Reevaluation of the “Junk DNA” Concept for Repetitive Mobile Genetic Elements in Genomes of Advanced Organisms

 

REFERENCES

 

Adelman, K. and E. Egan (2017). "Non-coding RNA: More uses for genomic junk." Nature 543(7644): 183-185. http://www.ncbi.nlm.nih.gov/pubmed/28277509.

Amaral, P. P., M. E. Dinger, et al. (2013). "Non-coding RNAs in homeostasis, disease and stress responses: an evolutionary perspective." Brief Funct Genomics 12(3): 254-278. http://www.ncbi.nlm.nih.gov/pubmed/23709461.

Barry, G., J. A. Briggs, et al. (2014). "The long non-coding RNA Gomafu is acutely regulated in response to neuronal activation and involved in schizophrenia-associated alternative splicing." Mol Psychiatry 19(4): 486-494. http://www.ncbi.nlm.nih.gov/pubmed/23628989.

Biemont, C. (2010). "A brief history of the status of transposable elements: from junk DNA to major players in evolution." Genetics 186(4): 1085-1093. http://www.ncbi.nlm.nih.gov/pubmed/21156958.

Biemont, C. and C. Vieira (2006). "Genetics: junk DNA as an evolutionary force." Nature 443(7111): 521-524. http://www.ncbi.nlm.nih.gov/pubmed/17024082.

Britten, R., Kohne, DE (1968). "Repeated sequences in DNA. Hundreds of thousands of copies of DNA sequences have been incorporated into the genomes of higher organisms." Science 161: 529-540. http://www.ncbi.nlm.nih.gov/pubmed/4874239.

Britten, R. J. (1996). "Cases of ancient mobile element DNA insertions that now affect gene regulation." Mol Phylogenet Evol 5(1): 13-17. http://www.ncbi.nlm.nih.gov/pubmed/8673282.

Britten, R. J. (1996). "DNA sequence insertion and evolutionary variation in gene regulation." Proc Natl Acad Sci U S A 93(18): 9374-9377. http://www.ncbi.nlm.nih.gov/pubmed/8790336.

Britten, R. J. (2004). "Coding sequences of functioning human genes derived entirely from mobile element sequences." Proc Natl Acad Sci U S A 101(48): 16825-16830. http://www.ncbi.nlm.nih.gov/pubmed/15546984.

Britten, R. J. (2006). "Transposable elements have contributed to thousands of human proteins." Proc Nat Acad Sci USA 103(6): 1798-1803. .

Britten, R. J. (2010). "Transposable element insertions have strongly affected human evolution." Proc Natl Acad Sci U S A 107(46): 19945-19948. http://www.ncbi.nlm.nih.gov/pubmed/21041622.

Britten, R. J. and E. H. Davidson (1971). "Repetitive and non-repetitive DNA sequences and a speculation on the origins of evolutionary novelty." Q Rev Biol 46(2): 111-138. http://www.ncbi.nlm.nih.gov/pubmed/5160087.

Britten, R. J. and D. E. Kohne (1970). "Repeated Segments of DNA." Scientific American 222(4): 24-31. http://www.ncbi.nlm.nih.gov/pubmed/5417826.

Carey, N. (2015). Junk DNA: A Journey Through the Dark Matter of the Genome, Columbia University Press. .

Clark, M. B., A. Choudhary, et al. (2013). "The dark matter rises: the expanding world of regulatory RNAs." Essays Biochem 54: 1-16. http://www.ncbi.nlm.nih.gov/pubmed/23829523.

Dhamija, S. and S. Diederichs (2016). "From junk to master regulators of invasion: lncRNA functions in migration, EMT and metastasis." Int J Cancer. http://www.ncbi.nlm.nih.gov/pubmed/26875870.

Doolittle, W. F. (2013). "Is junk DNA bunk? A critique of ENCODE." Proc Natl Acad Sci U S A 110(14): 5294-5300. http://www.ncbi.nlm.nih.gov/pubmed/23479647.

Doolittle, W. F. and T. D. P. Brunet (2017). "On causal roles and selected effects: our genome is mostly junk." BMC Biol 15(1): 116. http://www.ncbi.nlm.nih.gov/pubmed/29207982.

Dridi, S. (2012). "Alu mobile elements: from junk DNA to genomic gems." Scientifica (Cairo) 2012: 545328. http://www.ncbi.nlm.nih.gov/pubmed/24278713.

Gbadegesin, M. A. (2012). "Transposable elements in the genomes: parasites, junks or drivers of evolution?" Afr J Med Med Sci 41 Suppl: 13-25. http://www.ncbi.nlm.nih.gov/pubmed/23678632.

Ge, S. X. (2017). "Exploratory bioinformatics investigation reveals importance of "junk" DNA in early embryo development." BMC Genomics 18(1): 200. http://www.ncbi.nlm.nih.gov/pubmed/28231763.

