scholarly journals Allele-Specific DNA Methylation and Its Interplay with Repressive Histone Marks at Promoter-Mutant TERT Genes

Cell Reports ◽  
2020 ◽  
Vol 31 (8) ◽  
pp. 107718
Author(s):  
Josh Lewis Stern ◽  
Richard D. Paucek ◽  
Franklin W. Huang ◽  
Mahmoud Ghandi ◽  
Ronald Nwumeh ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Histone Marks ◽  
Allele Specific ◽  
Promoter Mutant

scholarly journals Allele-Specific DNA Methylation and Its Interplay with Repressive Histone Marks at Promoter-Mutant TERT Genes

Cell Reports ◽  
2017 ◽  
Vol 21 (13) ◽  
pp. 3700-3707 ◽  
Author(s):  
Josh Lewis Stern ◽  
Richard D. Paucek ◽  
Franklin W. Huang ◽  
Mahmoud Ghandi ◽  
Ronald Nwumeh ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Histone Marks ◽  
Allele Specific ◽  
Promoter Mutant

scholarly journals Ectopic targeting of CG DNA methylation in Arabidopsis with the bacterial SssI methyltransferase

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Wanlu Liu ◽  
Javier Gallego-Bartolomé ◽  
Yuxing Zhou ◽  
Zhenhui Zhong ◽  
Ming Wang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Zinc Finger ◽  
Zinc Finger Protein ◽  
Basic Research ◽  
Crop Plant ◽  
Open Chromatin ◽  
Histone Marks ◽  
It Impacts ◽  
Finger Protein

AbstractThe ability to target epigenetic marks like DNA methylation to specific loci is important in both basic research and in crop plant engineering. However, heritability of targeted DNA methylation, how it impacts gene expression, and which epigenetic features are required for proper establishment are mostly unknown. Here, we show that targeting the CG-specific methyltransferase M.SssI with an artificial zinc finger protein can establish heritable CG methylation and silencing of a targeted locus in Arabidopsis. In addition, we observe highly heritable widespread ectopic CG methylation mainly over euchromatic regions. This hypermethylation shows little effect on transcription while it triggers a mild but significant reduction in the accumulation of H2A.Z and H3K27me3. Moreover, ectopic methylation occurs preferentially at less open chromatin that lacks positive histone marks. These results outline general principles of the heritability and interaction of CG methylation with other epigenomic features that should help guide future efforts to engineer epigenomes.

scholarly journals Gene expression profiling of epigenetic chromatin modification enzymes and histone marks by cigarette smoke: implications for COPD and lung cancer

2016 ◽  
Vol 311 (6) ◽  
pp. L1245-L1258 ◽  
Author(s):  
Isaac K. Sundar ◽  
Irfan Rahman
Keyword(s):  
Gene Expression ◽  
Lung Cancer ◽  
Dna Methylation ◽  
Cigarette Smoke ◽  
Histone Modifications ◽  
Expression Patterns ◽  
Chromatin Modification ◽  
Gene Expression Patterns ◽  
Validation Data ◽  
Histone Marks

Chromatin-modifying enzymes mediate DNA methylation and histone modifications on recruitment to specific target gene loci in response to various stimuli. The key enzymes that regulate chromatin accessibility for maintenance of modifications in DNA and histones, and for modulation of gene expression patterns in response to cigarette smoke (CS), are not known. We hypothesize that CS exposure alters the gene expression patterns of chromatin-modifying enzymes, which then affects multiple downstream pathways involved in the response to CS. We have, therefore, analyzed chromatin-modifying enzyme profiles and validated by quantitative real-time PCR (qPCR). We also performed immunoblot analysis of targeted histone marks in C57BL/6J mice exposed to acute and subchronic CS, and of lungs from nonsmokers, smokers, and patients with chronic obstructive pulmonary disease (COPD). We found a significant increase in expression of several chromatin modification enzymes, including DNA methyltransferases, histone acetyltransferases, histone methyltransferases, and SET domain proteins, histone kinases, and ubiquitinases. Our qPCR validation data revealed a significant downregulation of Dnmt1, Dnmt3a, Dnmt3b, Hdac2, Hdac4, Hat1, Prmt1, and Aurkb. We identified targeted chromatin histone marks (H3K56ac and H4K12ac), which are induced by CS. Thus CS-induced genotoxic stress differentially affects the expression of epigenetic modulators that regulate transcription of target genes via DNA methylation and site-specific histone modifications. This may have implications in devising epigenetic-based therapies for COPD and lung cancer.

scholarly journals Prediction of smoking by multiplex bisulfite PCR with long amplicons considering allele-specific effects on DNA methylation

2018 ◽  
Vol 10 (1) ◽  
Author(s):  
Nikolay Kondratyev ◽  
Arkady Golov ◽  
Margarita Alfimova ◽  
Tatiana Lezheiko ◽  
Vera Golimbet
Keyword(s):  
Dna Methylation ◽  
Specific Effects ◽  
Allele Specific

scholarly journals Allelic H3K27me3 to allelic DNA methylation switch maintains noncanonical imprinting in extraembryonic cells

2019 ◽  
Vol 5 (12) ◽  
pp. eaay7246 ◽  
Author(s):  
Zhiyuan Chen ◽  
Qiangzong Yin ◽  
Azusa Inoue ◽  
Chunxia Zhang ◽  
Yi Zhang
Keyword(s):  
Dna Methylation ◽  
De Novo ◽  
Genetic Manipulation ◽  
Paternal Allele ◽  
Gene Promoters ◽  
Maternal Allele ◽  
Mammalian Development ◽  
Placental Development ◽  
Early Embryos ◽  
Allele Specific

Faithful maintenance of genomic imprinting is essential for mammalian development. While germline DNA methylation–dependent (canonical) imprinting is relatively stable during development, the recently found oocyte-derived H3K27me3-mediated noncanonical imprinting is mostly transient in early embryos, with some genes important for placental development maintaining imprinted expression in the extraembryonic lineage. How these noncanonical imprinted genes maintain their extraembryonic-specific imprinting is unknown. Here, we report that maintenance of noncanonical imprinting requires maternal allele–specific de novo DNA methylation [i.e., somatic differentially methylated regions (DMRs)] at implantation. The somatic DMRs are located at the gene promoters, with paternal allele–specific H3K4me3 established during preimplantation development. Genetic manipulation revealed that both maternal EED and zygotic DNMT3A/3B are required for establishing somatic DMRs and maintaining noncanonical imprinting. Thus, our study not only reveals the mechanism underlying noncanonical imprinting maintenance but also sheds light on how histone modifications in oocytes may shape somatic DMRs in postimplantation embryos.

scholarly journals Comprehensive mapping of the effects of azacitidine on DNA methylation, repressive/permissive histone marks and gene expression in primary cells from patients with MDS and MDS-related disease

Oncotarget ◽  
2017 ◽  
Vol 8 (17) ◽  
pp. 28812-28825 ◽  
Author(s):  
Magnus Tobiasson ◽  
Hani Abdulkadir ◽  
Andreas Lennartsson ◽  
Shintaro Katayama ◽  
Francesco Marabita ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Primary Cells ◽  
Histone Marks ◽  
Related Disease ◽  
Comprehensive Mapping
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