ArticleNature communications2022
Massively parallel reporter perturbation assays uncover temporal regulatory architecture during neural differentiation.
Article in Nature communications, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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Who cites it
36 citing papers in PubMed.
- Post-genome-wide association study variant-to-function challenges in asthma research.The Journal of allergy and clinical immunology · 2026Review
- Dynamic neuro-immune regulation of psychiatric risk loci in human neurons.Nature communications · 2026Article
- Lentiviral single-cell MPRA of synthetic enhancers reveals motif affinity-based encoding of cell state specificity.Genome biology · 2026Article
- Functional motif detection via in silico ablation using AlphaGenome.Briefings in bioinformatics · 2026Article
- Massively parallel reporter assay-informed modeling improves prediction of context-specific enhancer-gene regulatory interactions.Nucleic acids research · 2026Article
- An in vivo parallelized reporter assay to uncover tissue-specific splicing regulatory sequences in a multicellular animal.Nucleic acids research · 2026Article
- A massively parallel reporter assay ofbioRxiv : the preprint server for biology · 2026Article
- Article
- Predictive modeling of gene expression and localization of DNA binding site using deep convolutional neural networks.PLoS computational biology · 2026Article
- keju: powerful and accurate inference in Massively Parallel Reporter Assays.bioRxiv : the preprint server for biology · 2026Article
- Multiplexed assays of variant effect for clinical variant interpretation.Nature reviews. Genetics · 2026Review
- Applications of high-throughput reporter assays to gene regulation studies.Current opinion in structural biology · 2025Review
- A dual enhancer-attenuator element ensures transient Cdx2 expression during mouse posterior body formation.Developmental cell · 2025Article
- U-rich elements drive pervasive cryptic splicing in 3' UTR massively parallel reporter assays.Nature communications · 2025Article
- Massively parallel reporter assays and mouse transgenic assays provide correlated and complementary information about neuronal enhancer activity.Nature communications · 2025Article
- Just a SNP away: The future ofCell insight · 2025Review
- Functional dissection of metabolic trait-associated gene regulation in steady state and stimulated human skeletal muscle cells.bioRxiv : the preprint server for biology · 2025Article
- Prediction of Enhancer-Gene Interactions Using Chromatin-Conformation Capture and Epigenome Data Using STARE.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Structural framework to address variant-gene relationship in primary open-angle glaucoma.Vision research · 2025Review
- Network Analysis of Enhancer-Promoter Interactions Highlights Cell-Type-Specific Mechanisms of Transcriptional Regulation Variation.International journal of molecular sciences · 2024Article
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Authors and funding
7 authors.
Funding
Abstract
Gene regulatory elements play a key role in orchestrating gene expression during cellular differentiation, but what determines their function over time remains largely unknown. Here, we perform perturbation-based massively parallel reporter assays at seven early time points of neural differentiation to systematically characterize how regulatory elements and motifs within them guide cellular differentiation. By perturbing over 2,000 putative DNA binding motifs in active regulatory regions, we delineate four categories of functional elements, and observe that activity direction is mostly determined by the sequence itself, while the magnitude of effect depends on the cellular environment. We also find that fine-tuning transcription rates is often achieved by a combined activity of adjacent activating and repressing elements. Our work provides a blueprint for the sequence components needed to induce different transcriptional patterns in general and specifically during neural differentiation.
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