scholarly journals Frequent lack of repressive capacity of promoter DNA methylation identified through genome-wide epigenomic manipulation

2017 ◽  
Author(s):  
Ethan Ford ◽  
Matthew R. Grimmer ◽  
Sabine Stolzenburg ◽  
Ozren Bogdanovic ◽  
Alex de Mendoza ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Fusion Protein ◽  
Rna Polymerase Ii ◽  
Zinc Finger ◽  
Gene Promoters ◽  
Natural Conditions ◽  
Promoter Regions ◽  
Genome Wide ◽  
Promoter Dna Methylation ◽  
Promoter Dna

AbstractIt is widely assumed that the addition of DNA methylation at CpG rich gene promoters silences gene transcription. However, this conclusion is largely drawn from the observation that promoter DNA methylation inversely correlates with gene expression in natural conditions. The effect of induced DNA methylation on endogenous promoters has yet to be comprehensively assessed. Here, we induced the simultaneous methylation of thousands of promoters in the genome of human cells using an engineered zinc finger-DNMT3A fusion protein, enabling assessment of the effect of forced DNA methylation upon transcription, histone modifications, and DNA methylation persistence after the removal of the fusion protein. We find that DNA methylation is frequently insufficient to transcriptionally repress promoters. Furthermore, DNA methylation deposited at promoter regions associated with H3K4me3 is rapidly erased after removal of the zinc finger-DNMT3A fusion protein. Finally, we demonstrate that induced DNA methylation can exist simultaneously on promoter nucleosomes that possess the active histone modification H3K4me3, or DNA bound by the initiated form of RNA polymerase II. These findings suggest that promoter DNA methylation is not generally sufficient for transcriptional inactivation, with implications for the emerging field of epigenome engineering.One Sentence SummaryGenome-wide epigenomic manipulation of thousands of human promoters reveals that induced promoter DNA methylation is unstable and frequently does not function as a primary instructive biochemical signal for gene silencing and chromatin reconfiguration.

scholarly journals Genome-wide Mapping Reveals Conservation of Promoter DNA Methylation Following Chicken Domestication

2015 ◽  
Vol 5 (1) ◽  
Author(s):  
Qinghe Li ◽  
Yuanyuan Wang ◽  
Xiaoxiang Hu ◽  
Yaofeng Zhao ◽  
Ning Li
Keyword(s):  
Dna Methylation ◽  
Genome Wide ◽  
Promoter Dna Methylation ◽  
Promoter Dna

Limited Effect of TET2 Mutations on Promoter DNA Methylation in Chronic Myelomonocytic Leukemia

Blood ◽  
2011 ◽  
Vol 118 (21) ◽  
pp. 1365-1365
Author(s):  
Jumpei Yamazaki ◽  
Rodolphe F Taby ◽  
Aparna Vasanthakumar ◽  
Trisha Macrae ◽  
Kelly R Ostler ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Myeloid Leukemia ◽  
Cpg Island ◽  
Cpg Islands ◽  
Chronic Myelomonocytic Leukemia ◽  
Gene Promoters ◽  
Wild Type ◽  
Promoter Dna Methylation ◽  
Promoter Dna ◽  
Myelomonocytic Leukemia

Abstract Abstract 1365 TET2 enzymatically converts 5-methylcytosine to 5-hydroxymethylcytosine, possibly leading to loss of DNA methylation. TET2 mutations are common in myeloid leukemia and were proposed to contribute to leukemogenesis through DNA methylation. To expand on this concept, we studied chronic myelomonocytic leukemia (CMML) samples. TET2 missense or nonsense mutations were detected in 53% (16/30 patients). By contrast, only 1/30 patients had a mutation in IDH1 or IDH2, and none of them had a mutation in DNMT3A. By bisulfite pyrosequencing, global methylation measured by the LINE-1 assay and DNA methylation levels of 10 promoter CpG islands frequently abnormal in myeloid leukemia were not different between TET2 mutant and wild-type cases. This was also true for 9 out of 11 gene promoters reported by others as differentially methylated by TET2 mutations. We confirmed only two non-CpG island promoters, AIM2 and SP140, as hypermethylated in patients with mutant TET2. These were the only two gene promoters (out of 14 475 genes) previously found to be hypermethylated in TET2 mutant cases. This finding shows that hypermethylation of both AIM2 and SP140 are bona fide markers of TET2 mutant cases in CMML. On the other hand, total 5-methylcytosine levels in TET2 mutant cases were significantly higher than TET2 wild-type cases. Thus, TET2 mutations have a limited impact on promoter DNA methylation in CMML. To confirm this, we performed genome-wide analysis using a next-generation sequencing method for DNA methylation levels in three TET2 mutant cases. TET2 mutant CMMLs had an average of 230 (1.9%) promoter CpG island sites hypermethylated compared to normal blood, which is close to what is generally observed when one compares cancer to normal. By contrast, all three cases had near normal to increased levels of methylation outside CpG islands. The median methylation levels in non-promoter, non-CpG island sites was 88.7% in normal blood compared to 91.7%, 92.1% and 94.6% in the three TET2 mutant cases. Thus, TET2 mutant CMMLs escape the general hypomethylation phenomenon seen in many cancers. All together, our data suggest that TET2 mutant CMML cases may have distinct DNA methylation patterns primarily outside gene promoters. Disclosures: No relevant conflicts of interest to declare.

