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Method: Identification of determinants of differential chromatin accessibility through a massively parallel genome-integrated reporter assay
- Jennifer Hammelman,
- Konstantin Krismer,
- Budhaditya Banerjee,
- David K. Gifford,
- and Richard I. Sherwood
Genome Res. October 2020 30: 1468-1480; Published in Advance September 24, 2020, doi:10.1101/gr.263228.120
...factors to bind and activate previously inactive genes. Massively parallel reporter assays (MPRAs) (Inoue and Ahituv 2015; White 2015) have been developed to measure the change to gene expression from the action of promoters (Mogno et al. 2013; Grossman et al. 2017) or enhancers (Melnikov et al. 2012...
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Method: Iterative improvement of deep learning models using synthetic regulatory genomics
- André M. Ribeiro-dos-Santos and
- Matthew T. Maurano
Genome Res. November 2025 35: 2539-2549; Published in Advance October 22, 2025, doi:10.1101/gr.280540.125
...function at the endogenous genomic locus.Sources of training data beyond the reference sequence are limited by the scale of sequence amenable to manipulation, as well as its relevance to the regulation architecture of the endogenous locus. Massively parallel reporter assays (MPRAs) transiently transfected...
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Method: Sequence-based correction of barcode bias in massively parallel reporter assays
- Dongwon Lee,
- Ashish Kapoor,
- Changhee Lee,
- Michael Mudgett,
- Michael A. Beer,
- and Aravinda Chakravarti
Genome Res. September 2021 31: 1638-1645; Published in Advance July 20, 2021, doi:10.1101/gr.268599.120
...versus episomal encoding of enhancer activity. Genome Res 27: 38–52. doi:10.1101/gr.212092.116 ↵Kheradpour P, Ernst J, Melnikov A, Rogov P, Wang L, Zhang X, Alston J, Mikkelsen TS, Kellis M. 2013. Systematic dissection of regulatory motifs in 2000 predicted human enhancers using a massively parallel...
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Review: A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest
- Andrew D. Bates,
- Dawid Grzela,
- Maciej Studzian,
- Louise Brennan,
- Moli Williams,
- Conor Fawcett,
- Beth Hammond,
- Manreen Grewal,
- Marcin Ratajewski,
- Lukasz Pulaski,
- and Urszula L. McClurg
Genome Res. March 2026 36: 433-459; Published in Advance February 17, 2026, doi:10.1101/gr.281154.125
...).Predicted regulatory sites can be validated experimentally using reporter gene assays. In this assay, the transcriptional activity of a predicted promoter, or an enhancer, of a specific GOI can be investigated using plasmids that include the predicted regulatory sequence upstream of a reporter gene (for...
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Research: Genome-wide strand asymmetry in massively parallel reporter activity favors genic strands
- Brian S. Roberts,
- E. Christopher Partridge,
- Bryan A. Moyers,
- Vikram Agarwal,
- Kimberly M. Newberry,
- Beth K. Martin,
- Jay Shendure,
- Richard M. Myers,
- and Gregory M. Cooper
Genome Res. May 2021 31: 866-876; Published in Advance April 20, 2021, doi:10.1101/gr.270751.120
...Institute for Precision Medicine, University of Washington, Seattle, Washington 98195, USA Corresponding authors: rmyers@hudsonalpha.org, gcooper@hudsonalpha.orgAbstractMassively parallel reporter assays (MPRAs) are useful tools to characterize regulatory elements in human s. An aspect of MPRAs...
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Research: A massively parallel reporter assay reveals context-dependent activity of homeodomain binding sites in vivo
- Andrew E.O. Hughes,
- Connie A. Myers,
- and Joseph C. Corbo
Genome Res. October 2018 28: 1520-1531; Published in Advance August 29, 2018, doi:10.1101/gr.231886.117
...parallel reporter assay to determine how local sequence context shapes the regulatory activity of CRX binding sites in mouse photoreceptors. We assayed inactivating mutations in more than 1700 TF binding sites and found that dimeric CRX binding sites act as stronger enhancers than monomeric CRX binding...
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Research: A massively parallel 3′ UTR reporter assay reveals relationships between nucleotide content, sequence conservation, and mRNA destabilization
- Adam J. Litterman,
- Robin Kageyama,
- Olivier Le Tonqueze,
- Wenxue Zhao,
- John D. Gagnon,
- Hani Goodarzi,
- David J. Erle,
- and K. Mark Ansel
Genome Res. June 2019 29: 896-906; Published in Advance May 31, 2019, doi:10.1101/gr.242552.118
...secondary structures had predictive power for regulatory activity in our massively parallel reporter assay independent of GC content. We ran a linear regression of predicted folding energy versus GC content and identified sequences that were predicted to be “better” (above trend) or “worse” (below trend...
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Method: The SeqSplice multiplexed minigene splicing assay for characterization and quantitation of variant-induced BRCA1 and BRCA2 splice isoforms
- Daffodil M. Canson,
- Michael T. Parsons,
- Gemma Moir-Meyer,
- Troy Dumenil,
- Gemma Montalban,
- Erica Lin,
- Terri P. McVeigh,
- Aimee L. Davidson,
- Shaun M. Bouckaert,
- Matt Trau,
- Darren Korbie,
- and Amanda B. Spurdle
Genome Res. September 2025 35: 2104-2115; Published in Advance August 6, 2025, doi:10.1101/gr.279557.124
...% (191/204) specificity and only 6% (13/204) false-positive predictions for variants producing ≤5% alternative transcripts relative to the baseline level expressed by WT constructs (Fig. 4B).Variant clinical significanceWe found 46% (123/265) of variants assayed were reported in ClinVar (https...
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Research: The role of transposon activity in shaping cis-regulatory element evolution after whole-genome duplication
- Øystein Monsen,
- Lars Grønvold,
- Alex Datsomor,
- Thomas Harvey,
- James Kijas,
- Alexander Suh,
- Torgeir R. Hvidsten,
- and Simen Rød Sandve
Genome Res. March 2025 35: 475-488; Published in Advance February 12, 2025, doi:10.1101/gr.278931.124
...-CRE evolution shaping gene coexpression (Fig. 5F). Taken together, we find evidence for a small proportion (3%–5%) of the TE subfamilies spreading CREs that regulate nearby genes.Functional validation of TE-CREs using massively parallel reporter assayTo be able to directly assess regulatory potential of TE...
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Method: Massively parallel cis-regulatory analysis in the mammalian central nervous system
- Susan Q. Shen,
- Connie A. Myers,
- Andrew E.O. Hughes,
- Leah C. Byrne,
- John G. Flannery,
- and Joseph C. Corbo
Genome Res. February 2016 26: 238-255; Published in Advance November 17, 2015, doi:10.1101/gr.193789.115
...of hundreds of thousands of CREs in cell lines and primary tissues (The ENCODE Project Consortium 2012; Shen et al. 2012; Romanoski et al. 2015). As an avenue for the experimental validation of these predictions, massively parallel reporter assays (MPRAs, e.g., CRE-seq) have been developed, in which barcoded...

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