ArticleCell systems2024
Optimized reporters for multiplexed detection of transcription factor activity.
Article in Cell systems, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- Disentangling factors affecting bacterial transcriptional regulatory network inference.iScience · 2026Article
- Systematic comparison of estimates of transcription factor activity by ATAC-seq and multiplexed reporter assays.Molecular systems biology · 2026Article
- Precancerous microenvironment: A signalling perspective.Current opinion in cell biology · 2026Review
- Decoding GPCR signaling in living cells to advance early therapeutic discovery for neurological disorders.Frontiers in molecular neuroscience · 2026Review
- Applications of high-throughput reporter assays to gene regulation studies.Current opinion in structural biology · 2025Review
- Protocol for multiplexed transcription factor activity detection using optimized barcoded reporters and an automated computational pipeline.STAR protocols · 2025Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
In any given cell type, dozens of transcription factors (TFs) act in concert to control the activity of the genome by binding to specific DNA sequences in regulatory elements. Despite their considerable importance, we currently lack simple tools to directly measure the activity of many TFs in parallel. Massively parallel reporter assays (MPRAs) allow the detection of TF activities in a multiplexed fashion; however, we lack basic understanding to rationally design sensitive reporters for many TFs. Here, we use an MPRA to systematically optimize transcriptional reporters for 86 TFs and evaluate the specificity of all reporters across a wide array of TF perturbation conditions. We thus identified critical TF reporter design features and obtained highly sensitive and specific reporters for 62 TFs, many of which outperform available reporters. The resulting collection of "prime" TF reporters can be used to uncover TF regulatory networks and to illuminate signaling pathways. A record of this paper's transparent peer review process is included in the supplemental information.
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Registered trials
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