Enough talk (see this previous post and links within), on to the peer-reviewed science. Below you will find a list of references that I hope will contribute to the fall of the term “junk-DNA“, – some of it may (currently) lack a known function, but it is not junk !!!

Disclaimer: This is a list of useful references when arguing against the common overestimation of the amount of “junk”-DNA. By listing these I am not claiming anything beyond what I have already posted on this blog or in a comment somewhere. Also and importantly, I have not myself  had the time to review these articles as thoroughly as I would have wanted to, – some have been read carefully, others lightly and yet others just skimmed through. Thus, you are more than welcome to comment on these references if you have opinions on any of them, or find them unsuited for this list.

The list will be continuously expanded, and if you have references you would like to add, please notify me with a comment to the post.

The references are unsorted. Feel free to copy, rearrange and use as desired…

Last updated 5/8-13:

1. Alu elements as regulators of gene expression. Häsler J, Strub K, Nucleic Acids Res. 2006;34(19):5491-7. Epub 2006 Oct 4.
2. RNA editing, DNA recoding and the evolution of human cognition
   Trends in Neurosciences, , Volume 31, Issue 5, May 2008, Pages 227-233
   John S. Mattick, Mark F. Mehler
3. Evolution of the mammalian transcription factor binding repertoire via transposable elements, Bourque, Guillaume, Leong, Bernard, Vega, Vinsensius B., Chen, Xi, Lee, Yen Ling, Srinivasan, Kandhadayar G., Chew, Joon-Lin, Ruan, Yijun, Wei, Chia-Lin, Ng, Huck Hui, Liu, Edison T. Genome Res. 2008 0: gr.080663.108. DOI: 10.1101/gr.080663.108
4. Lin L, Shen S, Tye A, Cai JJ, Jiang P, et al. 2008 Diverse Splicing Patterns of Exonized Alu Elements in Human Tissues. PLoS Genetics 4(10): e1000225 doi:10.1371/journal.pgen.1000225
5. Dispensability of mammalian DNA. McLean C, Bejerano G., Genome Res. 2008 Oct 2. [Epub ahead of print]
6. Functional Demarcation of Active and Silent Chromatin Domains in Human HOX Loci by Noncoding RNAs. John L. Rinn et al., Cell 129, 1311–1323, June 29, 2007
7. A Strategy for Probing the Function of Noncoding RNAs Finds a Repressor of NFAT. A. T. Willingham, A. P. Orth, S. Batalov, E. C. Peters, B. G. Wen, P. Aza-Blanc, J. B. Hogenesch, and P. G. Schultz (2 September 2005). Science 309 (5740), 1570. [DOI: 10.1126/science.1115901]
8. Dinger, M. E. et al. Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation, Genome Res. doi: 10.1101/gr.078378.108
   (2008).
9. Non-coding RNAs in the nervous system, Mark F. Mehler and John S. Mattick, J Physiol Volume 575, Number 2, 333-341, September 1, 2006 DOI: 10.1113/jphysiol.2006.113191
10. Specific expression of long noncoding RNAs in the mouse brain, Tim R. Mercer* et al., PNAS  January 15, 2008   vol. 105  no. 2  716-721
11. RNA Maps Reveal New RNA Classes and a Possible Function for Pervasive Transcription, Philipp Kapranov et al., Science 8 June 2007: Vol. 316. no. 5830, pp. 1484 – 1488 DOI: 10.1126/science.1138341
12. Intergenic transcription is required to repress the Saccharomyces cerevisiae SER3 gene, Joseph A. Martens, Lisa Laprade and Fred Winston, Nature 429, 571-574 (3 June 2004) | doi:10.1038/nature02538
13. Regulation of an intergenic transcript controls adjacent gene transcription in Saccharomyces cerevisiae, Joseph A. Martens, Pei-Yun Jenny Wu and Fred Winston, GENES & DEVELOPMENT 19:2695-2704, 2005
14. Neuronal Untranslated BC1 RNA: Targeted Gene Elimination in Mice, Boris V. Skryabin et al., Molecular and Cellular Biology, September 2003, p. 6435-6441, Vol. 23, No. 18 0270-7306/03/$08.00+0 DOI: 10.1128/MCB.23.18.6435-6441.2003
