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Perspective: Challenges and considerations for reproducibility of STARR-seq assays
- Maitreya Das,
- Ayaan Hossain,
- Deepro Banerjee,
- Craig Alan Praul,
- and Santhosh Girirajan
Genome Res. April 2023 33: 479-495; Published in Advance May 2, 2023, doi:10.1101/gr.277204.122
...the include DNase-seq (Boyle et al. 2008), ATAC-seq (Buenrostro et al. 2013), and ChIP-seq (Robertson et al. 2007). However, these methods are limited to only providing the location of candidate enhancers and do not assess their functional activity.Self-transcribing active regulatory region sequencing (STARR-seq...
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Method: ATAC-STARR-seq reveals transcription factor–bound activators and silencers within chromatin-accessible regions of the human genome
- Tyler J. Hansen and
- Emily Hodges
Genome Res. August 2022 32: 1529-1541; Published in Advance July 20, 2022, doi:10.1101/gr.276766.122
..., these data highlight the multilayered capabilities of ATAC-STARR-seq to comprehensively investigate the regulatory landscape of the human all from a single DNA fragment source.Transcription is regulated by transcription factors (TFs) and the DNA sequences they bind, called cis-regulatory elements. Enhancers...
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Method: Uncovering methylation-dependent genetic effects on regulatory element function in diverse genomes
- Rachel M. Petersen,
- Christopher M. Vockley,
- and Amanda J. Lea
Genome Res. August 2025 35: 1781-1793; Published in Advance July 14, 2025, doi:10.1101/gr.279957.124
...regulatory region sequencing (STARR-seq) was developed as a type of MPRA; in this assay, regions of interest are inserted within the 3′ UTR, such that active regulatory elements drive expression of transcripts that include the focal sequence itself. Within a cellular environment, regulatory activity thus...
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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
...screening of regulatory activity. (A) Schematic overview of the ATAC-STARR-seq MPRA experiment. (B) Barplot of the origin of sequence fragments included in the analyses. (C) Regulatory activity (inducer or repressor) of MPRA sequence fragments from TE and non-TE sequences. (D) Fisher's exact test results...
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Research: Dissecting the regulatory activity and sequence content of loci with exceptional numbers of transcription factor associations
- Ryne C. Ramaker,
- Andrew A. Hardigan,
- Say-Tar Goh,
- E. Christopher Partridge,
- Barbara Wold,
- Sara J. Cooper,
- and Richard M. Myers
Genome Res. July 2020 30: 939-950; Published in Advance July 2, 2020, doi:10.1101/gr.260463.119
...models and to identify the sequence elements most important in controlling regulatory activity at HOT loci, we performed a self-transcribing active regulatory region sequencing (STARR-seq)–based mutagenesis assay on 245 genomic loci that had previously shown activity in massively parallel or single...
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Method: Quantifying the regulatory effect size of cis-acting genetic variation using allelic fold change
- Pejman Mohammadi,
- Stephane E. Castel,
- Andrew A. Brown,
- and Tuuli Lappalainen
Genome Res. November 2017 27: 1872-1884; Published in Advance October 11, 2017, doi:10.1101/gr.216747.116
...approach may be biased toward better discovery of independently acting eQTLs, and future work applying our method to distinct eQTLsdiscoveredbyothermethodswill be required to fully quantify the joint effects of cis-regulatory variants in human populations. Discussion Despite over a decade of eQTL analysis...
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Resource: MPRAbase a Massively Parallel Reporter Assay database
- Jingjing Zhao,
- Fotis A Baltoumas,
- Maxwell A Konnaris,
- Ioannis Mouratidis,
- Zhe Liu,
- Jasmine Sims,
- Vikram Agarwal,
- Georgios A Pavlopoulos,
- Ilias Georgakopoulos-Soares,
- and Nadav Ahituv
Genome Res. April 22, 2025 gr.280387.124; Published in Advance April 22, 2025, doi:10.1101/gr.280387.124
...: 5317. Kim Y-S, Johnson GD, Seo J, Barrera A, Cowart TN, Majoros WH, Ochoa A, Allen AS, Reddy TE. 2021. Correcting signal biases and detecting regulatory elements in STARR-seq data. Genome Res 31: 877–889. Kircher M, Xiong C, Martin B, Schubach M, Inoue F, Bell RJA, Costello JF, Shendure J, Ahituv N...
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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
...upstream or downstream from a reporter gene tagged by unique DNA sequences. However, tag sequences may themselves affect reporter gene expression and lead to major potential biases in the measured cis-regulatory activity. Here, we present a sequence-based method for correcting tag-sequence-specific effects...
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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
...properties, such as mutational correction, have also been shown to be strand-biased (Green et al. 2003). Furthermore, MPRAs may have features within their designs that predispose to strand asymmetry from nonregulatory effects. For example, in STARR-seq, the tested regulatory element is itself transcribed...
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Research: High-throughput functional comparison of promoter and enhancer activities
- Thomas A. Nguyen,
- Richard D. Jones,
- Andrew R. Snavely,
- Andreas R. Pfenning,
- Rory Kirchner,
- Martin Hemberg,
- and Jesse M. Gray
Genome Res. August 2016 26: 1023-1033; Published in Advance June 16, 2016, doi:10.1101/gr.204834.116
...Fos) (Fisch et al. 1987). The enhancer test is conceptually identical to STARR-seq, which is able to specifically detect enhancer but not promoter activity, because any RNA transcripts that initiate within genomic tiles are not amplified for quantification (Fig. 1B; Arnold et al. 2013). For each experiment...

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