Genome-Wide Quantitative Enhancer Activity Maps Identified by STARR-seq

By Cosmas D. Arnold, D. Gerlach, Christoph Stelzer, Łukasz M. Boryń, Martina Rath, Alexander Stark. Science, 2013

1,093 citations recorded by the source corpus.

Subfields: Molecular Biology, Plant Science

View Paper: https://www.semanticscholar.org/paper/4dc2928f0af6b81a4ab079256d073d5da696f6e8

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Citations in the corpus

Modification of enhancer chromatin: what, how and why? (2013, background): “Moreover, although limited in scope of validation, existing studies strongly support predictive power of epigenomic annotation in enhancer discovery (Arnold et al., 2013; Blow et al., 2010; Bonn et al., 2012; May et al., 2012; Visel et al., 2009).”
Transcriptional enhancers: from properties to genome-wide predictions (2014, methodology): “…discrepancy between the activity of a sequence in its endogenous genomic context and that in a reporter plasmid cannot be explained by genomic integration per se: results from plasmid-based assays agreed well with results from genomically integrated reporters in both yeast 129 and insect cells 72 .”
New developments on the Encyclopedia of DNA Elements (ENCODE) data portal (2019, methodology): “To more directly assess the function of ENCODE elements, new assays are underway, including massively parallel reporter assays (33), CRISPR screens (34) and STARR-seq (35).”
Regulation of disease-associated gene expression in the 3D genome (2016, neutral): “…although these sequences appar ently intrinsically harboured the capacity to act as an enhancer, many of them were actively repressed at their endogen ous location in the genome, showing that chromatin can add an additional regulatory layer to control the activity of noncoding sequences 49,50”
EnhancerAtlas 2.0: an updated resource with enhancer annotation in 586 tissue/cell types across nine species (2019, background): “In addition, we obtained STARR-seq datasets from the GEO Datasets (36).”
Genome-wide prediction of cis-regulatory regions using supervised deep learning methods (2016, methodology): “Using STARRseq data, a new experimental approach for screening candidate enhancer sequences [18], dinucleotide repeat motifs (DRMs) were found to be enriched in broadly active enhancers, leading to a proposition that a small set of TF binding site motifs and DRMs might be sufficient for enhancer pre”