ReviewBiology open2022
The importance of considering regulatory domains in genome-wide analyses - the nearest gene is often wrong!
Review in Biology open, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 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
12 citing papers in PubMed.
- Genetic predisposition to unwanted side effects under antidepressants and antipsychotics: a molecular-genetic study of 902 patients over 6 weeks.European archives of psychiatry and clinical neuroscience · 2026Article
- Enhancing TFEA.ChIP with ENCODE regulatory maps for generalizable transcription factor enrichment.Briefings in bioinformatics · 2026Article
- Genetic determinants of antidepressant and antipsychotic drug response.European archives of psychiatry and clinical neuroscience · 2025Article
- Update on the genetics of allergic diseases.The Journal of allergy and clinical immunology · 2025Review
- Activation of Wnt/β-catenin signaling is critical for the tumorigenesis of choroid plexus.Neuro-oncology · 2025Article
- Integrative 3D genomics with multi-omics analysis and functional validation of genetic regulatory mechanisms of abdominal fat deposition in chickens.Nature communications · 2024Article
- Article
- Evidence of innate training in bovine γδ T cells following subcutaneous BCG administration.Frontiers in immunology · 2024Article
- One model fits all: Combining inference and simulation of gene regulatory networks.PLoS computational biology · 2023Article
- Characterization of transcriptional enhancers in the chicken genome using CRISPR-mediated activation.Frontiers in genome editing · 2023Article
- Transcriptomic analysis reveals the dynamic changes of transcription factors during early development of chicken embryo.BMC genomics · 2022Article
- A Systems Biology Approach on the Regulatory Footprint of Human Endogenous Retroviruses (HERVs).Diseases (Basel, Switzerland) · 2022Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The expression of a large number of genes is regulated by regulatory elements that are located far away from their promoters. Identifying which gene is the target of a specific regulatory element or is affected by a non-coding mutation is often accomplished by assigning these regions to the nearest gene in the genome. However, this heuristic ignores key features of genome organisation and gene regulation; in that the genome is partitioned into regulatory domains, which at some loci directly coincide with the span of topologically associated domains (TADs), and that genes are regulated by enhancers located throughout these regions, even across intervening genes. In this review, we examine the results from genome-wide studies using chromosome conformation capture technologies and from those dissecting individual gene regulatory domains, to highlight that the phenomenon of enhancer skipping is pervasive and affects multiple types of genes. We discuss how simply assigning a genomic region of interest to its nearest gene is problematic and often leads to incorrect predictions and highlight that where possible information on both the conservation and topological organisation of the genome should be used to generate better hypotheses. The article has an associated Future Leader to Watch interview.
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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.