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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106 Heat stress alters oocyte genome-wide DNA methylation patterns revealed at single base resolution

Reproduction Fertility and Development ◽

10.1071/rdv34n2ab106 ◽

2022 ◽

Vol 34 (2) ◽

pp. 290

Author(s):

M. Moura ◽

C. Carvalho ◽

F. de Barros ◽

F. Mossa ◽

D. Bebbere ◽

...

Keyword(s):

Dna Methylation ◽

Heat Stress ◽

Single Base ◽

Genome Wide ◽

Single Base Resolution ◽

Methylation Patterns

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Inference of Crosstalk Effects between DNA Methylation and lncRNA Regulation in NSCLC

BioMed Research International ◽

10.1155/2018/7602794 ◽

2018 ◽

Vol 2018 ◽

pp. 1-6 ◽

Cited By ~ 5

Author(s):

Binhua Tang

Keyword(s):

Clinical Trial ◽

Dna Methylation ◽

Lung Carcinoma ◽

Analytic Functions ◽

Nsclc Tissue ◽

Genome Wide Analysis ◽

Clinical Trial Research ◽

Omics Integration ◽

Genome Wide ◽

Tissue Profiling

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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Neuroinflammatory Signaling in the Pathogenesis of Alzheimer’s Disease

Current Neuropharmacology ◽

10.2174/1570159x19666210826130210 ◽

2021 ◽

Vol 19 ◽

Author(s):

Md. Sahab Uddin ◽

Md. Tanvir Kabir ◽

Maroua Jalouli ◽

Md. Ataur Rahman ◽

Philippe Jeandet ◽

...

Keyword(s):

Alzheimer’S Disease ◽

Alzheimer's Disease ◽

Innate Immune ◽

Misfolded Proteins ◽

Inflammatory Signaling ◽

Genome Wide Analysis ◽

Genome Wide ◽

Immunological Mechanisms ◽

The Brain

: Alzheimer’s disease (AD) is a chronic neurodegenerative disease characterized by the formation of intracellular neurofibrillary tangles (NFTs) and extracellular amyloid plaques. Growing evidence has suggested that AD pathogenesis is not only limited to the neuronal compartment but also strongly interacts with immunological processes in the brain. On the other hand, aggregated and misfolded proteins can bind with pattern recognition receptors located on astroglia and microglia and can in turn induce an innate immune response, characterized by the release of inflammatory mediators, ultimately playing a role in both the severity and the progression of the disease. It has been reported by genome-wide analysis that several genes which elevate the risk for sporadic AD encode for factors controlling the inflammatory response and glial clearance of misfolded proteins. Obesity and systemic inflammation are examples of external factors which may interfere with the immunological mechanisms of the brain and can induce disease progression. In this review, we discussed the mechanisms and essential role of inflammatory signaling pathways in AD pathogenesis. Indeed, interfering with immune processes and modulation of risk factors may lead to future therapeutic or preventive AD approaches.

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Timing Polymerase Pausing with TV-PRO-seq

10.1101/461442 ◽

2018 ◽

Author(s):

Jie Zhang ◽

Massimo Cavallaro ◽

Daniel Hebenstreit

Keyword(s):

High Resolution ◽

Human Cells ◽

Rrna Genes ◽

Dna Motifs ◽

Single Base ◽

Chromatin States ◽

Genome Wide ◽

A Genome ◽

Single Base Resolution ◽

Polymerase Pausing

Transcription of many genes in metazoans is subject to polymerase pausing, which corresponds to the transient arrest of transcriptionally engaged polymerase. It occurs mainly at promoter proximal regions and is not well understood. In particular, a genome-wide measurement of pausing times at high resolution has been lacking.We present here an extension of PRO-seq, time variant PRO-seq (TV-PRO-seq), that allowed us to estimate genome-wide pausing times at single base resolution. Its application to human cells reveals that promoter proximal pausing is surprisingly short compared to other regions and displays an intricate pattern. We also find precisely conserved pausing profiles at tRNA and rRNA genes and identified DNA motifs associated with pausing time. Finally, we show how chromatin states reflect differences in pausing times.

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