scholarly journals Methylation analysis of a marsupial X-linked CpG island by bisulfite genomic sequencing.

1996 ◽  
Vol 6 (2) ◽  
pp. 114-123 ◽  
Author(s):  
D A Loebel ◽  
P G Johnston
Keyword(s):  
Cpg Island ◽  
Genomic Sequencing ◽  
Methylation Analysis ◽  
Bisulfite Genomic Sequencing

scholarly journals DNA methylation analysis by digital bisulfite genomic sequencing and digital MethyLight

2008 ◽  
Vol 36 (14) ◽  
pp. 4689-4698 ◽  
Author(s):  
D. J. Weisenberger ◽  
B. N. Trinh ◽  
M. Campan ◽  
S. Sharma ◽  
T. I. Long ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Genomic Sequencing ◽  
Methylation Analysis ◽  
Bisulfite Genomic Sequencing ◽  
Dna Methylation Analysis

DNA methylation mapping by tag-modified bisulfite genomic sequencing

2006 ◽  
Vol 355 (1) ◽  
pp. 50-61 ◽  
Author(s):  
Weiguo Han ◽  
Stephane Cauchi ◽  
James G. Herman ◽  
Simon D. Spivack
Keyword(s):  
Dna Methylation ◽  
Genomic Sequencing ◽  
Bisulfite Genomic Sequencing

scholarly journals Chemistry of Bisulfite Genomic Sequencing; Advances and Issues

2007 ◽  
Vol 51 (1) ◽  
pp. 47-48 ◽  
Author(s):  
H. Hayatsu ◽  
K. Negishi ◽  
M. Shiraishi ◽  
K. Tsuji ◽  
K. Moriyama
Keyword(s):  
Genomic Sequencing ◽  
Bisulfite Genomic Sequencing

Bisulfite genomic sequencing of DNA from dried blood spot microvolume samples

2012 ◽  
Vol 6 (3) ◽  
pp. 306-309 ◽  
Author(s):  
Hongmei Xu ◽  
Yun Zhao ◽  
Zhiping Liu ◽  
Wei Zhu ◽  
Yueqin Zhou ◽  
...  
Keyword(s):  
Dried Blood Spot ◽  
Genomic Sequencing ◽  
Bisulfite Genomic Sequencing ◽  
Blood Spot

Genome-Wide DNA Methylation Analysis Shows Enrichment of Differential Methylation in “Open Seas” and Enhancers and Reveals Hypomethylation in DNMT3A Mutated Cytogenetically Normal AML (CN-AML)

Blood ◽  
2012 ◽  
Vol 120 (21) ◽  
pp. 653-653 ◽  
Author(s):  
Ying Qu ◽  
Andreas Lennartsson ◽  
Verena I. Gaidzik ◽  
Stefan Deneberg ◽  
Sofia Bengtzén ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Cpg Island ◽  
Cpg Islands ◽  
Differential Methylation ◽  
Methylation Analysis ◽  
Cpg Sites ◽  
Genome Wide ◽  
Genomic Regions ◽  
Methylation Patterns

Abstract Abstract 653 DNA methylation is involved in multiple biologic processes including normal cell differentiation and tumorigenesis. In AML, methylation patterns have been shown to differ significantly from normal hematopoietic cells. Most studies of DNA methylation in AML have previously focused on CpG islands within the promoter of genes, representing only a very small proportion of the DNA methylome. In this study, we performed genome-wide methylation analysis of 62 AML patients with CN-AML and CD34 positive cells from healthy controls by Illumina HumanMethylation450K Array covering 450.000 CpG sites in CpG islands as well as genomic regions far from CpG islands. Differentially methylated CpG sites (DMS) between CN-AML and normal hematopoietic cells were calculated and the most significant enrichment of DMS was found in regions more than 4kb from CpG Islands, in the so called open sea where hypomethylation was the dominant form of aberrant methylation. In contrast, CpG islands were not enriched for DMS and DMS in CpG islands were dominated by hypermethylation. DMS successively further away from CpG islands in CpG island shores (up to 2kb from CpG Island) and shelves (from 2kb to 4kb from Island) showed increasing degree of hypomethylation in AML cells. Among regions defined by their relation to gene structures, CpG dinucleotide located in theoretic enhancers were found to be the most enriched for DMS (Chi χ2<0.0001) with the majority of DMS showing decreased methylation compared to CD34 normal controls. To address the relation to gene expression, GEP (gene expression profiling) by microarray was carried out on 32 of the CN-AML patients. Totally, 339723 CpG sites covering 18879 genes were addressed on both platforms. CpG methylation in CpG islands showed the most pronounced anti-correlation (spearman ρ =-0.4145) with gene expression level, followed by CpG island shores (mean spearman rho for both sides' shore ρ=-0.2350). As transcription factors (TFs) have shown to be crucial for AML development, we especially studied differential methylation of an unbiased selection of 1638 TFs. The most enriched differential methylation between CN-AML and normal CD34 positive cells were found in TFs known to be involved in hematopoiesis and with Wilms tumor protein-1 (WT1), activator protein 1 (AP-1) and runt-related transcription factor 1 (RUNX1) being the most differentially methylated TFs. The differential methylation in WT 1 and RUNX1 was located in intragenic regions which were confirmed by pyro-sequencing. AML cases were characterized with respect to mutations in FLT3, NPM1, IDH1, IDH2 and DNMT3A. Correlation analysis between genome wide methylation patterns and mutational status showed statistically significant hypomethylation of CpG Island (p<0.0001) and to a lesser extent CpG island shores (p<0.001) and the presence of DNMT3A mutations. This links DNMT3A mutations for the first time to a hypomethylated phenotype. Further analyses correlating methylation patterns to other clinical data such as clinical outcome are ongoing. In conclusion, our study revealed that non-CpG island regions and in particular enhancers are the most aberrantly methylated genomic regions in AML and that WT 1 and RUNX1 are the most differentially methylated TFs. Furthermore, our data suggests a hypomethylated phenotype in DNMT3A mutated AML. Disclosures: No relevant conflicts of interest to declare.

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