A Unified Architecture of Transcriptional Regulatory Elements
By R. Andersson, Albin Sandelin, Charles G. Danko. 2015
210 citations recorded by the source corpus.
Gene expression is precisely controlled in time and space through the integration of signals that act at gene promoters and gene-distal enhancers. Classically, promoters and enhancers are considered separate classes of regulatory elements, often distinguished by histone modifications. However, recent studies have revealed broad similarities between enhancers and promoters, blurring the distinction: active enhancers often initiate transcription, and some gene promoters have the potential of enhancing transcriptional output of other promoters. Here, we propose a model in which promoters and enhancers are considered a single class of functional element, with a unified architecture for transcription initiation. The context of interacting regulatory elements, and surrounding sequences, determine local transcriptional output as well as the enhancer and promoter activities of individual elements.
Subfields: Molecular Biology
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In Molecular Biology
- Casey S. Greene
- Wenqiang Shi
- Yifan Peng
- Brett K. Beaulieu-Jones
- G. Way
- Amr M. Alexandari
- Yifeng Li
- Zhiyong Lu
Citations in the corpus
- Opportunities and obstacles for deep learning in biology and medicine (2017, background): “There is no universal enhancer sequence signal or marker for enhancers, and some literature suggests that enhancers and promoters may be just categories along a spectrum [173].”
- Genome-wide prediction of cis-regulatory regions using supervised deep learning methods (2016, background): “Recent studies confirmed that sequence properties can be important for the recognition of promoters and enhancers [3, 5, 24].”
- GeneHancer: genome-wide integration of enhancers and target genes in GeneCards (2017, result): “This overlap is also in line with reported difficulties in differentiation between enhancers and promoters via chromatin profiling assays (73).”
- Fast, scalable prediction of deleterious noncoding variants from functional and population genomic data (2016, unknown): “This approach of annotating enhancers based on enhancer-associated RNAs (eRNAs) has been shown to identify elements that have active roles in gene regulation in a cell-type-specific fashion with high genomic resolution 35–37 .”