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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
...within accessible chromatin, and recently described methods have combined assays that capture these regions—such as assay for transposase-accessible chromatin using sequencing (ATAC-seq)—with self-transcribing active regulatory region sequencing (STARR-seq) to selectively assay the regulatory potential...
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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
...at the 3′ untranslated region (UTR). Different locations of tags and CREs have also been explored. Self-transcribing active regulatory region sequencing (STARR-seq) (Arnold et al. 2013) places CREs downstream from the reporter's transcript start site and uses the transcribed CREs as “tags.” More recently...
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Research: Multiplex enhancer-reporter assays uncover unsophisticated TP53 enhancer logic
- Annelien Verfaillie,
- Dmitry Svetlichnyy,
- Hana Imrichova,
- Kristofer Davie,
- Mark Fiers,
- Zeynep Kalender Atak,
- Gert Hulselmans,
- Valerie Christiaens,
- and Stein Aerts
Genome Res. July 2016 26: 882-895; Published in Advance May 18, 2016, doi:10.1101/gr.204149.116
...; Supplemental Table S3). The main difference in STARR-seq is that the tested regions are inserted at the 3′ of the transcription start site, causing the enhancers to transcribe themselves rather than relying on barcodes. STARR-seq yields reproducible expression values for 975 peaks, of which 242 peaks are TP53...
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Research: A systematic comparison reveals substantial differences in chromosomal versus episomal encoding of enhancer activity
- Fumitaka Inoue,
- Martin Kircher,
- Beth Martin,
- Gregory M. Cooper,
- Daniela M. Witten,
- Michael T. McManus,
- Nadav Ahituv,
- and Jay Shendure
Genome Res. January 2017 27: 38-52; Published in Advance November 9, 2016, doi:10.1101/gr.212092.116
...with different subsets of ENCODE annotations. The results of chromosomally based reporter assays are also more reproducible and more strongly predictable by both ENCODE annotations and sequence-based models. With a linear model that combines chromatin annotations and sequence information, we achieve a Pearson...
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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
...-CREs in Atlantic salmon, we carried out massive parallel reporter assays (MPRAs), specifically an ATAC-STARR-seq experiment, in salmon primary liver cells (Fig. 6A). This method assesses the ability of random DNA fragments from accessible chromatin to modulate transcription levels (Wang et al. 2018). In total, 4...
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Research: Sequence determinants of polyadenylation-mediated regulation
- Ilya Vainberg Slutskin,
- Adina Weinberger,
- and Eran Segal
Genome Res. October 2019 29: 1635-1647; Published in Advance September 17, 2019, doi:10.1101/gr.247312.118
...parallel reporter assay to inspect the effect of over 12,000 rationally designed polyadenylation sequences (PASs) on reporter gene expression and cleavage efficiency. We find that the PAS sequence can modulate gene expression by over five orders of magnitude. By using a uniquely designed scanning...

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