Transposable Elements Re-wire and Fine-tune the Transcriptome

Overview

Journal PLoS Genet

Specialty Genetics

Date 2013 Jan 30

PMID 23358118

Citations 103

Authors

Michael Cowley

Rebecca J Oakey

Affiliations

Soon will be listed here.

Abstract

What good are transposable elements (TEs)? Although their activity can be harmful to host genomes and can cause disease, they nevertheless represent an important source of genetic variation that has helped shape genomes. In this review, we examine the impact of TEs, collectively referred to as the mobilome, on the transcriptome. We explore how TEs-particularly retrotransposons-contribute to transcript diversity and consider their potential significance as a source of small RNAs that regulate host gene transcription. We also discuss a critical role for the mobilome in engineering transcriptional networks, permitting coordinated gene expression, and facilitating the evolution of novel physiological processes.

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References

Wong S, Wolfe K . Birth of a metabolic gene cluster in yeast by adaptive gene relocation. Nat Genet. 2005; 37(7):777-82. DOI: 10.1038/ng1584. View

Druker R, Bruxner T, Lehrbach N, Whitelaw E . Complex patterns of transcription at the insertion site of a retrotransposon in the mouse. Nucleic Acids Res. 2004; 32(19):5800-8. PMC: 528799. DOI: 10.1093/nar/gkh914. View

Polavarapu N, Marino-Ramirez L, Landsman D, McDonald J, Jordan I . Evolutionary rates and patterns for human transcription factor binding sites derived from repetitive DNA. BMC Genomics. 2008; 9:226. PMC: 2397414. DOI: 10.1186/1471-2164-9-226. View

Nekrutenko A, Li W . Transposable elements are found in a large number of human protein-coding genes. Trends Genet. 2001; 17(11):619-21. DOI: 10.1016/s0168-9525(01)02445-3. View

Esnault C, Maestre J, Heidmann T . Human LINE retrotransposons generate processed pseudogenes. Nat Genet. 2000; 24(4):363-7. DOI: 10.1038/74184. View

Suzuki S, Ono R, Narita T, Pask A, Shaw G, Wang C . Retrotransposon silencing by DNA methylation can drive mammalian genomic imprinting. PLoS Genet. 2007; 3(4):e55. PMC: 1851980. DOI: 10.1371/journal.pgen.0030055. View

Morgan H, Sutherland H, Martin D, Whitelaw E . Epigenetic inheritance at the agouti locus in the mouse. Nat Genet. 1999; 23(3):314-8. DOI: 10.1038/15490. View

Sorek R, Ast G, Graur D . Alu-containing exons are alternatively spliced. Genome Res. 2002; 12(7):1060-7. PMC: 186627. DOI: 10.1101/gr.229302. View

Huang C, Schneider A, Lu Y, Niranjan T, Shen P, Robinson M . Mobile interspersed repeats are major structural variants in the human genome. Cell. 2010; 141(7):1171-82. PMC: 2943426. DOI: 10.1016/j.cell.2010.05.026. View

10.

Vinckenbosch N, Dupanloup I, Kaessmann H . Evolutionary fate of retroposed gene copies in the human genome. Proc Natl Acad Sci U S A. 2006; 103(9):3220-5. PMC: 1413932. DOI: 10.1073/pnas.0511307103. View

11.

Shearwin K, Callen B, Barry Egan J . Transcriptional interference--a crash course. Trends Genet. 2005; 21(6):339-45. PMC: 2941638. DOI: 10.1016/j.tig.2005.04.009. View

12.

Li J, Akagi K, Hu Y, Trivett A, Hlynialuk C, Swing D . Mouse endogenous retroviruses can trigger premature transcriptional termination at a distance. Genome Res. 2012; 22(5):870-84. PMC: 3337433. DOI: 10.1101/gr.130740.111. View

13.

Stewart C, Kural D, Stromberg M, Walker J, Konkel M, Stutz A . A comprehensive map of mobile element insertion polymorphisms in humans. PLoS Genet. 2011; 7(8):e1002236. PMC: 3158055. DOI: 10.1371/journal.pgen.1002236. View

14.

Nagle D, McGrail S, Vitale J, Woolf E, Dussault Jr B, DiRocco L . The mahogany protein is a receptor involved in suppression of obesity. Nature. 1999; 398(6723):148-52. DOI: 10.1038/18210. View

15.

Pan Q, Shai O, Lee L, Frey B, Blencowe B . Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat Genet. 2008; 40(12):1413-5. DOI: 10.1038/ng.259. View

16.

Tang W, Gunn T, McLaughlin D, Barsh G, Schlossman S, Duke-Cohan J . Secreted and membrane attractin result from alternative splicing of the human ATRN gene. Proc Natl Acad Sci U S A. 2000; 97(11):6025-30. PMC: 18552. DOI: 10.1073/pnas.110139897. View

17.

Fedoroff N . How jumping genes were discovered. Nat Struct Biol. 2001; 8(4):300-1. DOI: 10.1038/86161. View

18.

Kazazian Jr H, Wong C, Youssoufian H, Scott A, Phillips D, Antonarakis S . Haemophilia A resulting from de novo insertion of L1 sequences represents a novel mechanism for mutation in man. Nature. 1988; 332(6160):164-6. DOI: 10.1038/332164a0. View

19.

Ramani A, Calarco J, Pan Q, Mavandadi S, Wang Y, Nelson A . Genome-wide analysis of alternative splicing in Caenorhabditis elegans. Genome Res. 2010; 21(2):342-8. PMC: 3032936. DOI: 10.1101/gr.114645.110. View

20.

Burns K, Boeke J . Human transposon tectonics. Cell. 2012; 149(4):740-52. PMC: 3370394. DOI: 10.1016/j.cell.2012.04.019. View