Genome-wide 5-hydroxymethylome analysis of a rodent hepatocarcinogen model reveals that 5-hydroxymethylcytosine-dependent active DNA demethylation may be functionally important in the early stages of carcinogenesis.
See research article http://genomebiology.com/2012/13/10/R93
Epigenomics, the determination of epigenetic landscapes on a genome-wide scale, has progressed at an astounding rate over the past decade. Recent technological developments have enabled base-pair resolution of various epigenomic features, leading to new insights into epigenetic regulation.
epigenomics; chromatin immunoprecipitation; ChIP-exo; micrococcal nuclease mapping; deoxyribonuclease I mapping
Somatic cell reprogramming to induced pluripotent stem (iPS) cells by defined factors is a form of engineered reverse development carried out in vitro. Recent investigation has begun to elucidate the molecular mechanisms whereby these factors function to reset the epigenome.
Studies describing intricate patterns of DNA methylation in nematode and ciliate are controversial due to the uncertainty of genomic evolutionary conservation of DNA methylation enzymes.
See related research articles http://genomebiology.com/2012/13/10/R99 and http://genomebiology.com/2012/13/10/R100
Heritable phenotypic differences caused by epigenetic modifications, rather than DNA sequence mutations, pose a challenge to our understanding of natural variation. Here, we review what is known about plant epialleles and the role of epigenetics in evolution.
DNA methylation; epialleles; epigenetics; genetics; plant evolution
A new study takes an evolutionary approach to investigate to what extent nucleosome positioning is determined by underlying sequence or by trans-acting factors.
Evolution; genome-wide organization; nucleosome positioning; poly(dA:dT) sequences; yeast
Genome-wide association studies and comparative genomics have established major loci and specific polymorphisms affecting human skin, hair and eye color. Environmental changes have had an impact on selected pigmentation genes as populations have expanded into different regions of the globe.
Meta-omics approaches such as metagenomics, metatranscriptomics and metaproteogenomics have the potential to improve our understanding of how the human microbiome affects digestive health and disease.
See research article http://www.genomebiology.com/2012/13/9/R79
A report on the 13th International Congress on Yeasts (ICY), held at Madison, Wisconsin, USA, 26-30 August 2012.
A report on the 20th International Conference on Intelligent Systems for Molecular Biology (ISMB), held at Long Beach, California, USA, July 15-17, 2012.
Biomarkers; complex diseases; computational medicine; drug repositioning; mechanism classifiers; next-generation sequencing; off-target mechanisms; translational bioinformatics
The genome sequence of tomato (Solanum lycopersicum), one of the most important vegetable crops, has recently been decoded. We address implications of the tomato genome for plant breeding, genomics and evolutionary studies, and its potential to fuel future crop biology research.
Genome; Arabidopsis; Tomato; Solanaceae; Biodiversity; Genomics; QTL; Omics
A report on the Galaxy Community Conference at the University of Illinois, Chicago, July 25-27, 2012.
Galaxy; workflows; data integration; tool integration; next generation sequencing
Recent reports describe the genome sequencing of Thellungiella salsuginea and Thellungiella parvula, two extremophile crucifers closely related to the stress-sensitive model plant Arabidopsis thaliana.
Abiotic stress; adaptation; comparative genomics; extremophile plants; genome evolution
Advances in genetics and genomics have improved our understanding of autism spectrum disorders. As many genes have been implicated, we look to points of convergence among these genes across biological systems to better understand and treat these disorders.
Whole-genome methylation analysis of newborns and centenarians reveals widespread epigenetic alterations, and provides new insight into age-related methylation pattern changes.
Caenorhabditis elegans piRNAs promote genome surveillance by triggering siRNA-mediated silencing of nonself DNA in competition with licensing programs that support endogenous gene expression.
piRNA; siRNA; Piwi; C. elegans; germline; genome surveillance; epigenetics; gene silencing; transposable elements
Purification of proteins cross-linked to mRNAs has identified 800 mRNA-binding proteins and their characteristics.
CLIP; 4-thiouridine; RBP; RNA-binding domain; disordered proteins
A report on the Bio-IT World Asia meeting, Marina Bay Sands, Singapore, 6-8 June 2012.
With new technologies, concerns about gene patent claims regarding isolated DNA are becoming less relevant, but broad method claims could be more problematic.
Gene patent; sequencing; isolated DNA; method; abstract; diagnostics; obviousness; Myriad; Prometheus; Classen
Longitudinal cohort studies are ideal for investigating how epigenetic patterns change over time and relate to changing exposure patterns and the development of disease. We highlight the challenges and opportunities in this approach.
Epigenomics; DNA methylation; life course; longitudinal studies