To examine methylation in developing germ cells, spermatogonia from 2 day- and 6 day-old Oct4-GFP (green fluorescent protein) mice were isolated using fluorescence activated cell sorting. Results: As compared to liver, four loci were hypomethylated and five loci were hypermethylated in spermatozoa, supporting previous results indicating a unique methylation pattern in male germ cells. Only one region was hypomethylated and no regions were hypermethylated in day 6 spermatogonia as compared to mature spermatozoa, signifying that the bulk of DNA methylation is established prior to type A spermatogonia. The methylation in day 2 spermatogonia, germ cells that are just commencing mitosis, revealed differences of 15-20% compared to day 6 spermatogonia at five regions indicating that the most crucial phase of DNA methylation acquisition occurs prenatally. Conclusion: Together, these studies provide further evidence that germ cell methylation patterns differ from those in somatic tissues and suggest that much of methylation at intergenic sites is acquired during prenatal germ cell development. (Supported by CIHR)

Identification of exotic genetic components and DNA methylation pattern analysis of three cotton introgression lines from Gossypium bickii

2011 ◽  
Vol 45 (2) ◽  
pp. 204-210 ◽  
Author(s):  
Shou-Pu He ◽  
Jun-Ling Sun ◽  
Chao Zhang ◽  
Xiong-Ming Du
Keyword(s):  
Dna Methylation ◽  
Pattern Analysis ◽  
Methylation Pattern ◽  
Introgression Lines ◽  
Genetic Components ◽  
Dna Methylation Pattern

scholarly journals DNA methylation pattern is associated with elevated expression of DGAT2 in hybrid tilapia

2021 ◽  
Author(s):  
Huan Zhong ◽  
Yi Zhou ◽  
Hong Zhang ◽  
Wei Xiao
Keyword(s):  
Dna Methylation ◽  
Methylation Pattern ◽  
Elevated Expression ◽  
Dna Methylation Pattern

scholarly journals Whole-Genome Methylation Analysis Revealed ART-Specific DNA Methylation Pattern of Neuro- and Immune-System Pathways in Chinese Human Neonates

2021 ◽  
Vol 12 ◽  
Author(s):  
Zongzhi Liu ◽  
Wei Chen ◽  
Zilong Zhang ◽  
Junyun Wang ◽  
Yi-Kun Yang ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Immune System ◽  
Cord Blood ◽  
Genetic Model ◽  
Housekeeping Genes ◽  
Normal Pregnancy ◽  
Methylation Pattern ◽  
Whole Genome ◽  
Maternal Cell ◽  
Dna Methylation Pattern

The DNA methylation of human offspring can change due to the use of assisted reproductive technology (ART). In order to find the differentially methylated regions (DMRs) in ART newborns, cord blood maternal cell contamination and parent DNA methylation background, which will add noise to the real difference, must be removed. We analyzed newborns’ heel blood from six families to identify the DMRs between ART and natural pregnancy newborns, and the genetic model of methylation was explored, meanwhile we analyzed 32 samples of umbilical cord blood of infants born with ART and those of normal pregnancy to confirm which differences are consistent with cord blood data. The DNA methylation level was lower in ART-assisted offspring at the whole genome-wide level. Differentially methylated sites, DMRs, and cord blood differentially expressed genes were enriched in the important pathways of the immune system and nervous system, the genetic patterns of DNA methylation could be changed in the ART group. A total of three imprinted genes and 28 housekeeping genes which were involved in the nervous and immune systems were significant different between the two groups, six of them were detected both in heel blood and cord blood. We concluded that there is an ART-specific DNA methylation pattern involved in neuro- and immune-system pathways of human ART neonates, providing an epigenetic basis for the potential long-term health risks in ART-conceived neonates.

Serum/plasma DNA methylation pattern and early detection of breast cancer

2015 ◽  
Vol 4 (2) ◽  
pp. 120
Author(s):  
AliM Ardekani ◽  
Hamed Abdolghafoorian ◽  
Arootin Gharibiyan ◽  
SeyedAhmad Hashemi ◽  
Mahdie Hadi
Keyword(s):  
Breast Cancer ◽  
Dna Methylation ◽  
Early Detection ◽  
Methylation Pattern ◽  
Plasma Dna ◽  
Dna Methylation Pattern
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