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Article
Map** the microbiome milieu
This month’s Genome Watch discusses the application of spatial transcriptomics to investigate the arrangements of microbial communities and their effects on the host.
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Open AccessDynamic enhancer landscapes in human craniofacial development
The genetic basis of human facial variation and craniofacial birth defects remains poorly understood. Distant-acting transcriptional enhancers control the fine-tuned spatiotemporal expression of genes during c...
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Article
Open AccessTopologically associating domain boundaries are required for normal genome function
Topologically associating domain (TAD) boundaries partition the genome into distinct regulatory territories. Anecdotal evidence suggests that their disruption may interfere with normal gene expression and caus...
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Article
Persistence and plasticity in bacterial gene regulation
Organisms orchestrate cellular functions through transcription factor (TF) interactions with their target genes, although these regulatory relationships are largely unknown in most species. Here we report a hi...
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Mutant phenotypes for thousands of bacterial genes of unknown function
One-third of all protein-coding genes from bacterial genomes cannot be annotated with a function. Here, to investigate the functions of these genes, we present genome-wide mutant fitness data from 32 diverse b...
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Open AccessResequencing and annotation of the Nostoc punctiforme ATTC 29133 genome: facilitating biofuel and high-value chemical production
Cyanobacteria have the potential to produce bulk and fine chemicals and members belonging to Nostoc sp. have received particular attention due to their relatively fast growth rate and the relative ease with whic...
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Large-scale discovery of enhancers from human heart tissue
Len Pennacchio, Axel Visel and colleagues use an epigenomic approach to identify a large number of candidate enhancers from human heart tissue. This work will facilitate further studies into the role of enhanc...
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ChIP-Seq identification of weakly conserved heart enhancers
Len Pennacchio and colleagues used ChIP-Seq with the enhancer-associated protein p300 to identify 3,000 candidate cardiac transcriptional enhancers in embryonic mice at E11.5. Notably, most candidate heart enh...
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Targeted deletion of the 9p21 non-coding coronary artery disease risk interval in mice
It has been know for several years that genetic variations in a stretch of DNA on chromosome 9p21 are linked to the incidence of coronary artery disease. The nature of this link has remained unknown, not least...
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Article
ChIP-seq accurately predicts tissue-specific activity of enhancers
A major yet unresolved quest in decoding the human genome is the identification of the regulatory sequences that control the spatial and temporal expression of genes. Distant-acting transcriptional enhancers a...
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Article
Open AccessRNA editing of human microRNAs
MicroRNAs (miRNAs) are short RNAs of around 22 nucleotides that regulate gene expression. The primary transcripts of miRNAs contain double-stranded RNA and are therefore potential substrates for adenosine to i...
