ArticleNature methods2014
Function-based identification of mammalian enhancers using site-specific integration.
Article in Nature methods, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 50 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
50 citing papers in PubMed.
- Synthetic Regulatory Genomics.Annual review of genomics and human genetics · 2026Review
- Multi-scale dissection, compaction and derivatization of mammalian developmental enhancers.bioRxiv : the preprint server for biology · 2026Article
- Crosstalk BetweenCancers · 2026Review
- Chamber-specific chromatin architecture guides functional interpretation of disease-associated Cis-regulatory elements in human cardiomyocytes.Nature communications · 2026Article
- Fine-tuning mechanical constraints reveals uncoupled patterning and gene expression programs in murine gastruloids.Development (Cambridge, England) · 2025Article
- Uncovering hidden enhancers through unbiased in vivo testing.Nature communications · 2025Article
- Multiplex profiling of developmental cis-regulatory elements with quantitative single-cell expression reporters.Nature methods · 2024Article
- High-throughput assays to assess variant effects on disease.Disease models & mechanisms · 2024Article
- MAE-seq refines regulatory elements across the genome.Nucleic acids research · 2024Article
- Cis-Regulatory Elements in Mammals.International journal of molecular sciences · 2023Review
- From Genotype to Phenotype: How Enhancers Control Gene Expression and Cell Identity in Hematopoiesis.HemaSphere · 2023Review
- Review
- Exploring the Role of Enhancer-Mediated Transcriptional Regulation in Precision Biology.International journal of molecular sciences · 2023Review
- A genome-wide relay of signalling-responsive enhancers drives hematopoietic specification.Nature communications · 2023Article
- Identification and characterization of enhancer elements controlling cell type-specific and signalling dependent chromatin programming during hematopoietic development.Stem cell investigation · 2023Review
- Efficient Selection of Enhancers and Promoters from MIA PaCa-2 Pancreatic Cancer Cells by ChIP-lentiMPRA.International journal of molecular sciences · 2022Article
- Enhancer-gene specificity in development and disease.Development (Cambridge, England) · 2022Review
- High-Resolution Mapping of Multiway Enhancer-Promoter Interactions Regulating Pathogen Detection.Molecular cell · 2020Article
- Article
- Long-range enhancer-promoter contacts in gene expression control.Nature reviews. Genetics · 2019Review
Corrections and comments
- Commented on by
Authors and funding
12 authors.
Funding
Abstract
The accurate and comprehensive identification of functional regulatory sequences in mammalian genomes remains a major challenge. Here we describe site-specific integration fluorescence-activated cell sorting followed by sequencing (SIF-seq), an unbiased, medium-throughput functional assay for the discovery of distant-acting enhancers. Targeted single-copy genomic integration into pluripotent cells, reporter assays and flow cytometry are coupled with high-throughput DNA sequencing to enable parallel screening of large numbers of DNA sequences. By functionally interrogating >500 kilobases (kb) of mouse and human sequence in mouse embryonic stem cells for enhancer activity we identified enhancers at pluripotency loci including NANOG. In in vitro-differentiated cardiomyocytes and neural progenitor cells, we identified cardiac enhancers and neuronal enhancers, respectively. SIF-seq is a powerful and flexible method for de novo functional identification of mammalian enhancers in a potentially wide variety of cell types.
Indexed as
Identifiers
What OpenQuestion holds
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.