Rapid dissection and model-based optimization of inducible enhancers in human cells using a massively parallel reporter assay
By A. Melnikov, A. Murugan, Xiaolan Zhang, Tiberiu Teşileanu, Li Wang, P. Rogov, Soheil Feizi, Andreas Gnirke, C. Callan, Justin B. Kinney and 3 more. Nature Biotechnology, 2012
377 citations recorded by the source corpus.
Learning to read and write the transcriptional regulatory code is of central importance to progress in genetic analysis and engineering. Here, we describe a massively parallel reporter assay (MPRA) that enables systematic dissection of transcriptional regulatory elements by integrating microarray-based DNA synthesis and high-throughput tag sequencing. We apply MPRA to compare more than 27,000 distinct variants of two inducible enhancers in human cells: a synthetic cAMP-regulated enhancer and the virus-inducible interferon beta enhancer. We first show that the resulting data define accurate maps of functional transcription factor binding sites in both enhancers at single-nucleotide resolution. We then use the data to train quantitative sequence-activity models (QSAMs) of the two enhancers. We show that QSAMs from two cellular states can be combined to identify novel enhancer variants that optimize potentially conflicting objectives, such as maximizing induced activity while minimizing basal activity.
Subfields: Biophysics, Molecular Biology
View Paper: https://www.semanticscholar.org/paper/9f45b869a4ff1a1a10ddfe789f1a46999e290814
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Citations in the corpus
- EnhancerAtlas 2.0: an updated resource with enhancer annotation in 586 tissue/cell types across nine species (2019, background): “Two representatives, STARRseq (self-transcribing active regulatory region sequencing) and MPRA (massively parallel reporter assay), produced a library of reporter DNA sequence constructs as well as the unique tags or barcodes to assess the enhancer activities of tested regulatory regions (5,17).”
- 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).”