Maintenance of Transposon-free Regions Throughout Vertebrate Evolution

Overview

Journal BMC Genomics

Publisher Biomed Central

Specialty Genetics

Date 2007 Dec 21

PMID 18093339

Citations 22

Authors

Cas Simons

Igor V Makunin

Michael Pheasant

John S Mattick

Affiliations

Soon will be listed here.

Abstract

Background: We 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.

Results: Here 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.

Conclusion: We 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.

Citing Articles

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Mendizabal-Castillero M, Merlo M, Cross I, Rodriguez M, Rebordinos L Animals (Basel). 2022; 12(24).

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The Role of Transposable Elements of the Human Genome in Neuronal Function and Pathology.

Chesnokova E, Beletskiy A, Kolosov P Int J Mol Sci. 2022; 23(10).

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Megaevolutionary dynamics and the timing of evolutionary innovation in reptiles.

Simoes T, Vernygora O, Caldwell M, Pierce S Nat Commun. 2020; 11(1):3322.

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Genome-wide de novo L1 Retrotransposition Connects Endonuclease Activity with Replication.

Flasch D, Macia A, Sanchez L, Ljungman M, Heras S, Garcia-Perez J Cell. 2019; 177(4):837-851.e28.

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Seed genome hypomethylated regions are enriched in transcription factor genes.

Chen M, Lin J, Hur J, Pelletier J, Baden R, Pellegrini M Proc Natl Acad Sci U S A. 2018; 115(35):E8315-E8322.

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