Birds do it,bees do it,worms and ciliates do it too: DNA methylation from unexpected corners of the tree of life

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     

Of RNA-binding proteins and their targets: interaction determines expression

Combining the prediction of interactions between mRNAs and RNA-binding proteins with experimental expression profiles uncovers novel regulatory paradigms concerning proliferation and differentiation processes.See related research, http://genomebiology.com/2014/15/1/R13     

The complex binding of PRDM9

A recent study investigates the in vitro DNA binding behavior of PRDM9, a zinc finger protein involved in the localization of recombination hotspots in mammals.Please see related research article: http://genomebiology.com/2013/14/4/R35     

Host genetic architecture and the landscape of microbiome composition: humans weigh in

Comparative analyses of the control of mammalian microbiomes by host genetic architecture reveal striking conserved features that have implications for the evolution of host–microbiome interactions.See related Research article: http://www.genomebiology.com/2015/16/1/191     

Identification of evolutionarily meaningful information within the mammalian RNA editing landscape

A large comparative genomic sequence study has determined the extent of conservation between RNA editing sites within the mammalian evolutionary tree.See related research by Pinto et al., http://genomebiology.com/2014/15/1/R5     

Timber! Felling the loblolly pine genome

Conventional short read sequences derived from haploid DNA were extended into long super-reads enabling assembly of the massive 22 Gbp loblolly pine, Pinus taeda, genome.See related research http://genomebiology.com/2014/15/3/R59     

Insecticide resistance comes of age

A new study integrates biochemistry, genetics and structural biology to reveal the mechanism of metabolic resistance in a vector mosquito in unprecedented detail.See related research http://genomebiology.com/2014/15/2/R27     

Rising from the crypt: decreasing DNA methylation during differentiation of the small intestine

The differentiation of intestinal stem cells involves few DNA methylation changes, assayed by bisulfite sequencing, in contrast to other adult somatic stem cell hierarchies.Please see related Research article: http://genomebiology.com/2013/14/5/R50     

Binding the boundaries of chromatin domains

A new study proposes an integrated framework to improve our understanding of the multiple functions of insulator elements, and their architectural role in the genome.See related research; http://genomebiology.com/2014/15/6/R82     

Interactome analysis brings splicing into focus

The spliceosome is a huge molecular machine that assembles dynamically onto its pre-mRNA substrates. A new study based on interactome analysis provides clues about how splicing-regulatory proteins modulate assembly of the spliceosome to either activate or repress splicing.Please see related Research article: http://www.genomebiology.com/2015/16/1/119/abstract     

Bringing non-human primate research into the post-genomic era: how monkeys are teaching us about elite controllers of HIV/AIDS

Whole-genome sequencing of Mauritian cynomolgus macaques reveals novel candidate loci for controlling simian immunodeficiency virus replication.See related Research, http://genomebiology.com/2014/15/11/478     

What can epigenomics do for you?

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     

International plant molecular biology: a bright future for green science

A new study in this issue of Genome Biology sheds light on why some pseudogenes persist in rodent, and other mammalian, genomes. Please see related Research article by Marques et al http://genomebiology.com/2012/13/11/R102     

SNES makes sense? Single-cell exome sequencing evolves

Technologies for single-cell sequencing are improving steadily. A recent study describes a new method for interrogating all coding sequences of the human genome at single-cell resolution.See related research by Leung et al., http://genomebiology.com/2015/16/1/55     

Smaug destroys a huge treasure

Smaug, a protein repressing translation and inducing mRNA decay, directly controls an unexpectedly large number of maternal mRNAs driving early Drosophila development.See related research, http://genomebiology.com/2014/15/1/R4Regulation of translation and mRNA stability is a key aspect of early metazoan development. One of the best studied factors involved in these processes is the Drosophila protein Smaug. In this issue of Genome Biology, Chen et al. [1] report that a large number of maternal mRNAs in the fly embryo are probably regulated directly by Smaug.     

Balance of DNA methylation and demethylation in cancer development

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/R93Epigenetic information is crucial for eukaryotic organisms as it impacts a broad range of biological processes from gene regulation to disease pathogenesis. This information is mainly embodied in DNA methylation, carried by 5-methylcytosine (5mC, the fifth base), and various histone modifications. It is well-established that epigenetics can play critical roles in cancer development; a highly distorted epigenome (including aberrant DNA methylation and histone modification patterns) is now accepted to be a general feature of many cancers [1,2]. Understanding the molecular mechanisms of epigenetic alterations at the early stages of tumorigenesis may therefore be important in developing new cancer treatments.A cell''s DNA methylation pattern is a dynamic status balanced by methylation and demethylation, and aberrant DNA methylation has been attributed to either excessive methylation or deficient demethylation. A study by Meehan, Moggs and colleagues, published in this issue of Genome Biology [3], now links active demethylation with the early stages of carcinogenesis by investigating the non-genotoxic carcinogen phenobarbital (PB)-induced rodent hepatocarcinogen model.     

An enigmatic satellite

McLaughlin and Chadwick describe an X-linked tandem repeat that is transcribed, conserved and defies X inactivation. Is it selfish, functional or just an oddity?See research article: http://genomebiology.com/2011/12/4/R37