Absence of a simple code: how transcription factors read the genome.
By Matthew Slattery, Tianyin Zhou, Lin Yang, Ana Carolina Dantas Machado, Raluca Gordân, R. Rohs. 2014
504 citations recorded by the source corpus.
Transcription factors (TFs) influence cell fate by interpreting the regulatory DNA within a genome. TFs recognize DNA in a specific manner; the mechanisms underlying this specificity have been identified for many TFs based on 3D structures of protein-DNA complexes. More recently, structural views have been complemented with data from high-throughput in vitro and in vivo explorations of the DNA-binding preferences of many TFs. Together, these approaches have greatly expanded our understanding of TF-DNA interactions. However, the mechanisms by which TFs select in vivo binding sites and alter gene expression remain unclear. Recent work has highlighted the many variables that influence TF-DNA binding, while demonstrating that a biophysical understanding of these many factors will be central to understanding TF function.
Subfields: Molecular Biology
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In Molecular Biology
- Jasper Snoek
- H. K. Long
- David R. Kelley
- Johannes Rinn
- J. Wysocka
- S. Prescott
- Howard Y. Chang
- Anshul B Kundaje
Citations in the corpus
- Ever-changing landscapes: transcriptional enhancers in development and evolution (2016, background): “Impact of Sequences that Affect DNA Shape In addition to the core TF motif recognition, emerging evidence supports the role of local DNA shape in influencing binding affinity, site accessibility, and binding site choice, known as ‘‘shape readout’’ (Slattery et al., 2014).”
- Basset: learning the regulatory code of the accessible genome with deep convolutional neural networks (2015, background): “These observations suggest that convolutional neural networks offer a simple and affective approach to automatically capture the subtle influences on functional activity provided by local sequence composition (Slattery et al. 2014).”