Non-CpG DNA methylation

This 2017 Korean review compared and contrasted CpG and non-CpG DNA methylation: “Non-CpG methylation is restricted to specific cell types, such as pluripotent stem cells, oocytes, neurons, and glial cells..accumulation of methylation at non-CpG sites and CpG sites in neurons seems to be involved in development and disease etiology. Non-CpG methylation is established during postnatal … Continue reading Non-CpG DNA methylation

The epigenetic clock now includes skin

The originator of the 2013 epigenetic clock improved its coverage with this 2018 UCLA human study: “We present a new DNA methylation-based biomarker (based on 391 CpGs) that was developed to accurately measure the age of human fibroblasts, keratinocytes, buccal cells, endothelial cells, skin and blood samples. We also observe strong age correlations in sorted neurons, … Continue reading The epigenetic clock now includes skin

Hijacking the epigenetic clock paradigm

This 2018 German human study’s last sentence was: “Additionally we found an association between DNAm [DNA methylation] age acceleration and rLTL [relative leukocyte telomere length], suggesting that this epigenetic clock, at least partially and possibly better than other epigenetic clocks, reflects biological age.” Statements in the study that contradicted, qualified, and limited the concluding sentence … Continue reading Hijacking the epigenetic clock paradigm

Hidden hypotheses of epigenetic studies

This 2018 UK review discussed three pre-existing conditions of epigenetic genome-wide association studies: “Genome-wide technology has facilitated epigenome-wide association studies (EWAS), permitting ‘hypothesis-free’ examinations in relation to adversity and/or mental health problems. Results of EWAS are in fact conditional on several a priori hypotheses: EWAS coverage is sufficient for complex psychiatric problems; Peripheral tissue is … Continue reading Hidden hypotheses of epigenetic studies

Measuring epigenetic changes at a single-cell level

This 2018 Canadian cell study described the development of a single-cell protocol to: “Profile primitive hematopoietic cells of mouse and human origin to identify epigenetically distinct subpopulations. Deep sampling of the CpG content of individual HSCs allowed for the near complete reconstitution of regulatory states from epigenetically defined subpopulations of HSCs and revealed a high … Continue reading Measuring epigenetic changes at a single-cell level

A study of our evolutionary remnants

This 2018 Michigan human cell study subject was factors affecting the expression of human endogenous retroviruses: “We provide a comprehensive genomic and epigenomic map of the more than 500,000 endogenous retroviruses (ERVs) and fragments that populate the intergenic regions of the human genome. The repressive epigenetic marks associated with the ERVs, particularly long terminal repeats … Continue reading A study of our evolutionary remnants

Little evidence for mitochondrial DNA methylation

This 2018 Japanese rodent study used three different techniques to detect mitochondrial DNA methylation: “Whilst 5-methylcytosine (5mC) is a major epigenetic mark in the nuclear DNA in mammals, whether or not mitochondrial DNA (mtDNA) receives 5mC modification remains controversial. We used bisulfite sequencing, McrBC digestion analyses and liquid chromatography mass spectrometry, which are distinctly differing … Continue reading Little evidence for mitochondrial DNA methylation

The epigenetic clock theory of aging

My 400th blog post curates a 2018 US/UK paper by two of the coauthors of Using an epigenetic clock to distinguish cellular aging from senescence. The authors reviewed the current state of epigenetic clock research, and proposed a new theory of aging: “The proposed epigenetic clock theory of ageing views biological ageing as an unintended … Continue reading The epigenetic clock theory of aging

Dealing with big data in epigenetic studies

There’s been a long-standing need for tools and mathematical techniques which effectively deal with the large amount of data present in epigenetic studies. Complete experimental conditions and results aren’t accurately described when researchers fail to transform large sets of data into information. This 2018 Baltimore review/promotional paper described an approach that promised to resolve the … Continue reading Dealing with big data in epigenetic studies

Obtaining convictions with epigenetic statistics?

This 2018 Austrian review subject was forensic applications of epigenetic clock methodologies: “The methylation-sensitive analysis of carefully selected DNA markers (CpG sites) has brought the most promising results by providing prediction accuracies of ±3–4 years, which can be comparable to, or even surpass those from, eyewitness reports. This mini-review puts recent developments in age estimation … Continue reading Obtaining convictions with epigenetic statistics?