ArticleNature communications2018
High-resolution genome-wide functional dissection of transcriptional regulatory regions and nucleotides in human.
Article in Nature communications, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 91 papers.
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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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Who cites it
91 citing papers in PubMed, 186 citations in OpenAlex.
- Multi-scale dissection, compaction and derivatization of mammalian developmental enhancers.bioRxiv : the preprint server for biology · 2026Article
- Enhancer hubs govern chromatin topology and Th17 cell identity.bioRxiv : the preprint server for biology · 2026Article
- The distribution of fitness effects of new mutations in regulatory regions of thebioRxiv : the preprint server for biology · 2026Article
- Functional interrogation of candidate cis-regulatory elements at the LDLR locus.PLoS genetics · 2026Article
- Designing synthetic regulatory elements using the generative AI framework DNA-Diffusion.Nature genetics · 2026Article
- Comprehensive evaluation of diverse massively parallel reporter assays to functionally characterize human enhancers genome-wide.Genome biology · 2025Article
- Applications of high-throughput reporter assays to gene regulation studies.Current opinion in structural biology · 2025Review
- Super-silencers are crucial for development and carcinogenesis in B cells.Nature communications · 2025Article
- Spatial-scERA: a method for reconstructing spatial single-cell enhancer activity in multicellular organisms.Nucleic acids research · 2025Article
- The landscape of fitness effects of putatively functional noncoding mutations in humans.bioRxiv : the preprint server for biology · 2025Article
- Variant-to-function approaches for adipose tissue: Insights into cardiometabolic disorders.Cell genomics · 2025Review
- ChromActivity: integrative epigenomic and functional characterization assay based annotation of regulatory activity across diverse human cell types.Genome biology · 2025Article
- BINDER achieves accurate identification of hierarchical TADs by comprehensively characterizing consensus TAD boundaries.Genome research · 2025Article
- The role of transposon activity in shapingGenome research · 2025Article
- Enhancer reprogramming: critical roles in cancer and promising therapeutic strategies.Cell death discovery · 2025Review
- Histone H4 lysine 20 monomethylation is not a mark of transcriptional silencers.bioRxiv : the preprint server for biology · 2025Article
- AnFrontiers in genetics · 2025Article
- HDI-STARR-seq: Condition-specific enhancer discovery in mouse liver in vivo.BMC genomics · 2024Article
- Massively parallel reporter assays identify enhancer elements in oesophageal Adenocarcinoma.NAR cancer · 2024Article
- An autoimmune transcriptional circuit drives FOXP3Science translational medicine · 2024Article
31 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors at 1 institution in 2 countries.
Funding
Abstract
Genome-wide epigenomic maps have revealed millions of putative enhancers and promoters, but experimental validation of their function and high-resolution dissection of their driver nucleotides remain limited. Here, we present HiDRA (High-resolution Dissection of Regulatory Activity), a combined experimental and computational method for high-resolution genome-wide testing and dissection of putative regulatory regions. We test ~7 million accessible DNA fragments in a single experiment, by coupling accessible chromatin extraction with self-transcribing episomal reporters (ATAC-STARR-seq). By design, fragments are highly overlapping in densely-sampled accessible regions, enabling us to pinpoint driver regulatory nucleotides by exploiting differences in activity between partially-overlapping fragments using a machine learning model (SHARPR-RE). In GM12878 lymphoblastoid cells, we find ~65,000 regions showing enhancer function, and pinpoint ~13,000 high-resolution driver elements. These are enriched for regulatory motifs, evolutionarily-conserved nucleotides, and disease-associated genetic variants from genome-wide association studies. Overall, HiDRA provides a high-throughput, high-resolution approach for dissecting regulatory regions and driver nucleotides.
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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.