Covisualization of Global DNA Methylation/Hydroxymethylation and Protein Biomarkers for Ultrahigh-Definition Epigenetic Phenotyping of Stem Cells

2019 ◽  
pp. 79-92
Author(s):  
Jian Tajbakhsh
Keyword(s):  
Dna Methylation ◽  
Stem Cells ◽  
Global Dna Methylation ◽  
Protein Biomarkers

scholarly journals Lead Exposure Disrupts Global DNA Methylation in Human Embryonic Stem Cells and Alters Their Neuronal Differentiation

2014 ◽  
Vol 139 (1) ◽  
pp. 142-161 ◽  
Author(s):  
Marie-Claude Senut ◽  
Arko Sen ◽  
Pablo Cingolani ◽  
Asra Shaik ◽  
Susan J. Land ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Stem Cells ◽  
Embryonic Stem Cells ◽  
Neuronal Differentiation ◽  
Human Embryonic Stem Cells ◽  
Lead Exposure ◽  
Embryonic Stem ◽  
Global Dna Methylation

scholarly journals X Chromosome Dosage Modulates Multiple Molecular and Cellular Properties of Mouse Pluripotent Stem Cells Independently of Global DNA Methylation Levels

2018 ◽  
Author(s):  
Juan Song ◽  
Adrian Janiszewski ◽  
Natalie De Geest ◽  
Lotte Vanheer ◽  
Irene Talon ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Stem Cells ◽  
X Chromosome ◽  
Pluripotent Stem Cells ◽  
Gene Dosage ◽  
Embryonic Stem ◽  
Chromatin Accessibility ◽  
Global Dna Methylation ◽  
Open Chromatin ◽  
Mammalian Development

ABSTRACTDuring early mammalian development, the two X-chromosomes in female cells are active. Dosage compensation between XX female and XY male cells is then achieved by X-chromosome inactivation in female cells. Reprogramming female mouse somatic cells into induced pluripotent stem cells (iPSCs) leads to X-chromosome reactivation. The extent to which increased X-chromosome dosage (X-dosage) in female iPSCs leads to differences in the molecular and cellular properties of XX and XY iPSCs is still unclear. We show that chromatin accessibility in mouse iPSCs is modulated by X-dosage. Specific sets of transcriptional regulator motifs are enriched in chromatin with increased accessibility in XX or XY iPSCs. We show that the transcriptome, growth and pluripotency exit are also modulated by X-dosage in iPSCs. To understand the mechanisms by which increased X-dosage modulates the molecular and cellular properties of mouse pluripotent stem cells, we used heterozygous deletions of the X-linked gene Dusp9 in XX embryonic stem cells. We show that X-dosage regulates the transcriptome, open chromatin landscape, growth and pluripotency exit largely independently of global DNA methylation. Our results uncover new insights into X-dosage in pluripotent stem cells, providing principles of how gene dosage modulates the epigenetic and genetic mechanisms regulating cell identity.

scholarly journals X-Chromosome Dosage Modulates Multiple Molecular and Cellular Properties of Mouse Pluripotent Stem Cells Independently of Global DNA Methylation Levels

2019 ◽  
Vol 12 (2) ◽  
pp. 333-350 ◽  
Author(s):  
Juan Song ◽  
Adrian Janiszewski ◽  
Natalie De Geest ◽  
Lotte Vanheer ◽  
Irene Talon ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Stem Cells ◽  
X Chromosome ◽  
Pluripotent Stem Cells ◽  
Global Dna Methylation

Abstract 1379: Identification of global DNA methylation signatures in glioblastoma-derived cancer stem cells

2014 ◽  
Author(s):  
Eun Joon Lee ◽  
Prakash Rath ◽  
Jimei Liu ◽  
Dungsheng Ryu ◽  
Alan Free ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Stem Cells ◽  
Cancer Stem Cells ◽  
Global Dna Methylation

scholarly journals Direct readout of heterochromatic H3K9me3 regulates DNMT1-mediated maintenance DNA methylation

2020 ◽  
Vol 117 (31) ◽  
pp. 18439-18447
Author(s):  
Wendan Ren ◽  
Huitao Fan ◽  
Sara A. Grimm ◽  
Yiran Guo ◽  
Jae Jin Kim ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Stem Cells ◽  
Histone Modifications ◽  
Dna Methyltransferase ◽  
Histone H3 ◽  
Genomic Stability ◽  
Epigenetic Modifications ◽  
Global Dna Methylation ◽  
Replication Foci ◽  
Direct Readout

In mammals, repressive histone modifications such as trimethylation of histone H3 Lys9 (H3K9me3), frequently coexist with DNA methylation, producing a more stable and silenced chromatin state. However, it remains elusive how these epigenetic modifications crosstalk. Here, through structural and biochemical characterizations, we identified the replication foci targeting sequence (RFTS) domain of maintenance DNA methyltransferase DNMT1, a module known to bind the ubiquitylated H3 (H3Ub), as a specific reader for H3K9me3/H3Ub, with the recognition mode distinct from the typical trimethyl-lysine reader. Disruption of the interaction between RFTS and the H3K9me3Ub affects the localization of DNMT1 in stem cells and profoundly impairs the global DNA methylation and genomic stability. Together, this study reveals a previously unappreciated pathway through which H3K9me3 directly reinforces DNMT1-mediated maintenance DNA methylation.

scholarly journals Identification of Global DNA Methylation Signatures in Glioblastoma-Derived Cancer Stem Cells

2015 ◽  
Vol 42 (7) ◽  
pp. 355-371 ◽  
Author(s):  
Eun-Joon Lee ◽  
Prakash Rath ◽  
Jimei Liu ◽  
Dungsung Ryu ◽  
Lirong Pei ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Stem Cells ◽  
Cancer Stem Cells ◽  
Global Dna Methylation
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