Inferring gene expression from ribosomal promoter sequences, a crowdsourcing approach
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Activity-dependent changes in gene expression are implicated in the pathogenesis of Huntington's disease (Gambazzi et al., 2010; Spektor et al., 2002; Luthi-Carter et al., 2000). One of the most important facets of transcriptional dysfunction in HD appears ...
Sequence-specific binding of a transcription factor to DNA is the central event in any transcriptional regulatory network. However, relatively little is known about the evolutionary plasticity of transcription factors. For example, the exact functional con ...
TORC1 is a conserved multisubunit kinase complex that regulates many aspects of eukaryotic growth including the biosynthesis of ribosomes. The TOR protein kinase resident in TORC1 is responsive to environmental cues and is potently inhibited by the natural ...
Cognitive abilities and disorders unique to humans are thought to result from adaptively driven changes in brain transcriptomes, but little is known about the role of cis-regulatory changes affecting transcription start sites (TSS). Here, we mapped in huma ...
BACKGROUND: To understand cancer-related modifications to transcriptional programs requires detailed knowledge about the activation of signal-transduction pathways and gene expression programs. To investigate the mechanisms of target gene regulation by hum ...
Finding sequences that control expression of genes is central to understanding genome function. Previous studies have used evolutionary conservation as an indicator of regulatory potential. Here, we present a method for the unbiased in vivo screen of putat ...
Tightly regulated gene expression systems represent invaluable tools for studying gene function and for the validation of drug targets in bacteria. While several regulated bacterial promoters have been characterized, few of them have been successfully used ...
Small nucleolar RNAs (snoRNAs) play a key role in ribosomal RNA biogenesis, yet factors controlling their expression are unknown. We found that the majority of Saccharomyces snoRNA promoters display an aRCCCTaa sequence motif at the upstream border of a TA ...
An emerging model views gene regulation as a competition for regulatory sequences between transcription factors and nucleosomes at thermodynamic equilibrium. A computational model of the DNA affinity of nucleosomes was recently developed allowing to predic ...