Technical articles that are geared for researchers in the field. Explore in detail new techniques and tips for topics like NGS in epigenetics, m6A RNA methylation, CRISPR/Cas9 epigenetic editing, chromatin immunoprecipitation, and more.
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Neurogenesis is a highly coordinated process with sequential waves of tightly controlled changes in gene expression. N6-Methyladenosine (m6A), is believed to play a role in the epitranscriptomic mechanism that controls mammalian cortical neurogenesis. M6A is the most abundant modification in mRNA and is found in most eukaryotic cells. It is installed by the methyltransferase complex, consisting of methyltransferase-like 3 (Mettl3) and methyltransferase-like 14 (Mettl14) as the SAM-binding sub-unit. The role of m6A modification in cancer has previously been investigated. Now, [more…]
Although cells have the same genetic material, they can function differently. Single-cell RNA sequencing has revealed how heterogeneous the transriptome of an individual cell may be with a homogeneous cell population or tissue. Single-cell genome sequencing has provided insights into genomic variations that occur in physiology and in diseases. Today we can probe the majority of epigenetic dimensions with single-cell resolution through multiple methods (Table 1). Studying individual cells offers insight into molecular components of the genome and its functional [more…]
Every day our cells undergo substantial amounts of DNA damage from exogenous and endogenous sources. UV light, in particular, can cause an estimated 100,000 lesions per cell every day. Left unrepaired, these DNA lesions could lead to induction of senescence, cell death or mutations, which could be responsible for the development of cancer, neurodegeneration and several other diseases. However, our organisms have developed a mechanism to recognize the DNA damage caused by UV light and other damaging agents, in the [more…]
Have you ever thought of how the day-night cycle can epigenetically affect plants? Latest research from Zhang et al. has shown a possible mechanism of how histone variants can negatively regulate gene expression in day-night cycles of rice seedling tissues. This paves a way for an exciting area of research of how histone variants can be differentially deposited in a very short time span, in order to fine tune the transcription due to the environmental stimuli in plants. Histones variants, [more…]
Recently Dr. Yu Xue’s group, at the Huazhong University of Science and Technology in Wuhan, China, developed a database designated as Eukaryotic Writers, Erasers and Readers protein of Histone Acetylation and Methylation system Database (WERAM). WERAM is a comprehensive database containing integrated information on the writers, erasers, and readers of histone acetylation and methylation. Namely writers are the enzymes that catalyze acetylation and methylation, the erasers are the enzymes that remove these marks, and the readers are proteins that recognize and interact [more…]
Gene expression is controlled on several levels from DNA sequence to post-transcriptional changes. Epigenetics demonstrate that gene expression can be controlled by chemical changes in the DNA such as methylation. Since the discovery of epigenetics, researchers have been attempting to produce effective methods to alter the methylation status of select genes. This would enable researchers to effectively turn on or off target genes without affecting the genetic code. Liu et al. (2016) have repurposed the CRISPR/Cas9 system to edit DNA [more…]
Circulating cell-free DNA (cfDNA) are small DNA fragments found circulating in plasma or serum, as well as other bodily fluids. The cfDNA isolated from plasma usually contains fragments of about ~170-500 bp, mostly corresponding to ~170 bp mononucleosomal and ~300 bp dinucleosomal DNA fragments [1,2], thought to arise mostly from apoptotic cells. In addition, larger fragments (>1,000 bp) are often detected, thought to arise mostly from necrotic cells. In healthy individuals, the levels of cfDNA in plasma/serum are generally low, ranging between [more…]
Over the past decade discoveries about the role of epigenetic mechanisms in learning and memory have changed the way scientists think about cognition 1. The most well characterized to date are histone acetylation and DNA methylation, but more recently discovered epigenetic mechanisms are continuing to shape researchers’ understandings of transcriptional regulation in post-mitotic neurons. Chromatin is made up of nucleosomes, which are 147 base pairs of DNA wrapped around a histone octomer. The canonical histones that organize DNA at the [more…]
A new single-cell genomics protocol that is potentially transformative for epigenetics research has been developed by scientists in the UK and Belgium. Applying this method, it is now possible to study the epigenome and transcriptome of a single cell at the same time. This novel approach could enhance our understanding of the link between gene expression and DNA methylation in single cells. Also, the knowledge of this relationship may clarify the mechanisms underlying normal development, and changes that occur with [more…]
Planaria, or flatworms, are often used as a model organism to investigate the fascinating process of how tissues and organs can regenerate. The flatworm has numerous stem cells called neoblasts and, when it’s injured, this intriguing creature can actually restore its own body parts. Researchers conducted the study at the Stowers Institute for Medical Research in the lab of Alejandro Sánchez Alvarado, Ph.D., a Howard Hughes Medical Institute investigator. In two related studies, they examined stem cell differentiation and the [more…]