How Understanding an Individual’s Epigenetics Can Help Measure and Treat Addiction

January 3, 2017 WhatIsEpigenetics

For a long time humans have wondered if chemicals causing drug and alcohol addiction could be active in the genes and potentially passed on to the next generation. Although this was not scientifically proven until recent years, the fear of suffering from addictive diseases led children of addicts and former addicts to avoid alcohol and drugs completely. One of the scientific studies that give weight to this family history hypothesis on addiction was conducted at the Indiana University School of [more…]

A Histone Extraction Protocol

January 23, 2014 WhatIsEpigenetics

The following histone extraction protocol was written by scientists at Epigentek and is a recommended and optimized procedure for their histone modification assays, successfully utilized by many research labs. Use these easy to follow steps to ensure proper isolation of histone proteins. For tissues (treated and untreated), weigh the sample and cut the sample into small pieces (1-2 mm3) with a scalpel or scissors. Transfer tissue pieces to a Dounce homogenizer.  Add TEB buffer (PBS containing 0.5% Triton X 100, 2 [more…]

Our Parents’ Lives Could Influence Memories Through Epigenetics

January 7, 2014 WhatIsEpigenetics

The scientists at Emory University School of Medicine showed new evidence that our parents’ behaviors before we are born may have a bigger influence on us than we previously imagined, although we know our parents have a big impact on our lives. The scientists used olfactory molecular specificity to examine the inheritance of parental traumatic exposure, a phenomenon that has been frequently observed, but not understood. They subjected F0 mice to odor fear conditioning before conception and found that subsequently [more…]

Folate Deficiency in a Father’s Diet Could Cause Negative Pregnancy Outcomes by Changing Sperm Epigenome

December 18, 2013 WhatIsEpigenetics

Scientists at McGill University, Canada reported that folate deficiency in a father’s diet could increase birth defects in the offspring by altering sperm epigenome. These defects include craniofacial and musculoskeletal malformations. The scientists fed male mice either a folate-deficient or folate-sufficient diet throughout life and then performed genome-wide DNA methylation analysis and subsequent functional analysis to identify differential methylation in sperm of genes implicated in development, and chronic diseases such as cancer, diabetes, autism and schizophrenia. They found that >300 [more…]

The Epigenetic Landscape is a Key Determinant of Gene Expression Reprogramming in Cardiac Hypertrophy

December 4, 2013 WhatIsEpigenetics

The epigenetic signature for cardiac hypertrophy, which can progress to heart failure through an adaptive response of the myocardium to stress, is still poorly understood. The scientists at Humanitas Clinical and Research Center, Rozzano, Italy report on the genome-wide distribution of seven histone modifications in adult mouse cardiomyocytes subjected to a prohypertrophy stimulus in vivo. They found a set of promoters with an epigenetic pattern that distinguishes specific functional classes of genes regulated in hypertrophy and identified 9,207 candidate active [more…]

Transposase-Accessible Chromatin Assay for Fast and Sensitive Epigenomic Profiling

November 18, 2013 WhatIsEpigenetics

Scientists at Stanford University School of Medicine have developed a rapid and sensitive method for integrative epigenomic analysis called assay for transposase-accessible chromatin using sequencing (ATAC-seq).This assay is based on direct in vitro transposition of sequencing adaptors into native chromatin, which captures open chromatin sites using a simple two-step protocol with 500–50,000 cells and reveals the interplay between genomic locations of open chromatin, DNA-binding proteins, individual nucleosomes and chromatin compaction at nucleotide resolution. By using ATAC-seq, the scientists discovered classes of DNA-binding [more…]

Accurately Telling the Age of Human Tissues and Cells by DNA Methylation Clock

November 11, 2013 WhatIsEpigenetics

External signs of the human body’s age can be given by wrinkles and graying hair. However, these signs may not be accurate to tell the age of human tissues and cells that construct your body. Geneticist and biomathematician Steve Horvath at the University of California Los Angeles has developed a multi-tissue predictor of age that enables one to estimate the age of most tissues and cell types based on DNA methylation that can selectively switch off genes. This age predictor was [more…]

Simple Blood Test of DNA Methylation Markers Promises Early Diagnosis of Pancreatic Cancer

November 1, 2013 WhatIsEpigenetics

The scientists at Johns Hopkins University used a genome-wide pharmacologic transcriptome approach to identify two novel cancer-specific DNA methylation markers in cultured pancreatic cancer cells: BNC1 and ADAMTS1. Using a nanoparticle-enabled MOB (Methylation On Beads) technology, they found that these two markers are also frequently detected in serum samples of pancreatic cancer patients (N = 42) with a sensitivity for BNC1 of 79% and for ADAMTS1 of 48%, while the specificity was 89% for BNC1 and 92% for ADAMTS1. Overall [more…]

New Technique Available to Measure m6A Levels for RNA Methylation Studies

October 22, 2013 WhatIsEpigenetics

Researchers at Epigentek recently developed a new and breakthrough approach to identify the “fifth base” of RNA, N6-methyladenosine (m6A) to efficiently study RNA methylation in a practical and cost-effective manner. The technology is based on a high throughput and strip-well microplate format and is made commercially available as the EpiQuik m6A RNA Methylation Quantification Kit, the first of its kind. It was commonly believed that messenger RNA (mRNA) contains four nucleobases — guanine, adenine, uracil, and cytosine. However in 2012, [more…]

Targeted DNA demethylation and activation of endogenous genes using programmable TALE-TET1 fusion proteins

October 16, 2013 WhatIsEpigenetics

The scientists at MIT describe an approach for efficient targeted demethylation of specific CpGs in human cells using fusions of engineered transcription activator–like effector (TALE) repeat arrays and the TET1 hydroxylase catalytic domain. Using these TALE-TET1 fusions, they demonstrated that modification of critical methylated promoter CpG positions can lead to substantial increases in the expression of endogenous human genes. Genome-wide studies have defined cell type–specific patterns of DNA methylation that are important for regulating gene expression in both normal development2 [more…]

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