Ado-Mediated Depletion of Taurine Impairs Mitochondrial Respiratory Capacity and Alters the Chromatin Landscape of Inguinal Adipose Tissue.

Non-shivering thermogenesis (NST) has strong potential to combat obesity; however, a safe molecular approach to activate this process has not yet been identified. The sulfur amino acid taurine has the ability to safely activate NST and confer protection against obesity and metabolic disease in both mice and humans, but the mechanism of this action is unknown. In this study, we discover that a suite of taurine biosynthetic enzymes, especially that of cysteamine dioxygenase (ADO), significantly increases in response to β adrenergic signaling in inguinal adipose tissue (IWAT) in order to increase intracellular concentrations of taurine.

Dynamic regulation of chromatin accessibility during melanocyte stem cell activation.

Melanocyte stem cells (McSCs) of the hair follicle are necessary for hair pigmentation and can serve as melanoma cells of origin when harboring cancer-driving mutations. McSCs can be released from quiescence, activated, and undergo differentiation into pigment-producing melanocytes during the hair cycle or due to environmental stimuli, such as ultraviolet-B (UVB) exposure. However, our current understanding of the mechanisms regulating McSC stemness, activation, and differentiation remains limited.

Confined migration induces heterochromatin formation and alters chromatin accessibility.

During migration, cells often squeeze through small constrictions, requiring extensive deformation. We hypothesized that nuclear deformation associated with such confined migration could alter chromatin organization and function. By studying cells migrating through microfluidic devices that mimic interstitial spaces , we found that confined migration results in increased H3K9me3 and H3K27me3 heterochromatin marks that persist for days.

Single-cell chromatin accessibility and lipid profiling reveals SCD1-dependent metabolic shift in adipocytes induced by bariatric surgery.

Obesity promotes type 2 diabetes and cardiometabolic pathologies. Vertical sleeve gastrectomy (VSG) is used to treat obesity resulting in long-term weight loss and health improvements that precede weight loss; however, the mechanisms underlying the immediate benefits remain incompletely understood. Because adipose plays a crucial role in energy homeostasis and utilization, we hypothesized that VSG exerts its influences, in part, by modulating adipose functional states.

methyl-ATAC-seq measures DNA methylation at accessible chromatin.

Chromatin features are characterized by genome-wide assays for nucleosome location, protein binding sites, three-dimensional interactions, and modifications to histones and DNA. For example, assay for transposase accessible chromatin sequencing (ATAC-seq) identifies nucleosome-depleted (open) chromatin, which harbors potentially active gene regulatory sequences; and bisulfite sequencing (BS-seq) quantifies DNA methylation. When two distinct chromatin features like these are assayed separately in populations of cells, it is impossible to determine, with certainty, where the features are coincident in the genome by simply overlaying data sets.

Imprinted DNA methylation reconstituted at a non-imprinted locus.

Background: In mammals, tight regulation of cytosine methylation is required for embryonic development and cellular differentiation. The trans-acting DNA methyltransferases that catalyze this modification have been identified and characterized; however, these proteins lack sequence specificity, leaving the mechanism of targeting unknown. A cis-acting regulator within the Rasgrf1 imprinting control region (ICR) is necessary for establishment and maintenance of local imprinted methylation.

Analysis of Combinatorial Epigenomic States.

Hundreds of distinct chemical modifications to DNA and histone amino acids have been described. Regulation exerted by these so-called epigenetic marks is vital to normal development, stability of cell identity through mitosis, and nongenetic transmission of traits between generations through meiosis. Loss of this regulation contributes to many diseases.

Long non-coding RNA regulation of reproduction and development.

Noncoding RNAs (ncRNAs) have long been known to play vital roles in eukaryotic gene regulation. Studies conducted over a decade ago revealed that maturation of spliced, polyadenylated coding mRNA occurs by reactions involving small nuclear RNAs and small nucleolar RNAs; mRNA translation depends on activities mediated by transfer RNAs and ribosomal RNAs, subject to negative regulation by micro RNAs; transcriptional competence of sex chromosomes and some imprinted genes is regulated in cis by ncRNAs that vary by species; and both small-interfering RNAs and piwi-interacting RNAs bound to Argonaute-family proteins regulate post-translational modifications on chromatin and local gene expression states. More recently, gene-regulating noncoding RNAs have been identified, such as long intergenic and long noncoding RNAs (collectively referred to as lncRNAs)--a class totaling more than 100,000 transcripts in humans, which include some of the previously mentioned RNAs that regulate dosage compensation and imprinted gene expression.

Role of PRDM16 and its PR domain in the epigenetic regulation of myogenic and adipogenic genes during transdifferentiation of C2C12 cells.

The positive regulatory domain containing 16 (PRDM16) is commonly regarded as a "switch" controlling the transdifferentiation of myoblasts to brown adipocytes. The N-positive regulatory (PR) domain, which is highly homologous to SET domain, is a characteristic structure for the PRDM family. Many SET domain containing proteins and several PRDM members have been found to possess histone methyltransferase activity, yet the role of PRDM16 and its PR domain in the epigenetic regulation of myogenic and adipogenic genes during myoblasts/adipocytes transdifferentiation remains unexplored.

Single molecule and single cell epigenomics.