scholarly journals Prenatal stress-induced programming of genome-wide promoter DNA methylation in 5-HTT-deficient mice

2014 ◽  
Vol 4 (10) ◽  
pp. e473-e473 ◽  
Author(s):  
K G Schraut ◽  
S B Jakob ◽  
M T Weidner ◽  
A G Schmitt ◽  
C J Scholz ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Prenatal Stress ◽  
Genome Wide ◽  
Promoter Dna Methylation ◽  
Promoter Dna ◽  
Deficient Mice

scholarly journals Loss of Fam60a, a Sin3a subunit, results in embryonic lethality and is associated with aberrant methylation at a subset of gene promoters

eLife ◽  
2018 ◽  
Vol 7 ◽  
Author(s):  
Ryo Nabeshima ◽  
Osamu Nishimura ◽  
Takako Maeda ◽  
Natsumi Shimizu ◽  
Takahiro Ide ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Embryonic Stem ◽  
Dna Demethylation ◽  
Specific Gene ◽  
Aberrant Methylation ◽  
Gene Promoters ◽  
Mouse Development ◽  
Promoter Regions ◽  
Corepressor Complex ◽  
Genome Wide

We have examined the role of Fam60a, a gene highly expressed in embryonic stem cells, in mouse development. Fam60a interacts with components of the Sin3a-Hdac transcriptional corepressor complex, and most Fam60a–/– embryos manifest hypoplasia of visceral organs and die in utero. Fam60a is recruited to the promoter regions of a subset of genes, with the expression of these genes being either up- or down-regulated in Fam60a–/– embryos. The DNA methylation level of the Fam60a target gene Adhfe1 is maintained at embryonic day (E) 7.5 but markedly reduced at E9.5 in Fam60a–/– embryos, suggesting that DNA demethylation is enhanced in the mutant. Examination of genome-wide DNA methylation identified several differentially methylated regions, which were preferentially hypomethylated, in Fam60a–/– embryos. Our data suggest that Fam60a is required for proper embryogenesis, at least in part as a result of its regulation of DNA methylation at specific gene promoters.

scholarly journals Divergent DNA methylation signatures of X chromosome regulation in marsupials and eutherians

2020 ◽  
Author(s):  
Devika Singh ◽  
Dan Sun ◽  
Andrew G. King ◽  
David E. Alquezar-Planas ◽  
Rebecca N. Johnson ◽  
...  
Keyword(s):  
Dna Methylation ◽  
X Chromosome ◽  
Specific Expression ◽  
X Chromosomes ◽  
Phascolarctos Cinereus ◽  
Male And Female ◽  
Inactive X Chromosome ◽  
Genome Wide ◽  
Promoter Dna Methylation ◽  
Promoter Dna

AbstractX chromosome inactivation (XCI) mediated by differential DNA methylation between sexes is well characterized in eutherian mammals. Although XCI is shared between eutherians and marsupials, the role of DNA methylation in marsupial XCI remains contested. Here we examine genome-wide signatures of DNA methylation from methylation maps across fives tissues from a male and female koala (Phascolarctos cinereus) and present the first whole genome, multi-tissue marsupial “methylome atlas.” Using these novel data, we elucidate divergent versus common features of marsupial and eutherian DNA methylation. First, tissue-specific differential DNA methylation in marsupials primarily occurs in gene bodies. Second, females show significant global reduction (hypomethylation) of X chromosome DNA methylation compared to males. We show that this pattern is also observed in eutherians. Third, on average, promoter DNA methylation shows little difference between male and female koala X chromosomes, a pattern distinct from that of eutherians. Fourth, the sex-specific DNA methylation landscape upstream of Rsx, the primary lncRNA associated with marsupial XCI, is consistent with the epigenetic regulation of female-(and presumably inactive X chromosome-) specific expression. Finally, we utilize the prominent female X chromosome hypomethylation and classify 98 previously unplaced scaffolds as X-linked, contributing an additional 14.6 Mb (21.5 %) to genomic data annotated as the koala X chromosome. Our work demonstrates evolutionarily divergent pathways leading to functionally conserved patterns of XCI in two deep branches of mammals.

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