Genome-wide analysis of cervical secretions obtained during embryo transfer reveals the association between DNA methylation and pregnancy outcomes

Intercellular crosstalk effects between DNA methylation and lncRNA regulation remain elusive in lung carcinoma epigenetics. We present an application toolkit MetLnc in integration and annotation for group-wise NSCLC tissue-based DNA methylation and lncRNA profiling resources, to comprehensively analyze differentially methylated loci and lncRNAs through genome-wide analysis. Together with multiple analytic functions, MetLnc acts as an efficient approach on epigenetic omics integration and interrogation. Via the benchmark with group-wise NSCLC tissue profiling and TCGA cohort resources, we study differentially methylated CpG loci and lncRNAs as meaningful clues for inferring crosstalk effects between DNA methylation and lncRNA regulation; together we conclude with investigated biomarkers for further epigenetics and clinical trial research.

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PGC7 suppresses TET3 for protecting DNA methylation

Nucleic Acids Research ◽

10.1093/nar/gkt1261 ◽

2013 ◽

Vol 42 (5) ◽

pp. 2893-2905 ◽

Cited By ~ 39

Author(s):

Chunjing Bian ◽

Xiaochun Yu

Keyword(s):

Dna Methylation ◽

Molecular Mechanism ◽

Biological Process ◽

Cpg Islands ◽

Binding Motifs ◽

Genome Wide Analysis ◽

Dna Motif ◽

Genome Wide

Abstract Ten-eleven translocation (TET) family enzymes convert 5-methylcytosine to 5-hydroxylmethylcytosine. However, the molecular mechanism that regulates this biological process is not clear. Here, we show the evidence that PGC7 (also known as Dppa3 or Stella) interacts with TET2 and TET3 both in vitro and in vivo to suppress the enzymatic activity of TET2 and TET3. Moreover, lacking PGC7 induces the loss of DNA methylation at imprinting loci. Genome-wide analysis of PGC7 reveals a consensus DNA motif that is recognized by PGC7. The CpG islands surrounding the PGC7-binding motifs are hypermethylated. Taken together, our study demonstrates a molecular mechanism by which PGC7 protects DNA methylation from TET family enzyme-dependent oxidation.

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Genome-wide analysis of DNA methylation in obese, lean and miniature pig breeds

Scientific Reports ◽

10.1038/srep30160 ◽

2016 ◽

Vol 6 (1) ◽

Cited By ~ 12

Author(s):

Yalan Yang ◽

Rong Zhou ◽

Yulian Mu ◽

Xinhua Hou ◽

Zhonglin Tang ◽

...

Keyword(s):

Dna Methylation ◽

Miniature Pig ◽

Genome Wide Analysis ◽

Pig Breeds ◽

Genome Wide

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Bacterial Epigenomics: Coming of Age

mSystems ◽

10.1128/msystems.00747-21 ◽

2021 ◽

Author(s):

Pedro H. Oliveira

Keyword(s):

Dna Methylation ◽

Coming Of Age ◽

Innate Immune ◽

Physiological Significance ◽

Single Base ◽

Genome Wide Analysis ◽

Genome Wide ◽

Single Base Resolution

Epigenetic DNA methylation in bacteria has been traditionally studied in the context of antiparasitic defense and as part of the innate immune discrimination between self and nonself DNA. However, sequencing advances that allow genome-wide analysis of DNA methylation at the single-base resolution are nowadays expanding and have propelled a modern epigenomic revolution in our understanding of the extent, evolution, and physiological significance of methylation.

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