Bisulfite-free approaches for DNA methylation profiling

2017 ◽  
Vol 9 (10) ◽  
pp. 1537-1549 ◽  
Author(s):  
Takaaki Kurinomaru ◽  
Ryoji Kurita
Keyword(s):  
Dna Methylation ◽  
Epigenetic Modification ◽  
Methylation Analysis ◽  
Research Fields ◽  
Free Dna ◽  
Wide Range ◽  
Dna Methylation Profiling ◽  
Dna Methylation Analysis ◽  
Methylation Profiling

The determination of epigenetic modification, especially that of 5-methylcytosine in the CpG sequence in mammals, has attracted attention because it should prove valuable in a wide range of research fields including diagnosis, drug discovery and therapy. In this review, we introduce the recent development of bisulfite-free DNA methylation analysis, which we classify into two categories, namely labelling-based and labelling-free assays.

scholarly journals Forensic Epigenetic Analysis: The Path Ahead

2019 ◽  
Vol 28 (4) ◽  
pp. 301-308 ◽  
Author(s):  
Sabeeha ◽  
Seyed E. Hasnain 
Keyword(s):  
Dna Methylation ◽  
Tissue Type ◽  
Methylation Analysis ◽  
Methylation Of Dna ◽  
Forensic Samples ◽  
Epigenetic Analysis ◽  
Dna Methylation Analysis ◽  
Methylation Profiling ◽  
Selection Of

Unlike DNA fingerprinting, which scores for differences in the genome that are phenotype neutral, epigenetic variations are gaining importance in forensic investigations. Methylation of DNA has a broad range of effects on the lifestyle, health status, and physical appearance of individuals. DNA methylation profiling of forensic samples is useful in determination of the cell or tissue type of the DNA source and also for estimation of age. The quality and quantity of the biosample available from the crime scene limits the possible number of DNA methylation tests and the selection of the technology that can be used. Several techniques have been used for DNA methylation analysis for epigenetic investigations of forensic biological samples. However, novel techniques are needed for multiplex analysis of epigenetic markers as the techniques that are currently available require a large amount of high-quality DNA and are also limited in their multiplexing capacities that are often insufficient to fully resolve a forensic query of interest.

scholarly journals DNA Methylation in Solid Tumors: Functions and Methods of Detection

2021 ◽  
Vol 22 (8) ◽  
pp. 4247
Author(s):  
Andrea Martisova ◽  
Jitka Holcakova ◽  
Nasim Izadi ◽  
Ravery Sebuyoya ◽  
Roman Hrstka ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Solid Tumors ◽  
Epigenetic Modification ◽  
Single Gene ◽  
Restriction Enzymes ◽  
Methylation Analysis ◽  
Cpg Dinucleotides ◽  
Sequencing Technologies ◽  
Genome Level ◽  
Dna Methylation Analysis

DNA methylation, i.e., addition of methyl group to 5′-carbon of cytosine residues in CpG dinucleotides, is an important epigenetic modification regulating gene expression, and thus implied in many cellular processes. Deregulation of DNA methylation is strongly associated with onset of various diseases, including cancer. Here, we review how DNA methylation affects carcinogenesis process and give examples of solid tumors where aberrant DNA methylation is often present. We explain principles of methods developed for DNA methylation analysis at both single gene and whole genome level, based on (i) sodium bisulfite conversion, (ii) methylation-sensitive restriction enzymes, and (iii) interactions of 5-methylcytosine (5mC) with methyl-binding proteins or antibodies against 5mC. In addition to standard methods, we describe recent advances in next generation sequencing technologies applied to DNA methylation analysis, as well as in development of biosensors that represent their cheaper and faster alternatives. Most importantly, we highlight not only advantages, but also disadvantages and challenges of each method.

scholarly journals Genome-Wide DNA Methylation Profiling in the Lotus (Nelumbo nucifera) Flower Showing its Contribution to the Stamen Petaloid

Plants ◽  
2019 ◽  
Vol 8 (5) ◽  
pp. 135 ◽  
Author(s):  
Zhongyuan Lin ◽  
Meihui Liu ◽  
Rebecca Njeri Damaris ◽  
Tonny Maraga Nyong’a ◽  
Dingding Cao ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Bisulfite Sequencing ◽  
Epigenetic Modification ◽  
Nelumbo Nucifera ◽  
Flower Formation ◽  
Relationship Analysis ◽  
Genome Wide ◽  
Dna Methylation Profiling ◽  
Methylation Profiling

DNA methylation is a vital epigenetic modification. Methylation has a significant effect on the gene expression influencing the regulation of different physiological processes. Current studies on DNA methylation have been conducted on model plants. Lotus (Nelumbo nucifera) is a basic eudicot exhibiting variations during development, especially in flower formation. DNA methylation profiling was conducted on different flower tissues of lotuses through whole genome bisulfite sequencing (WGBS) to investigate the effects of DNA methylation on its stamen petaloid. A map of methylated cytosines at the single base pair resolution for the lotus was constructed. When the stamen was compared with the stamen petaloid, the DNA methylation exhibited a global decrease. Genome-wide relationship analysis between DNA methylation and gene expression identified 31 different methylation region (DMR)-associated genes, which might play crucial roles in floral organ formation, especially in the stamen petaloid. One out of 31 DMR-associated genes, NNU_05638 was homolog with Plant U-box 33 (PUB33). The DNA methylation status of NNU_05638 promoter was distinct in three floral organs, which was confirmed by traditional bisulfite sequencing. These results provide further insights about the regulation of stamen petaloids at the epigenetic level in lotus.

