Ten Things You Should Know About Transposable Elements

Overview

Journal Genome Biol

Specialties Biology
Genetics

Date 2018 Nov 21

PMID 30454069

Citations 529

Authors

Guillaume Bourque

Kathleen H Burns

Mary Gehring

Vera Gorbunova

Andrei Seluanov

Molly Hammell

Michael Imbeault

Zsuzsanna Izsvak

Henry L Levin

Todd S Macfarlan

Dixie L Mager

Cedric Feschotte

Affiliations

Soon will be listed here.

Abstract

Transposable elements (TEs) are major components of eukaryotic genomes. However, the extent of their impact on genome evolution, function, and disease remain a matter of intense interrogation. The rise of genomics and large-scale functional assays has shed new light on the multi-faceted activities of TEs and implies that they should no longer be marginalized. Here, we introduce the fundamental properties of TEs and their complex interactions with their cellular environment, which are crucial to understanding their impact and manifold consequences for organismal biology. While we draw examples primarily from mammalian systems, the core concepts outlined here are relevant to a broad range of organisms.

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References

McCue A, Slotkin R . Transposable element small RNAs as regulators of gene expression. Trends Genet. 2012; 28(12):616-23. DOI: 10.1016/j.tig.2012.09.001. View

Lynch V, Nnamani M, Kapusta A, Brayer K, Plaza S, Mazur E . Ancient transposable elements transformed the uterine regulatory landscape and transcriptome during the evolution of mammalian pregnancy. Cell Rep. 2015; 10(4):551-61. PMC: 4447085. DOI: 10.1016/j.celrep.2014.12.052. View

Ohno S . So much "junk" DNA in our genome. Brookhaven Symp Biol. 1972; 23:366-70. View

Wang J, Xie G, Singh M, Ghanbarian A, Rasko T, Szvetnik A . Primate-specific endogenous retrovirus-driven transcription defines naive-like stem cells. Nature. 2014; 516(7531):405-9. DOI: 10.1038/nature13804. View

Stetson D, Ko J, Heidmann T, Medzhitov R . Trex1 prevents cell-intrinsic initiation of autoimmunity. Cell. 2008; 134(4):587-98. PMC: 2626626. DOI: 10.1016/j.cell.2008.06.032. View

Lohe A, Hartl D . Autoregulation of mariner transposase activity by overproduction and dominant-negative complementation. Mol Biol Evol. 1996; 13(4):549-55. DOI: 10.1093/oxfordjournals.molbev.a025615. View

Saha A, Mitchell J, Nishida Y, Hildreth J, Ariberre J, Gilbert W . A trans-dominant form of Gag restricts Ty1 retrotransposition and mediates copy number control. J Virol. 2015; 89(7):3922-38. PMC: 4403431. DOI: 10.1128/JVI.03060-14. View

Percharde M, Lin C, Yin Y, Guan J, Peixoto G, Bulut-Karslioglu A . A LINE1-Nucleolin Partnership Regulates Early Development and ESC Identity. Cell. 2018; 174(2):391-405.e19. PMC: 6046266. DOI: 10.1016/j.cell.2018.05.043. View

Casola C, Hucks D, Feschotte C . Convergent domestication of pogo-like transposases into centromere-binding proteins in fission yeast and mammals. Mol Biol Evol. 2007; 25(1):29-41. PMC: 2268608. DOI: 10.1093/molbev/msm221. View

10.

Jangam D, Feschotte C, Betran E . Transposable Element Domestication As an Adaptation to Evolutionary Conflicts. Trends Genet. 2017; 33(11):817-831. PMC: 5659911. DOI: 10.1016/j.tig.2017.07.011. View

11.

Miyoshi N, Stel J, Shioda K, Qu N, Odajima J, Mitsunaga S . Erasure of DNA methylation, genomic imprints, and epimutations in a primordial germ-cell model derived from mouse pluripotent stem cells. Proc Natl Acad Sci U S A. 2016; 113(34):9545-50. PMC: 5003264. DOI: 10.1073/pnas.1610259113. View

12.

Kubiak M, Makalowska I . Protein-Coding Genes' Retrocopies and Their Functions. Viruses. 2017; 9(4). PMC: 5408686. DOI: 10.3390/v9040080. View

13.

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

14.

Elbarbary R, Lucas B, Maquat L . Retrotransposons as regulators of gene expression. Science. 2016; 351(6274):aac7247. PMC: 4788378. DOI: 10.1126/science.aac7247. View

15.

Pardue M, DeBaryshe P . Retrotransposons that maintain chromosome ends. Proc Natl Acad Sci U S A. 2011; 108(51):20317-24. PMC: 3251079. DOI: 10.1073/pnas.1100278108. View

16.

Arkhipova I . Using bioinformatic and phylogenetic approaches to classify transposable elements and understand their complex evolutionary histories. Mob DNA. 2017; 8:19. PMC: 5718144. DOI: 10.1186/s13100-017-0103-2. View

17.

Ade C, Roy-Engel A, Deininger P . Alu elements: an intrinsic source of human genome instability. Curr Opin Virol. 2013; 3(6):639-45. PMC: 3982648. DOI: 10.1016/j.coviro.2013.09.002. View

18.

Wallau G, Vieira C, Loreto E . Genetic exchange in eukaryotes through horizontal transfer: connected by the mobilome. Mob DNA. 2018; 9:6. PMC: 5791352. DOI: 10.1186/s13100-018-0112-9. View

19.

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

20.

Martinez G, Panda K, Kohler C, Slotkin R . Silencing in sperm cells is directed by RNA movement from the surrounding nurse cell. Nat Plants. 2016; 2:16030. DOI: 10.1038/nplants.2016.30. View