ArticleBMC genomics2007
Maintenance of transposon-free regions throughout vertebrate evolution.
Article in BMC genomics, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 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
22 citing papers in PubMed, 40 citations in OpenAlex.
- Genomic Characterization ofAnimals : an open access journal from MDPI · 2022Article
- The Role of Transposable Elements of the Human Genome in Neuronal Function and Pathology.International journal of molecular sciences · 2022Review
- Megaevolutionary dynamics and the timing of evolutionary innovation in reptiles.Nature communications · 2020Article
- Genome-wide de novo L1 Retrotransposition Connects Endonuclease Activity with Replication.Cell · 2019Article
- Seed genome hypomethylated regions are enriched in transcription factor genes.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Risks and Recommendations in Prenatally Detected De Novo Balanced Chromosomal Rearrangements from Assessment of Long-Term Outcomes.American journal of human genetics · 2018Article
- Reorganisation of Hoxd regulatory landscapes during the evolution of a snake-like body plan.eLife · 2016Article
- The hourglass and the early conservation models--co-existing patterns of developmental constraints in vertebrates.PLoS genetics · 2013Article
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- Transposon-derived and satellite-derived repetitive sequences play distinct functional roles in Mammalian intron size expansion.Evolutionary bioinformatics online · 2012Article
- Distributions of transposable elements reveal hazardous zones in mammalian introns.PLoS computational biology · 2011Article
- Origin and evolution of TRIM proteins: new insights from the complete TRIM repertoire of zebrafish and pufferfish.PloS one · 2011Article
- Comparative analyses of vertebrate posterior HoxD clusters reveal atypical cluster architecture in the caecilian Typhlonectes natans.BMC genomics · 2010Article
- Genes devoid of full-length transposable element insertions are involved in development and in the regulation of transcription in human and closely related species.Journal of molecular evolution · 2010Article
- Paucity and preferential suppression of transgenes in late replication domains of the D. melanogaster genome.BMC genomics · 2010Article
- Annotation and visualization of endogenous retroviral sequences using the Distributed Annotation System (DAS) and eBioX.BMC bioinformatics · 2009Article
- Article
- Atypical relaxation of structural constraints in Hox gene clusters of the green anole lizard.Genome research · 2009Article
- Distribution of ancestral proto-Actinopterygian chromosome arms within the genomes of 4R-derivative salmonid fishes (Rainbow trout and Atlantic salmon).BMC genomics · 2008Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
Abstract
backgroundWe recently reported the existence of large numbers of regions up to 80 kb long that lack transposon insertions in the human, mouse and opossum genomes. These regions are significantly associated with loci involved in developmental and transcriptional regulation.
resultsHere we report that transposon-free regions (TFRs) are prominent genomic features of amphibian and fish lineages, and that many have been maintained throughout vertebrate evolution, although most transposon-derived sequences have entered these lineages after their divergence. The zebrafish genome contains 470 TFRs over 10 kb and a further 3,951 TFRs over 5 kb, which is comparable to the number identified in mammals. Two thirds of zebrafish TFRs over 10 kb are orthologous to TFRs in at least one mammal, and many have orthologous TFRs in all three mammalian genomes as well as in the genome of Xenopus tropicalis. This indicates that the mechanism responsible for the maintenance of TFRs has been active at these loci for over 450 million years. However, the majority of TFR bases cannot be aligned between distantly related species, demonstrating that TFRs are not the by-product of strong primary sequence conservation. Syntenically conserved TFRs are also more enriched for regulatory genes compared to lineage-specific TFRs.
conclusionWe suggest that TFRs contain extended regulatory sequences that contribute to the precise expression of genes central to early vertebrate development, and can be used as predictors of important regulatory regions.
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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.