On BioScience and Life and Such

Hammering nails in the “junk-DNA” coffin

In Uncategorized on October 28, 2008 at 2:12 pm


post to news.thinkgene.com

A replica of the coffin used for Abraham Linco...

Image via Wikipedia

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
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  1. Genomics, for over half a Century, has been pulled by two “horses”. One was “The Central Dogma of Molecular Biology” by Crick/Watson, the other was the “Junk DNA” misnomer by Ohno.

    Now, both of the horses are dead – please kindly stop flogging. It is not a very good use of time (unless you enjoy it).

    Now, in the age of HoloGenomics, better replace obsolete dogmas by “The Principle of Recursive Genome Function”, see in peer reviewed paper here, or on YouTube

    Pellionisz_at_junkdna.com

  2. I realize that the YouTube link is not working. Here is a link with a “visual leporello” Table of Contents.

    The science paper is here

    Pellionisz_at_junkdna.com

  3. The video was also featured on Scienceroll: http://tinyurl.com/5rmm8n

  4. Funny – if junk DNA research was suppressed or discouraged by a label, how is it that one can find hundreds of papers opn junk DNA function during this period of ‘suppression”?

    Spinning tales of martyrdom and ego-inflation just make some people look desperate and pathetic.

  5. slpage. So research is not completely suppressed, – which is good. I guess numbers of papers could have been thousands instead of hundreds if it wasn’t discouraged, if you find that funny, then so be it.

    I am not a “junk” DNA researcher myself so I’m hardly a martyr nor do I see that my posts in any possible way inflates my ego. Actually I’d say my ego is deflated a bit by now……and that of course may be viewed as pathetic by some.

    But, when it comes to desperate writings I’d say your comment fits the description better, since with regards to the amount of DNA being “junk” or not, your comment isn’t relevant at all…

  6. Also in Nature.blogs,wherein such as news were been posted, I commented critically news regarding Genomics, as by Sergio Stagnaro
    http://www.the-scientist.com/blog/display/55106/
    [Comment posted 2008-10-29 11:41:24].
    I frankly suspect that economics may contribute to hindering scientific advances, clinical in nature, which allow me to state that gene mutations parallel biological systems dysfunctions, bedside evaluated with a simple stethoscope! Earlier, on BMJ blog has been posted a message of mine at the URL: ” http://blogs.bmj.com/bmj/2008/10/28/laura-james-on-science-and-journalism/#comments
    regarding Ministerial Conference of Environment and Health in Madrid. Scientists need publicity, especially for spreading among individuals their own theories, rather than to obtain funding. Unfortunately, paramount theories are not expensive, but are not politically correct. For instance, in the Age of Genomics at the Zenith, who among journalists is authorized to give information that every gene mutation brings about necessarily alteration, i.e., dysfunction, in related biological system, adding that doctors can nowadays bedside evaluate all tissue functions, in reliable way,so that we can gather, since BIRTH, precise information not only with the aid of genomics, but also with a simple stethoscope?
    In a few words, in no expensive way, doctors are able to state rapidly if an individual is predisposed to diabetes, hypertension, osteoporosis, ATS (CVD), CANCER in well-defined biological system, a.s.o.
    Such as statements may you read, for instance, on http://www.nature.com, at URLs http://www.nature.com/news/2008/081006/full/news.2008.1152.html?q=2#last-comment
    http://blogs.nature.com/nm/spoonful/2008/03/gout_gene.html

    That is LIFE!

  7. Dear Nils, only now I read with pleasure your kind comment, regarding what I wrote elsewhere [Comment posted 2008-10-29 11:41:24]. You know, I have sent recently a Lettera Aperta (Open Letter) to Italian President On.Silvio Berlusconi. In a few words, I’ve illustrated what accounts for the reason taht the end of CLINICAL Medicine parallels the end of Medicine itself (e.g. Stagnaro Sergio. The Death of Clinical Medicine parallels Medicine End. Canadian Medical Association Journal (CMAJ) 2008; 178: 1523-1524, 10 June 2008. http://www.cmaj.ca/cgi/eletters/178/12/1523).
    Notoriously, today’s Medicine is ruled by Economics, so that mass-media “spread” every day Genomics expensive advancements, while CLINICAL progresses, paralleling the first,reliable, not expensive and useful for all individuals, rationalized enrolled in the primary prevention, are trivially silenced. An Italian famous journalist, even this morning, wrote me, once again, he is awaiting from years the consent (requested also today) of his Chief to interview me ……..

  8. A comment from a discussion over at Sandwalk:

    Doppelganger said…

    Nils,
    That you cite Andras Pellionisz’ historical revisionism-littered disaster of a paper in your litany of citations purportedly showing that there is less ‘junk-DNA’ than believed tells me that you don’t pay enough attention to the content of the papers on your list.

    and he goes on to say….

    I’m not sure that ‘controversial’ really engenders the true feeling most competwent scientsts have when they read his paper.

    It is childish, the figures contain typos, it is petty, it contains flat out lies, and the main theme has ZERO support. Why it is publication is a mystery, how it got past review smacks of a Sternberg-Meyer event.

    If you want to leave it on your list, feel free. But realize that doing so calls your scientific judgement into question.

  9. Scientific judgement…here is the point in Science!I do not recognize ar all the SCIENTIFIC method, based on logical deduction from a general principle, as the ONLY valid. That would be a dogma, in my opinion. Surely, I agree with corroboration or confutation of theories, whose “empirical”, final statements may be “judget”….at the condition that the Master demonstrates to know the utilized method. In Italy, but also elsewhere, there are Editors and Reviewers who judge articles done with methods, they ignore, in spite of negative or positive judgement.
    Middle Ages of today’s Medicine, as I wrote!

  10. […] in question added to junk DNA coffin post. ▶ Comment /* 0) { jQuery('#comments').show('', change_location()); […]

  11. […] nogal denigrerend ook wel junk DNA genoemd. Hoewel over de precieze rol van dit niet-coderend DNA het laatste woord nog niet gezegd is, lijken typfouten in dergelijk junk-DNA – zo is de huidige wetenschappelijke consensus […]

  12. […] updated: Hammering nails in the “junk-DNA” coffin with this Cell paper “Orchestrated Intron Retention Regulates Normal Granulocyte […]

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