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In brief

Subjects

Chromosome biology

Chromosome organization by a nucleoid-associated protein in live bacteria Wang, W. et al. Science 333, 1445–1449 (2011)

This study shows that, in vivo, the spatial organization of the Escherichia coli chromosome and the clustering of this bacterium's functional chromosomal domains depend largely on the presence of one nucleoid-associated protein (NAP). The authors used a combination of fluorescence microscopy and chromosome conformation capture assays to examine the subcellular distribution of five main NAPs in live cells. One NAP, the transcriptional silencer HNS, forms two compact, DNA-bound clusters that sequester various HNS-regulated operons; this long-range clustering is disrupted in hns-null mutants.

Transcriptomics

The human mitochondrial transcriptome Mercer, T. R. et al. Cell 146, 645–658 (2011)

The authors have generated a comprehensive profile of the human mitochondrial transcriptome. Using a combination of deep sequencing, parallel analysis of RNA ends and in vivo DNAse I footprinting, some little-known features of the atypical mitochondrial genome were characterized. These include the extensive involvement of post-translational modifications in regulating expression from the polycistronic transcripts, the existence of small RNA species and the nature of the sites that regulate transcription initiation. The ten data sets generated in this article and a meta-analysis of 20 existing data sets can be accessed at http://mitochondria.matticklab.com.

Epigenetics

Analysis of DNA methylation in a three-generation family reveals widespread genetic influence on epigenetic regulation Gertz, J. et al. PLoS Genet. 7, e1002228

Most variation in DNA methylation in the human epigenome is influenced by the underlying genomic sequence, according to this new study. The authors assessed DNA methylation across the genome in six members of a three-generation family and showed that 80% of the variation in this mark is explained by genotype. This finding suggests that genomic imprinting has a relatively minor influence on methylation patterns and has implications for understanding the functional effects of genetic variation.

Evolution

Three periods of regulatory innovation during vertebrate evolution Lowe, C. B. et al. Science 333, 1019–1024 (2011)

These authors used comparative genomics to infer that conserved non-exonic elements (CNEEs) — putative regulatory regions — have undergone three extended phases of evolution in vertebrates. They identified CNEEs and traced their evolution using genomic data from five vertebrate species, including humans. CNEEs appear to have been gained near to transcription factor genes during early vertebrate evolution. A second phase of innovations then occurred close to genes involved in extracellular signalling, and this was followed by a third period of changes close to genes that are required for post-translational modifications.

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In brief. Nat Rev Genet 12, 669 (2011). https://doi.org/10.1038/nrg3078

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