·      Distributed genome network innovation attributed to mobile DNA elements
(van de Lagemaat, Landry et al. 2003; Cowley and Oakey 2013)

Organisms

Phenotypes

References

18 Fungal Genomes

Whole-Genome Architecture and Transcriptional Profiles

(Castanera, Lopez-Varas et al. 2016)

Plants

Epigenetic Controls

(Bennetzen and Wang 2014)

Plants

C4 photosynthesis

(Cao, Xu et al. 2016)

Plants

Stress Response

(Negi, Rai et al. 2016)

Maize

Abiotic Stress Response

(Makarevitch, Waters et al. 2015)

Maize

Helitron transposons reshuffle the transcriptome

(Barbaglia, Klusman et al. 2012)

Cotton

Fiber cell development

(Wang, Huang et al. 2016)

Coffea

Drought stress response

(Lopes, Jjingo et al. 2013)

Drosophila

X chromosome dosage compensation

(Ellison and Bachtrog 2013)

Mammals

Estrogen receptor network

(Testori, Caizzi et al. 2012)

Mammals

Pregnancy

(Lynch, Leclerc et al. 2011)

Human

c-Myc regulatory subnetwork

(Wang, Bowen et al. 2009)

Human

Core embryonic stem cell development

(Kunarso, Chia et al. 2010)

 

 

      

 

REFERENCES

 

Barbaglia, A. M., K. M. Klusman, et al. (2012). "Gene capture by Helitron transposons reshuffles the transcriptome of maize." Genetics 190(3): 965-975. http://www.ncbi.nlm.nih.gov/pubmed/22174072.

Bennetzen, J. L. and H. Wang (2014). "The contributions of transposable elements to the structure, function, and evolution of plant genomes." Annu Rev Plant Biol 65: 505-530. http://www.ncbi.nlm.nih.gov/pubmed/24579996.

Cao, C., J. Xu, et al. (2016). "Evidence for the role of transposons in the recruitment of cis-regulatory motifs during the evolution of C4 photosynthesis." BMC Genomics 17(1): 201. http://www.ncbi.nlm.nih.gov/pubmed/26955946.

Castanera, R., L. Lopez-Varas, et al. (2016). "Transposable Elements versus the Fungal Genome: Impact on Whole-Genome Architecture and Transcriptional Profiles." PLoS Genet 12(6): e1006108. http://www.ncbi.nlm.nih.gov/pubmed/27294409.

Cowley, M. and R. J. Oakey (2013). "Transposable elements re-wire and fine-tune the transcriptome." PLoS Genet 9(1): e1003234. http://www.ncbi.nlm.nih.gov/pubmed/23358118.

Ellison, C. E. and D. Bachtrog (2013). "Dosage compensation via transposable element mediated rewiring of a regulatory network." Science 342(6160): 846-850. http://www.ncbi.nlm.nih.gov/pubmed/24233721.

Kunarso, G., N. Y. Chia, et al. (2010). "Transposable elements have rewired the core regulatory network of human embryonic stem cells." Nat Genet 42(7): 631-634. http://www.ncbi.nlm.nih.gov/pubmed/20526341.

Lopes, F. R., D. Jjingo, et al. (2013). "Transcriptional activity, chromosomal distribution and expression effects of transposable elements in coffea genomes." PLoS One 8(11): e78931. http://www.ncbi.nlm.nih.gov/pubmed/24244387.

Lynch, V. J., R. D. Leclerc, et al. (2011). "Transposon-mediated rewiring of gene regulatory networks contributed to the evolution of pregnancy in mammals." Nat Genet 43(11): 1154-1159. http://www.ncbi.nlm.nih.gov/pubmed/21946353.

Makarevitch, I., A. J. Waters, et al. (2015). "Transposable elements contribute to activation of maize genes in response to abiotic stress." PLoS Genet 11(1): e1004915. http://www.ncbi.nlm.nih.gov/pubmed/25569788.

Negi, P., A. N. Rai, et al. (2016). "Moving through the Stressed Genome: Emerging Regulatory Roles for Transposons in Plant Stress Response." Front Plant Sci 7: 1448. http://www.ncbi.nlm.nih.gov/pubmed/27777577.

Testori, A., L. Caizzi, et al. (2012). "The role of transposable elements in shaping the combinatorial interaction of transcription factors." BMC Genomics 13(1): 400. http://www.ncbi.nlm.nih.gov/pubmed/22897927.

van de Lagemaat, L. N., J. R. Landry, et al. (2003). "Transposable elements in mammals promote regulatory variation and diversification of genes with specialized functions." Trends Genet 19(10): 530-536. http://www.ncbi.nlm.nih.gov/pubmed/14550626.

Wang, J., N. J. Bowen, et al. (2009). "A c-Myc regulatory subnetwork from human transposable element sequences." Mol Biosyst 5(12): 1831-1839. http://www.ncbi.nlm.nih.gov/pubmed/19763338.

Wang, K., G. Huang, et al. (2016). "Transposable elements play an important role during cotton genome evolution and fiber cell development." Sci China Life Sci 59(2): 112-121. http://www.ncbi.nlm.nih.gov/pubmed/26687725.