Label-free DNA methylation analysis using opto-fluidic ring resonators

2010 ◽  
Vol 26 (3) ◽  
pp. 1016-1020 ◽  
Author(s):  
Jonathan D. Suter ◽  
Daniel J. Howard ◽  
Huidong Shi ◽  
Charles W. Caldwell ◽  
Xudong Fan
Keyword(s):  
Dna Methylation ◽  
Ring Resonators ◽  
Label Free ◽  
Methylation Analysis ◽  
Free Dna ◽  
Dna Methylation Analysis

Targeted deep DNA methylation analysis of circulating cell-free DNA in plasma using massively parallel semiconductor sequencing

Epigenomics ◽  
2015 ◽  
Vol 7 (3) ◽  
pp. 353-362 ◽  
Author(s):  
Felipe Vaca-Paniagua ◽  
Javier Oliver ◽  
Andre Nogueira da Costa ◽  
Philippe Merle ◽  
James McKay ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Massively Parallel ◽  
Methylation Analysis ◽  
Cell Free Dna ◽  
Free Dna ◽  
Semiconductor Sequencing ◽  
Dna Methylation Analysis ◽  
Circulating Cell Free Dna

scholarly journals Intimal sarcomas and undifferentiated cardiac sarcomas carry mutually exclusive MDM2, MDM4, and CDK6 amplifications and share a common DNA methylation signature

2021 ◽  
Author(s):  
Christian Koelsche ◽  
Jamal K. Benhamida ◽  
Felix K. F. Kommoss ◽  
Damian Stichel ◽  
David T. W. Jones ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Left Atrium ◽  
Molecular Data ◽  
Methylation Analysis ◽  
Mesenchymal Tumors ◽  
Therapeutic Implications ◽  
High Prevalence ◽  
Methylation Patterns ◽  
Dna Methylation Analysis ◽  
Methylation Profiling

AbstractUndifferentiated mesenchymal tumors arising from the inner lining (intima) of large arteries are classified as intimal sarcomas (ISA) with MDM2 amplification as their molecular hallmark. Interestingly, undifferentiated pleomorphic sarcomas (UPS) of the heart have recently been suggested to represent the cardiac analog of ISA due to morphological overlap and high prevalence of MDM2 amplifications in both neoplasms. However, little is known about ISAs and cardiac UPS without MDM2 amplifications and molecular data supporting their common classification is sparse. Here, we report a series of 35 cases comprising 25 ISAs of the pulmonary artery, one ISA of the renal artery and 9 UPS of the left atrium. Tumors were analyzed utilizing the Illumina Infinium MethylationEPIC BeadChip array, enabling copy number profile generation and unsupervised DNA methylation analysis. DNA methylation patterns were investigated using t-distributed stochastic neighbor embedding (t-SNE) analysis. Histologically, all ISAs and UPS of the left atrium resembled extra-cardiac UPS. All cases exhibited highly complex karyotypes with overlapping patterns between ISA and UPS. 29/35 cases showed mutually exclusive amplifications in the cell-cycle associated oncogenes MDM2 (25/35), MDM4 (2/35), and CDK6 (2/35). We further observed recurrent co-amplifications in PDGFRA (21/35), CDK4 (15/35), TERT (11/35), HDAC9 (9/35), and CCND1 (4/35). Sporadic co-amplifications occurred in MYC, MYCN, and MET (each 1/35). The tumor suppressor CDKN2A/B was frequently deleted (10/35). Interestingly, DNA methylation profiling (t-SNE) revealed an overlap of ISA and cardiac UPS. This “ISA” methylation signature was distinct from potential histologic and molecular mimics. In conclusion, our data reveal MDM4 and CDK6 amplifications in ISAs and UPS of the left atrium, lacking MDM2 amplification. We further report novel co-amplifications of various oncogenes, which may have therapeutic implications. Finally, the genetic and epigenetic concordance of ISAs and UPS of the left atrium further supports a shared pathogenesis and common classification.

Label-free DNA methylation analysis using the optofluidic ring resonator sensor

2009 ◽  
Author(s):  
Jonathan D. Suter ◽  
Daniel J. Howard ◽  
Charles W. Caldwell ◽  
Huidong Shi ◽  
Xudong Fan
Keyword(s):  
Dna Methylation ◽  
Ring Resonator ◽  
Label Free ◽  
Methylation Analysis ◽  
Free Dna ◽  
Dna Methylation Analysis
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