ArticleGenome research2017
A systematic comparison reveals substantial differences in chromosomal versus episomal encoding of enhancer activity.
Article in Genome research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 206 papers, 1 of them a synthesis that pooled it.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
206 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Meta-analysis of massively parallel reporter assays enables prediction of regulatory function across cell types.Human mutation · 2019Pooled it
- Massively parallel functional profiling prioritizes breast cancer risk variants and implicates CCDC88C in ER-positive breast cancer.HGG advances · 2026Article
- Massively parallel characterization of adolescent idiopathic scoliosis risk variants.Genome research · 2026Article
- KSHV-encoded vIRF3 cooperates with cellular IRF4 to drive super-enhancer activity through complex DNA elements.Nucleic acids research · 2026Article
- Non-Coding Negative Regulatory Features in Livestock Genomes: Functional Annotation and Causal Validation.Animals : an open access journal from MDPI · 2026Review
- Uniform processing and analysis of IGVF massively parallel reporter assay data with MPRAsnakeflow.Genome research · 2026Article
- Cross-Model Uncertainty-Aware Minimal Editing of Cis-Regulatory Elements for Cell-Type-Selective Design.Genes · 2026Article
- Dynamic neuro-immune regulation of psychiatric risk loci in human neurons.Nature communications · 2026Article
- Toward generalizable and interpretable AI in regulatory genomics.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
- Massively parallel characterization and predictive modelling of neuronal regulatory variation.bioRxiv : the preprint server for biology · 2026Article
- Lentiviral single-cell MPRA of synthetic enhancers reveals motif affinity-based encoding of cell state specificity.Genome biology · 2026Article
- Using a modular massively parallel reporter assay to discover context-dependent regulatory activity in type 2 diabetes-linked noncoding regions.HGG advances · 2026Article
- Unlocking the Regulatory Genome: Interpreting the Clinical Impact of Noncoding Variants in Genetic Cardiomyopathies.Circulation. Genomic and precision medicine · 2026Review
- Intrinsic promoter responsiveness dictates sensitivity to transcriptional activation by enhancers.bioRxiv : the preprint server for biology · 2026Article
- Article
- In Vitro Massively Parallel Screening of Human Regulatory Elements Involved in Postcranial Skeletal Development for Differential Activity Compared to Chimpanzee.Genome biology and evolution · 2026Article
- Chromosomal instability promotes cell migration and invasion via EFEMP1 secretion into extracellular vesicles.The EMBO journal · 2026Article
- Facilitators may represent a new class of regulatory elements.Current opinion in genetics & development · 2026Review
146 more citing papers are in PubMed but not listed here.
Corrections and comments
- Commented on by
- Erratum issued
Authors and funding
8 authors.
Funding
Abstract
Candidate enhancers can be identified on the basis of chromatin modifications, the binding of chromatin modifiers and transcription factors and cofactors, or chromatin accessibility. However, validating such candidates as bona fide enhancers requires functional characterization, typically achieved through reporter assays that test whether a sequence can increase expression of a transcriptional reporter via a minimal promoter. A longstanding concern is that reporter assays are mainly implemented on episomes, which are thought to lack physiological chromatin. However, the magnitude and determinants of differences in cis-regulation for regulatory sequences residing in episomes versus chromosomes remain almost completely unknown. To address this systematically, we developed and applied a novel lentivirus-based massively parallel reporter assay (lentiMPRA) to directly compare the functional activities of 2236 candidate liver enhancers in an episomal versus a chromosomally integrated context. We find that the activities of chromosomally integrated sequences are substantially different from the activities of the identical sequences assayed on episomes, and furthermore are correlated 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's R
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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.