The AIDS era has seen multiple advances in the power of genetics research; scores of host genetic protective factors have been nominated and several have translated to the bedside. We discuss how genomics may inform HIV/AIDS prevention, treatment and eradication.
A report on the 46th annual PopGroup conference, Glasgow, UK, December 18-21,
Genetics; evolution; coalescent theory; selective sweeps; blogging; gynodioecy; androdioecy
Examining NFAT transcription factor dynamics in single cells during signal propagation from cell membrane to the nucleus reveals unique modes of operation for protein isoforms.
Transcription factors; nuclear dynamics; signaling; NFAT; p53; NF-κB
Mouse genetics and computer simulations demonstrate that digit number and width are controlled by a Turing-type mechanism in which distal Hox genes modulate periodicity.
A growing resource of methicillin-resistant Staphylococcus aureus (MRSA) genomes uncovers intriguing phylogeographic and recombination patterns and highlights challenges in identifying the source of these phenomena.
The 1000 Genomes Project Consortium has recently published an important early contribution to a new generation of systematic surveys of rare human genetic variation.
A report of the fifth annual Personal Genomes and Medical Genomics meeting, held at Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA, November 14-17, 2012.
high-throughput sequencing; personal genomics; personalized medicine; pharmacogenomics; precision medicine
Processing of pre-miRNAs by Dicer is regulated by its dsRNA-binding protein partner, and leads to the generation of alternative miRNA forms with distinct target sets.
Recent studies have found methyl-6-adenosine in thousands of mammalian genes, and this modification is most pronounced near the beginning of the 3' UTR. We present a perspective on current work and new single-molecule sequencing methods for detecting RNA base modifications.
epigenetics; epigenomics; epitranscriptome; m6A; methyl-6-adenosine; methyladenosine; N6-methyladenosine; RNA modifications
A report on the 11th European Conference on Computational Biology (ECCB), Basel, Switzerland, September 9-12, 2012.
bioinformatics; genomics; proteomics; transcriptomics; interactions; networks
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