ArticlePLoS computational biology2010
Selection upon genome architecture: conservation of functional neighborhoods with changing genes.
Article in PLoS computational biology, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed, 60 citations in OpenAlex.
- Gene clustering drives the transcriptional coherence of disparate biological processes in eukaryotes.iScience · 2026Article
- Topologically associating domains and the evolution of three-dimensional genome architecture in rice.The Plant journal : for cell and molecular biology · 2025Article
- Protein family neighborhood analyzer-ProFaNA.PeerJ · 2023Article
- Genome Comparisons of the Fission Yeasts Reveal Ancient Collinear Loci Maintained by Natural Selection.Journal of fungi (Basel, Switzerland) · 2021Article
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- Inside the supergene of the bird with four sexes.Hormones and behavior · 2020Review
- Patterns of diverse gene functions in genomic neighborhoods predict gene function and phenotype.Scientific reports · 2019Article
- Large-scale mammalian genome rearrangements coincide with chromatin interactions.Bioinformatics (Oxford, England) · 2019Article
- Translating Flowering Time From Arabidopsis thaliana to Brassicaceae and Asteraceae Crop Species.Plants (Basel, Switzerland) · 2018Review
- Specialized plant biochemistry drives gene clustering in fungi.The ISME journal · 2018Article
- FOXO3 longevity interactome on chromosome 6.Aging cell · 2017Article
- Genome-wide identification of physically clustered genes suggests chromatin-level co-regulation in male reproductive development in Arabidopsis thaliana.Nucleic acids research · 2017Article
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- The Role of Transcription Factors at Antisense-Expressing Gene Pairs in Yeast.Genome biology and evolution · 2016Article
- Long non-coding RNAs in corticogenesis: deciphering the non-coding code of the brain.The EMBO journal · 2015Review
- The clustering of functionally related genes contributes to CNV-mediated disease.Genome research · 2015Article
- Identification of a plant isoflavonoid that causes biliary atresia.Science translational medicine · 2015Article
- Expression-based segmentation of the Drosophila genome.BMC genomics · 2013Article
- Genomic rearrangements and the evolution of clusters of locally adaptive loci.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
Corrections and comments
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Authors and funding
6 authors at 5 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
An increasing number of evidences show that genes are not distributed randomly across eukaryotic chromosomes, but rather in functional neighborhoods. Nevertheless, the driving force that originated and maintains such neighborhoods is still a matter of controversy. We present the first detailed multispecies cartography of genome regions enriched in genes with related functions and study the evolutionary implications of such clustering. Our results indicate that the chromosomes of higher eukaryotic genomes contain up to 12% of genes arranged in functional neighborhoods, with a high level of gene co-expression, which are consistently distributed in phylogenies. Unexpectedly, neighborhoods with homologous functions are formed by different (non-orthologous) genes in different species. Actually, instead of being conserved, functional neighborhoods present a higher degree of synteny breaks than the genome average. This scenario is compatible with the existence of selective pressures optimizing the coordinated transcription of blocks of functionally related genes. If these neighborhoods were broken by chromosomal rearrangements, selection would favor further rearrangements reconstructing other neighborhoods of similar function. The picture arising from this study is a dynamic genomic landscape with a high level of functional organization.
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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.