Hasler, J., T. Samuelsson, et al. (2007). "Useful 'junk': Alu RNAs in the human transcriptome." Cell Mol Life Sci 64(14): 1793-1800. http://www.ncbi.nlm.nih.gov/pubmed/17514354.

Kazazian, H. H. (2011). Mobile DNA: Finding Treasure in Junk, FT Press Science. .

Kim, Y. J., J. Lee, et al. (2012). "Transposable Elements: No More 'Junk DNA'." Genomics Inform 10(4): 226-233. http://www.ncbi.nlm.nih.gov/pubmed/23346034.

Liu, G., J. S. Mattick, et al. (2013). "A meta-analysis of the genomic and transcriptomic composition of complex life." Cell Cycle 12(13): 2061-2072. http://www.ncbi.nlm.nih.gov/pubmed/23759593.

Lunyak, V. V. and M. Atallah (2011). "Genomic relationship between SINE retrotransposons, Pol III-Pol II transcription, and chromatin organization: the journey from junk to jewel." Biochem Cell Biol 89(5): 495-504. http://www.ncbi.nlm.nih.gov/pubmed/21916613.

Lyon, M. F. (2000). "LINE-1 elements and X chromosome inactivation: a function for "junk" DNA?" Proc Natl Acad Sci U S A 97(12): 6248-6249. http://www.ncbi.nlm.nih.gov/pubmed/10841528.

Mercer, T. R. and J. S. Mattick (2013). "Structure and function of long noncoding RNAs in epigenetic regulation." Nat Struct Mol Biol 20(3): 300-307. http://www.ncbi.nlm.nih.gov/pubmed/23463315.

Morris, K. V. and J. S. Mattick (2014). "The rise of regulatory RNA." Nat Rev Genet 15(6): 423-437. http://www.ncbi.nlm.nih.gov/pubmed/24776770.

Muotri, A. R., M. C. Marchetto, et al. (2007). "The necessary junk: new functions for transposable elements." Hum Mol Genet 16 Spec No. 2: R159-167. http://www.ncbi.nlm.nih.gov/pubmed/17911158.

Novoa, E. M., C. E. Mason, et al. (2017). "Charting the unknown epitranscriptome." Nat Rev Mol Cell Biol 18(6): 339-340. http://www.ncbi.nlm.nih.gov/pubmed/28488699.

Ohno, S. (1972). "So much "junk" DNA in our genome." Brookhaven Symp Biol 23: 366-370. http://www.ncbi.nlm.nih.gov/pubmed/5065367.

Pandey, R. and M. Mukerji (2011). "From 'JUNK' to just unexplored noncoding knowledge: the case of transcribed Alus." Brief Funct Genomics 10(5): 294-311. http://www.ncbi.nlm.nih.gov/pubmed/21987713.

Pennisi, E. (2012). "Genomics. ENCODE project writes eulogy for junk DNA." Science 337(6099): 1159, 1161. http://www.ncbi.nlm.nih.gov/pubmed/22955811.

Smith, M. A., T. Gesell, et al. (2013). "Widespread purifying selection on RNA structure in mammals." Nucleic Acids Res. http://www.ncbi.nlm.nih.gov/pubmed/23847102.

Upton, K. R. and G. J. Faulkner (2014). "Blood from 'junk': the LTR chimeric transcript Pu.2 promotes erythropoiesis." Mob DNA 5: 15. http://www.ncbi.nlm.nih.gov/pubmed/24839466.

Veitia, R. A. and S. Bottani (2009). "Whole genome duplications and a 'function' for junk DNA? Facts and hypotheses." PLoS One 4(12): e8201. http://www.ncbi.nlm.nih.gov/pubmed/20011530.

Volff, J. N. (2006). "Turning junk into gold: domestication of transposable elements and the creation of new genes in eukaryotes." Bioessays 28(9): 913-922. http://www.ncbi.nlm.nih.gov/pubmed/16937363.

Walters, R. D., J. F. Kugel, et al. (2009). "InvAluable junk: the cellular impact and function of Alu and B2 RNAs." IUBMB Life 61(8): 831-837. http://www.ncbi.nlm.nih.gov/pubmed/19621349.

Werner, A., M. J. Piatek, et al. (2014). "Transpositional shuffling and quality control in male germ cells to enhance evolution of complex organisms." Ann N Y Acad Sci. http://www.ncbi.nlm.nih.gov/pubmed/25557795.

Werner, A., M. J. Piatek, et al. (2015). "Transpositional shuffling and quality control in male germ cells to enhance evolution of complex organisms." Ann N Y Acad Sci 1341: 156-163. http://www.ncbi.nlm.nih.gov/pubmed/25557795.

Zuckerkandl, E. and G. Cavalli (2007). "Combinatorial epigenetics, "junk DNA", and the evolution of complex organisms." Gene 390(1-2): 232-242. http://www.ncbi.nlm.nih.gov/pubmed/17223284.