ArticleNature biotechnology2018
A massively parallel reporter assay dissects the influence of chromatin structure on cis-regulatory activity.
Article in Nature biotechnology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 45 papers.
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Who cites it
45 citing papers in PubMed, 94 citations in OpenAlex.
- Mechanisms and functional implications of long-range enhancer-dependent gene regulation.Nature genetics · 2026Review
- Synthetic Regulatory Genomics.Annual review of genomics and human genetics · 2026Review
- Cumulative transcription factor binding and p300-mediated histone acetylation drive enhancer activation frequency.Nature genetics · 2026Article
- Article
- Large-scale discovery of potent, compact and erythroid specific enhancers for gene therapy vectors.Nature communications · 2025Article
- Using individual barcodes to increase quantification power of massively parallel reporter assays.BMC bioinformatics · 2025Article
- Just a SNP away: The future ofCell insight · 2025Review
- Rapid and quantitative functional interrogation of human enhancer variant activity in live mice.Nature communications · 2025Article
- Characterization and functional evaluation of goat PDX1 regulatory modules through comparative analysis of conserved interspecies homologs.Scientific reports · 2024Article
- A DNA base-specific sequence interposed between CRX and NRL contributes to RHODOPSIN expression.Scientific reports · 2024Article
- Article
- Decoding biology with massively parallel reporter assays and machine learning.Genes & development · 2024Review
- Massively parallel characterization of insulator activity across the genome.Nature communications · 2024Article
- Decoding polygenic diseases: advances in noncoding variant prioritization and validation.Trends in cell biology · 2024Review
- Multiplex profiling of developmental cis-regulatory elements with quantitative single-cell expression reporters.Nature methods · 2024Article
- Genomic context sensitizes regulatory elements to genetic disruption.Molecular cell · 2024Article
- Genomic context sensitizes regulatory elements to genetic disruption.bioRxiv : the preprint server for biology · 2024Article
- Strategies for dissecting the complexity of neurodevelopmental disorders.Trends in genetics : TIG · 2024Review
- Deep molecular learning of transcriptional control of a synthetic CRE enhancer and its variants.iScience · 2024Article
- Transcriptional precision in photoreceptor development and diseases - Lessons from 25 years of CRX research.Frontiers in cellular neuroscience · 2024Review
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
A gene's position in the genome can profoundly affect its expression because regional differences in chromatin modulate the activity of locally acting cis-regulatory sequences (CRSs). Here we study how CRSs and regional chromatin act in concert on a genome-wide scale. We present a massively parallel reporter gene assay that measures the activities of hundreds of different CRSs, each integrated at many specific genomic locations. Although genome location strongly affected CRS activity, the relative strengths of CRSs were maintained at all chromosomal locations. The intrinsic activities of CRSs also correlated with their activities in plasmid-based assays. We explain our data with a quantitative model in which expression levels are set by independent contributions from local CRSs and the regional chromatin environment, rather than by more complex sequence- or protein-specific interactions between these two factors. The methods we present will help investigators determine when regulatory information is integrated in a modular fashion and when regulatory sequences interact in more complex ways.
Identifiers
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.