ArticleGenome biology2004
The regulatory content of intergenic DNA shapes genome architecture.
Article in Genome biology, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 68 papers.
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Who cites it
68 citing papers in PubMed.
- UnlockingNAR genomics and bioinformatics · 2026Article
- Genetic Architecture of Perivascular Space Morphology in the Pediatric Brain.bioRxiv : the preprint server for biology · 2026Article
- The overlapping genetic architecture of psychiatric disorders and cortical brain structure.Nature. Mental health · 2025Article
- DAXX-dependent H3.3 deposition maintains myoblast cell identity independently of other histone chaperone complexes.iScience · 2025Article
- Cohesin organizes 3D DNA contacts surrounding active enhancers inGenome research · 2025Article
- Cohesin organizes 3D DNA contacts surrounding active enhancers inbioRxiv : the preprint server for biology · 2024Article
- Multioviz: an interactive platform for in silico perturbation and interrogation of gene regulatory networks.BMC bioinformatics · 2024Article
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- Detection of evolutionary conserved and accelerated genomic regions related to adaptation to thermal niches inEcology and evolution · 2024Article
- Dyads of GGC and GCC form hotspot colonies that coincide with the evolution of human and other great apes.BMC genomic data · 2024Article
- The Density of Regulatory Information Is a Major Determinant of Evolutionary Constraint on Noncoding DNA in Drosophila.Molecular biology and evolution · 2024Article
- Extended intergenic DNA contributes to neuron-specific expression of neighboring genes in the mammalian nervous system.Nature communications · 2022Article
- An expansion of the non-coding genome and its regulatory potential underlies vertebrate neuronal diversity.Neuron · 2022Article
- piRNAQuest V.2: an updated resource for searching through the piRNAome of multiple species.RNA biology · 2022Article
- Muscle allele-specific expression QTLs may affect meat quality traits in Bos indicus.Scientific reports · 2021Article
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- Ancient Genomic Regulatory Blocks Are a Source for Regulatory Gene Deserts in Vertebrates after Whole-Genome Duplications.Molecular biology and evolution · 2020Article
- Transcriptional Enhancers inGenetics · 2020Review
- piRNAs in Gastric Cancer: A New Approach Towards Translational Research.International journal of molecular sciences · 2020Review
8 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
backgroundFactors affecting the organization and spacing of functionally unrelated genes in metazoan genomes are not well understood. Because of the vast size of a typical metazoan genome compared to known regulatory and protein-coding regions, functional DNA is generally considered to have a negligible impact on gene spacing and genome organization. In particular, it has been impossible to estimate the global impact, if any, of regulatory elements on genome architecture.
resultsTo investigate this, we examined the relationship between regulatory complexity and gene spacing in Caenorhabditis elegans and Drosophila melanogaster. We found that gene density directly reflects local regulatory complexity, such that the amount of noncoding DNA between a gene and its nearest neighbors correlates positively with that gene's regulatory complexity. Genes with complex functions are flanked by significantly more noncoding DNA than genes with simple or housekeeping functions. Genes of low regulatory complexity are associated with approximately the same amount of noncoding DNA in D. melanogaster and C. elegans, while loci of high regulatory complexity are significantly larger in the more complex animal. Complex genes in C. elegans have larger 5' than 3' noncoding intervals, whereas those in D. melanogaster have roughly equivalent 5' and 3' noncoding intervals.
conclusionsIntergenic distance, and hence genome architecture, is highly nonrandom. Rather, it is shaped by regulatory information contained in noncoding DNA. Our findings suggest that in compact genomes, the species-specific loss of nonfunctional DNA reveals a landscape of regulatory information by leaving a profile of functional DNA in its wake.
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