Profiling DNA Methylation and Hydroxymethylation at Retrotransposable Elements

2016 ◽  
pp. 387-401 ◽  
Author(s):  
Lorenzo de la Rica ◽  
Jatinder S. Stanley ◽  
Miguel R. Branco
Keyword(s):  
Dna Methylation ◽  
Retrotransposable Elements

scholarly journals Global DNA methylation analysis in relapsed Pre-B cell acute lymphoblastic leukemia

2019 ◽  
Author(s):  
◽  
Alexei Jay Stuckel
Keyword(s):  
Dna Methylation ◽  
Acute Lymphoblastic Leukemia ◽  
Residual Disease ◽  
Lymphoblastic Leukemia ◽  
Aberrant Methylation ◽  
Retrotransposable Elements ◽  
Cell Acute Lymphoblastic Leukemia ◽  
Dna Methylation Analysis ◽  
Standard Risk ◽  
Prognostic Power

Reliable biomarkers for relapsed acute lymphoblastic leukemia are scarce. Currently, minimal residual disease (MRD) is the best method in predicting a relapse event, but is invasive to the patient. In addition, high quantity amount of cells are needed for flow-MRD and PCR-MRD requires stable IG-TCR rearrangements. An alternative MRD strategy may involve DNA based technologies involving mass spectrometry that have the potential to monitor the progression of ALL. There are also many recurrent karyotypes that stratify patients into either low-standard risk or high-risk of relapsing. However, many patients with favorable karyotypes (e.g. highhyperdiploidy, ETV6/RUNX1) still experience one or more relapse events. DNA methylation has the potential to serve as a biomarker throughout the course of the disease in several aspects. DNA methylation associated microarrays have demonstrated the ability to stratify patients into their recurrent cytogenetic subtype. Further, others have identified CpG loci that have the potential to stratify patients at diagnosis that are at risk of relapsing. This dissertation identified differential DNA methylation between matched diagnosis and relapsed patients by creating a methylome profile (MIRA-seq) for each patient. We are the first to report global hypomethylation that occurs at relapse, predominately within retrotransposable elements. In addition, genes that exhibited 5' regulatory aberrant methylation from diagnosis to relapse were identified. Some of the genes harboring epigenetic lesions may be considered an "epidriver" of ALL. A "driver" mutation can be defined as a mutation that can directly or indirectly offer a Darwinian advantage in terms of growth for leukemic blasts. The "epi" component refers to the nature of the mutation as epigenetic in origin and in the context of this study is synonymous with deviant or aberrant methylation. Further, our MIRA-seq study in canine acute leukemia observed epigenetic lesions of epidriver genes that were also present at diagnosis and relapse in human ALL. Lastly, MIRA-seq profiles from ALL patients at diagnosis who either did or did not go on to relapse were compared against each other in order to identify individual CpGs using pyrosequencing that were associated with relapse (prognostic). These combined efforts were done with the foresight of identifying potential novel targets that exist as epidrivers of ALL or loci that hold prognostic power at diagnosis. This dissertation builds upon others who have previously identified relapse-associated biomarkers with implications of improved patient care and risk stratification.

DNA methylation in satellite repeats disorders

2019 ◽  
Vol 63 (6) ◽  
pp. 757-771 ◽  
Author(s):  
Claire Francastel ◽  
Frédérique Magdinier
Keyword(s):  
Dna Methylation ◽  
Human Genome ◽  
Repetitive Dna ◽  
Dna Sequences ◽  
Satellite Repeats ◽  
Tremendous Progress ◽  
Genes Encoding ◽  
Dna Elements ◽  
Near Future

Abstract Despite the tremendous progress made in recent years in assembling the human genome, tandemly repeated DNA elements remain poorly characterized. These sequences account for the vast majority of methylated sites in the human genome and their methylated state is necessary for this repetitive DNA to function properly and to maintain genome integrity. Furthermore, recent advances highlight the emerging role of these sequences in regulating the functions of the human genome and its variability during evolution, among individuals, or in disease susceptibility. In addition, a number of inherited rare diseases are directly linked to the alteration of some of these repetitive DNA sequences, either through changes in the organization or size of the tandem repeat arrays or through mutations in genes encoding chromatin modifiers involved in the epigenetic regulation of these elements. Although largely overlooked so far in the functional annotation of the human genome, satellite elements play key roles in its architectural and topological organization. This includes functions as boundary elements delimitating functional domains or assembly of repressive nuclear compartments, with local or distal impact on gene expression. Thus, the consideration of satellite repeats organization and their associated epigenetic landmarks, including DNA methylation (DNAme), will become unavoidable in the near future to fully decipher human phenotypes and associated diseases.

15 LONGITUDINAL EVALUATION OF MUCOSAL DNA METHYLATION IN ULCERATIVE COLITIS SHOWS DISEASE-SPECIFIC CHANGES

2020 ◽  
Vol 158 (3) ◽  
pp. S50-S51
Author(s):  
Suresh Venkateswaran ◽  
Varun Kilaru ◽  
Hari Somineni ◽  
Jason Matthews ◽  
Jeffrey Hyams ◽  
...  
Keyword(s):  
Ulcerative Colitis ◽  
Dna Methylation ◽  
Longitudinal Evaluation ◽  
Disease Specific

Aberrant DNA Methylation Is Associated with Reduced Response to SRC Inhibition in Primary Human Vestibular Schwannoma Cells

2019 ◽  
Author(s):  
Christine Dinh ◽  
Juan Young ◽  
Olena Bracho ◽  
Rahul Mittal ◽  
Denise Yan ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Vestibular Schwannoma ◽  
Aberrant Dna Methylation

Global DNA Methylation is influenced by smoking behavior

2007 ◽  
Vol 40 (05) ◽  
Author(s):  
MAN Muschler ◽  
T Hillemacher ◽  
H Frieling ◽  
S Moskau ◽  
A Semmler ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Smoking Behavior ◽  
Global Dna Methylation

DNA Methylation Regulation

2020 ◽  
Author(s):  
Keyword(s):  
Dna Methylation

Maternal H3K27me3 controls DNA methylation-independent imprinting

2018 ◽  
Author(s):  
Inoue A ◽  
Jiang L ◽  
Lu F ◽  
Suzuki T ◽  
Zhang Y
Keyword(s):  
Dna Methylation
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