15. Pellionisz, A. (2008) The Principle of Recursive Genome Function. The Cerebellum (Springer), DOI 10.1007/s12311-008-0035-y
16. Evolution of the mammalian transcription factor binding repertoire via transposable elements, Guillaume Bourque, Bernard Leong, Vinsensius B. Vega, et al.
    Genome Res. published online August 5, 2008; doi:10.1101/gr.080663.108
17. Natural selection on gene function drives the evolution of LTR retrotransposon families in the rice genome. Regina S. Baucom et al. Genome Res. Published in Advance November 24, 2008, doi: 10.1101/gr.083360.108
18. Bekpen C, Marques-Bonet T, Alkan C, Antonacci F, Leogrande MB, et al. (2009) Death and Resurrection of the Human IRGM Gene. PLoS Genet 5(3): e1000403. doi:10.1371/journal.pgen.1000403.
19. Local DNA Topography Correlates with Functional Noncoding Regions of the Human Genome. Stephen C. J. Parker, Loren Hansen, Hatice Ozel Abaan, Thomas D. Tullius, Elliott H. Margulies. Published Online March 12, 2009. Science DOI: 10.1126/science.1169050.
20. A Functional Role for Transposases in a Large Eukaryotic Genome.
    Mariusz Nowacki, Brian P. Higgins, Genevieve M. Maquilan, Estienne C. Swart, Thomas G. Doak, Laura F. Landweber. Science 15 May 2009: Vol. 324. no. 5929, pp. 935 – 938 DOI: 10.1126/science.1170023.
21. Unstable Tandem Repeats in Promoters Confer Transcriptional Evolvability. Marcelo D. Vinces, Matthieu Legendre, Marina Caldara, Masaki Hagihara, Kevin J. Verstrepen. Science 29 May 2009: Vol. 324. no. 5931, pp. 1213 – 1216. DOI: 10.1126/science.1170097.
22. The regulated retrotransposon transcriptome of mammalian cells. Geoffrey J Faulkner1, Yasumasa Kimura2, Carsten O Daub2, Shivangi Wani1, Charles Plessy2, Katharine M Irvine3, Kate Schroder3, Nicole Cloonan1, Anita L Steptoe1, Timo Lassmann2, Kazunori Waki2, Nadine Hornig4,5, Takahiro Arakawa2, Hazuki Takahashi2, Jun Kawai2, Alistair R R Forrest2,6, Harukazu Suzuki2, Yoshihide Hayashizaki2, David A Hume7, Valerio Orlando4,5, Sean M Grimmond1 & Piero Carninci2. Nature Genetics 41, 563 – 571 (2009)
23. Distributions of selectively constrained sites and deleterious mutation rates in the hominid and murid genomes. Eory L, Halligan DL, Keightley PD. Mol Biol Evol.2009; 0: msp219v1-msp219
24. Characterization of viral and human RNAs smaller than canonical microRNAs. Zhihua Li, Sang Woo Kim, Yuefeng Lin, Patrick S. Moore, Yuan Chang, and Bino John. J. Virol. doi:10.1128/JVI.01325-09.
25. SVA retrotransposons: Evolution and genetic instability. Dustin C. Hancksa and Haig H. Kazazian Jr. Seminars in Cancer Biology, doi:10.1016/j.semcancer.2010.04.001
26. High-throughput sequencing reveals extensive variation in human-specific L1 content in individual human genomes. Adam D Ewing and Haig H Kazazian. Genome Res.  gr.106419.110; Published in Advance May 20, 2010, doi:10.1101/gr.106419.110
27. A coding-independent function of gene and pseudogene mRNAs regulates tumour biology. Laura Poliseno, Leonardo Salmena, Jiangwen Zhang, Brett Carver, William J. Haveman & Pier Paolo Pandolfi. Nature Volume:465, Pages: 1033–1038. Date published: (24 June 2010). doi:10.1038/nature09144
28. Orchestrated Intron Retention Regulates Normal Granulocyte Differentiation. Justin J.-L. Wong1, William Ritchie, Olivia A. Ebner, Matthias Selbach, Jason W.H. Wong, Yizhou Huang, Dadi Gao, Natalia Pinello, Maria Gonzalez, Kinsha Baidya, Annora Thoeng, Teh-Liane Khoo, Charles G. Bailey, Jeff Holst, John E.J. Rasko. Cell, Volume 154, Issue 3, 1 August 2013, Pages 583–595