A5004882158- Epigenetics and DNA Methylation
- Cancer Genomics and Diagnostics
- Muscle Physiology and Disorders
- Immune Cell Function and Interaction
- Blood Coagulation and Thrombosis Mechanisms
- Genomics and Phylogenetic Studies
- Genetic factors in colorectal cancer
- Cancer-related gene regulation
- Tissue Engineering and Regenerative Medicine
- Virus-based gene therapy research
- Veterinary Oncology Research
- T-cell and B-cell Immunology
- Neurogenetic and Muscular Disorders Research
- Colorectal Cancer Treatments and Studies
- Genetic Syndromes and Imprinting
- Breast Cancer Treatment Studies
- RNA modifications and cancer
- Immune responses and vaccinations
- Molecular Biology Techniques and Applications
- Congenital heart defects research
- Genetics, Aging, and Longevity in Model Organisms
- Metabolomics and Mass Spectrometry Studies
- Children's Rights and Participation
- Medicinal Plant Research
- Immunodeficiency and Autoimmune Disorders
Translational Genomics Research Institute
2024
HudsonAlpha Institute for Biotechnology
2012-2020
Intermountain Healthcare
2018
National Heart Lung and Blood Institute
2014
Jean Mayer Human Nutrition Research Center on Aging
2014
Tufts University
2014
University of Alabama at Birmingham
2014
Harvard University
2014
Framingham Heart Study
2014
Boston Children's Hospital
2014
DNA methylation is an epigenetic modification that changes with age in human tissues, although the mechanisms and specificity of this process are still poorly understood. We compared CpG across 283 blood, brain, kidney, skeletal muscle samples using arrays to identify tissue-specific effects.We found age-associated CpGs (ageCGs) both common tissues. Tissue-specific CGs frequently located outside islands decreased methylation, ageCGs show opposite trend. AgeCGs significantly associated...
Background— Genetic research regarding blood lipids has largely focused on DNA sequence variation; few studies have explored epigenetic effects. Genome-wide surveys of methylation may uncover factors influencing lipid metabolism. Methods and Results— To identify whether differential cytosine-(phosphate)-guanine dinucleotides (CpGs) correlated with phenotypes, we isolated from CD4+ T cells quantified the proportion sample at >450 000 CpGs by using Illumina Infinium HumanMethylation450...
Morphological variation in natural populations is a genomic test bed for studying the interface between molecular evolution and population genetics, but some of most interesting questions involve non-model organisms that lack well annotated reference genomes. Many felid species exhibit polymorphism melanism relative roles played by genetic drift, selection, interspecies hybridization remain uncertain. We identify mutations Agouti signaling protein (ASIP) or Melanocortin 1 receptor (MC1R) as...
The inheritance of gene expression patterns is dependent on epigenetic regulation, but the establishment and maintenance landscapes during T cell differentiation are incompletely understood. Here we show that two stage-specific Cd4 cis-elements, previously characterized enhancer E4p a novel E4m, coordinately promote transcription in mature thymic MHC-II-specific cells, part through canonical Wnt pathway. Specifically, licenses E4m to orchestrate DNA demethylation by TET1 TET3, which turn...
Abstract Satellite cells are skeletal muscle stem that provide myogenic progeny for myofiber growth and repair. Temporal expression of regulatory factors (MRFs) the paired box transcription factor Pax7 defines characteristic phases proliferation (Pax7 + /MyoD /myogenin − ) differentiation during myogenesis satellite cells. Here, using bromodeoxyuridine (BrdU) labeling triple immunodetection, we analyzed patterns MRFs MyoD, Myf5, or myogenin within S phase myoblasts prepared from posthatch...
DNA methylation levels vary markedly by cell-type makeup of a sample. Understanding these differences and estimating the sample is an important aspect studying methylation. from leukocytes in whole blood simple to obtain pervasive research. However, contain many distinct cell types subtypes. We propose two-stage model that estimates proportions six main (CD4+ T cells, CD8+ monocytes, B granulocytes, natural killer cells) as well subtypes cells. Unlike previous methods only estimate overall...
Abstract A genomic understanding of the oncogenic processes and individual variability human cancer has steadily fueled improvement in patient outcomes over past 20 years. Mutations within tumour tissues are routinely assessed through clinical diagnostic assays by academic commercial laboratories to facilitate diagnosis, prognosis effective treatment stratification. The application genomics unveiled a wealth mutation‐based biomarkers canine cancers, suggesting that transformative principles...
Abstract The epigenetic patterns that are established during early thymic development might determine mature T cell physiology and function, but the molecular basis topography of genetic elements involved not fully known. Here we show, using Cd4 locus as a paradigm for developmental programming, DNA demethylation licenses novel stimulus-responsive element is critical maintenance gene expression in effector cells. We document importance maintaining high CD4 parasitic infection show by driving...
<h3>Objective</h3> Copy number variants (CNVs) have been associated with the risk to develop multiple autoimmune diseases. Our objective was identify CNVs psoriatic arthritis (PsA) using a genome-wide analysis approach. <h3>Methods</h3> A total of 835 patients PsA and 1498 healthy controls were genotyped for Illumina HumanHap610 BeadChip genotyping platform. Genomic characterised CNstream software analysed association χ<sup>2</sup> test. The most significant genomic CNV associations...
DNA methylation at CpG sites is both heritable and influenced by environment, but the relative contributions of each to levels are unclear. We conducted a heritability analysis in human CD4+ cells across 975 individuals from 163 families Genetics Lipid-lowering Drugs Diet Network (GOLDN). Based on broad-sense (H2) value threshold 0.4, we identified 20,575 highly CpGs among 174,445 most variable autosomal (SD > 0.02). Tests for associations with genotype 2,145,360 SNPs using 717 showed that...
Mapping of allelic imbalance (AI) at heterozygous loci has the potential to establish links between genetic risk for disease and biological function. Leveraging multi-omics data AI analysis functional annotation, we discovered a novel variant rs1047643 8p23 in association with systemic lupus erythematosus (SLE). This displays dynamic chromatin accessibility expression on FDFT1 gene B cells SLE. We further found B-cell restricted super-enhancer (SE) that physically contacts this SNP-residing...
Current target enrichment systems for large-scale next-generation sequencing typically require synthetic oligonucleotides used as capture reagents to isolate sequences of interest. The majority are focused on gene coding regions or promoters en masse. Here we introduce development a customizable targeted system using biotinylated RNA probe baits transcribed from sheared bacterial artificial chromosome clone templates that enables large, contiguous blocks the genome applications. This adapted...