Dynamically regulated changes in chromatin states are vital for normal development and can produce disease when they go awry. Accordingly, much effort has been devoted to characterizing these states under normal and pathological conditions. Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is the most widely used method to characterize where in the genome transcription factors, modified histones, modified nucleotides and chromatin binding proteins are found; bisulfite sequencing (BS-seq) and its variants are commonly used to characterize the locations of DNA modifications.

Possible chemical initiators of cognitive dysfunction in phenylketonuria, Parkinson's disease and Alzheimer's disease.

Though a great deal is known of the pathophysiology of phenylketonuria (PKU), Parkinson's disease (PD) and Alzheimer's disease (AD) very little is known regarding possible chemical species responsible for initiating the cascade of events that ultimately cause cognitive dysfunction. Can these be viewed as inborn errors in metabolism, occurring at various stages in the life cycle, analogous to adult onset diabetes? One major deficiency in understanding such conditions is the paucity of information regarding the total metabolic pathway for various amino acids that may be implicated in their causation. For example in PKU, its etiology was reported in 1934 and dietary restriction of phenylalanine proved effective for individuals with unsatisfactory metabolism of phenylalanine.

Approaching the single molecule. Interview by Kristie Nybo.

Paul Soloway's development of single molecule approaches to study epigenetics caught our attention. Curious to know more, BioTechniques contacted him to find out about the ambition, character, and motivation that led to his success.

Single-molecule analysis of combinatorial epigenomic states in normal and tumor cells.

Proper placement of epigenetic marks on DNA and histones is fundamental to normal development, and perturbations contribute to a variety of disease states. Combinations of marks act together to control gene expression; therefore, detecting their colocalization is important, but because of technical challenges, such measurements are rarely reported. Instead, measurements of epigenetic marks are typically performed one at a time in a population of cells, and their colocalization is inferred by association.

Coordinate regulation of DNA methylation and H3K27me3 in mouse embryonic stem cells.

Chromatin is separated into functional domains distinguished by combinatorial patterns of post-translational histone modifications and DNA methylation. Recent studies examining multiple histone modifications have found numerous chromatin states with distinct profiles of chromatin marks and functional enrichments. There are data showing coordinate regulation between DNAme and H3K27me3, which are both involved in the establishment and maintenance of epigenetic gene silencing, but the data are conflicting.

Microfluidic extraction, stretching and analysis of human chromosomal DNA from single cells.

We describe a microfluidic device for the extraction, purification and stretching of human chromosomal DNA from single cells. A two-dimensional array of micropillars in a microfluidic polydimethylsiloxane channel was designed to capture a single human cell. Megabase-long DNA strands released from the cell upon lysis are trapped in the micropillar array and stretched under optimal hydrodynamic flow conditions.

Data mining as a discovery tool for imprinted genes.

This chapter serves as an introduction to the collection of genome-wide sequence and epigenomic data, as well as the use of these data in training generalized linear models (glm) to predicted imprinted status. This is meant to be an introduction to the method, so only the most straightforward examples will be covered. For instance, the examples given below refer to 11 classes of genomic regions (the entire gene body, introns, exons, 5' UTR, 3' UTR, and 1, 10, and 100 kb upstream and downstream of each gene).

Breed-dependent transcriptional regulation of 5'-untranslated GR (NR3C1) exon 1 mRNA variants in the liver of newborn piglets.

Glucocorticoids are vital for life and regulate an array of physiological functions by binding to the ubiquitously expressed glucocorticoid receptor (GR, also known as NR3C1). Previous studies demonstrate striking breed differences in plasma cortisol levels in pigs. However, investigation into the breed-dependent GR transcriptional regulation is hampered by lacking porcine GR promoter information.

Real-time analysis and selection of methylated DNA by fluorescence-activated single molecule sorting in a nanofluidic channel.

Epigenetic modifications, such as DNA and histone methylation, are responsible for regulatory pathways that affect disease. Current epigenetic analyses use bisulfite conversion to identify DNA methylation and chromatin immunoprecipitation to collect molecules bearing a specific histone modification. In this work, we present a proof-of-principle demonstration for a new method using a nanofluidic device that combines real-time detection and automated sorting of individual molecules based on their epigenetic state.

Sequences sufficient for programming imprinted germline DNA methylation defined.

Epigenetic marks are fundamental to normal development, but little is known about signals that dictate their placement. Insights have been provided by studies of imprinted loci in mammals, where monoallelic expression is epigenetically controlled. Imprinted expression is regulated by DNA methylation programmed during gametogenesis in a sex-specific manner and maintained after fertilization.

A survey for novel imprinted genes in the mouse placenta by mRNA-seq.

Many questions about the regulation, functional specialization, computational prediction, and evolution of genomic imprinting would be better addressed by having an exhaustive genome-wide catalog of genes that display parent-of-origin differential expression. As a first-pass scan for novel imprinted genes, we performed mRNA-seq experiments on embryonic day 17.5 (E17.

Role for piRNAs and noncoding RNA in de novo DNA methylation of the imprinted mouse Rasgrf1 locus.

Genomic imprinting causes parental origin-specific monoallelic gene expression through differential DNA methylation established in the parental germ line. However, the mechanisms underlying how specific sequences are selectively methylated are not fully understood. We have found that the components of the PIWI-interacting RNA (piRNA) pathway are required for de novo methylation of the differentially methylated region (DMR) of the imprinted mouse Rasgrf1 locus, but not other paternally imprinted loci.