How ‘Junk DNA’ Can Control Cell Development (one for the Creationists)

How ‘Junk DNA’ Can Control Cell Development (one for the Creationists) August 14, 2013

Having just had a small discussion on an Amazon book review concerning evolution, and with the science denier proposing as one of his 3 main arguments against evolution being ‘junk DNA’, I thought this article would be interesting; a recent paper described by Science Daily:

Aug. 2, 2013 — Researchers from the Gene and Stem Cell Therapy Program at Sydney’s Centenary Institute have confirmed that, far from being “junk,” the 97 per cent of human DNA that does not encode instructions for making proteins can play a significant role in controlling cell development.

And in doing so, the researchers have unravelled a previously unknown mechanism for regulating the activity of genes, increasing our understanding of the way cells develop and opening the way to new possibilities for therapy.

Using the latest gene sequencing techniques and sophisticated computer analysis, a research group led by Professor John Rasko AO and including Centenary’s Head of Bioinformatics, Dr William Ritchie, has shown how particular white blood cells use non-coding DNA to regulate the activity of a group of genes that determines their shape and function. The work is published today in the scientific journalCell.

“This discovery, involving what was previously referred to as “junk,” opens up a new level of gene expression control that could also play a role in the development of many other tissue types,” Rasko says. “Our observations were quite surprising and they open entirely new avenues for potential treatments in diverse diseases including cancers and leukemias.”

The researchers reached their conclusions through studying introns — non-coding sequences which are located inside genes.

As part of the normal process of generating proteins from DNA, the code for constructing a particular protein is printed off as a strip of genetic material known as messenger RNA (mRNA). It is this strip of mRNA which carries the instructions for making the protein from the gene in the nucleus to the protein factories or ribosomes in the body of the cell.

But these mRNA strips need to be processed before they can be used as protein blueprints. Typically, any non-coding introns must be cut out to produce the final sequence for a functional protein. Many of the introns also include a short sequence — known as the stop codon — which, if left in, stops protein construction altogether. Retention of the intron can also stimulate a cellular mechanism which breaks up the mRNA containing it.

Dr Ritchie was able to develop a computer program to sort out mRNA strips retaining introns from those which did not. Using this technique the lead molecular biologist of the team, Dr Justin Wong, found that mRNA strips from many dozens of genes involved in white blood cell function were prone to intron retention and consequent break down. This was related to the levels of the enzymes needed to chop out the intron. Unless the intron is excised, functional protein products are never produced from these genes. Dr Jeff Holst in the team went a step further to show how this mechanism works in living bone marrow.

So the researchers propose intron retention as an efficient means of controlling the activity of many genes. “In fact, it takes less energy to break up strips of mRNA, than to control gene activity in other ways,” says Rasko. “This may well be a previously-overlooked general mechanism for gene regulation with implications for disease causation and possible therapies in the future.”

Journal Reference:

  1. Justin J.-L. Wong, 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. Orchestrated Intron Retention Regulates Normal Granulocyte DifferentiationCell, 2013; 154 (3): 583 DOI: 10.1016/j.cell.2013.06.052
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  • Andy_Schueler

    Researchers from the Gene and Stem Cell Therapy Program at Sydney’s Centenary Institute have confirmed that, far from being “junk,” the 97 per cent of human DNA…

    Argh… Sometimes I wonder if there are any competent science journalists left.

    • SmilodonsRetreat

      I believe it’s the Scripps Institute that has a journalism internship, where they take aspiring science journalists and actually have them do field work as well as writing courses.

      Of course, I haven’t seen any graduates of that program (that I’m aware of) in the major science publishers.

      • Andy_Schueler

        Sounds promising.
        But when it comes to anything that is remotely related to junk DNA, it seems that science journalists just turn their brains off and try to spin a story based on this idiotic strawman: “Researchers have confirmed that, far from being “junk,” the 97 per cent of human DNA…”.

        The funny thing is, that the links right next to this article all go to articles that are build around the same strawman – researchers apparently confirmed the exact same thing in 2010 and 2009 before that, and the editors at Cell (which happens to be the most prestigious journal that a Biologist could hope to publish in) are apparently still stupid enough to publish the same story over and over and over again (and if whoever wrote this article would follow this trail (s)he might have found out that this strawman goes back to the fucking seventies…).
        Just thinking about this for a few seconds should have caused the author of this article to wonder whether researchers really try to demonstrate the exact same thing over and over and over again (and always get it published) or whether it just might be the case that they have no fucking clue what “junk DNA” means…

  • Richard Edwards

    I see Andy beat me to it. This article is a real face-palm moment for science journalism. Not only has it long, long, long, long, long been known that introns have functional importance but this “97 per cent of human DNA that does not encode instructions for making proteins” is not even the right number! Introns may make up 97% of genes (sounds a bit high) but only about a quarter of the genome is intronic sequence – see http://en.wikipedia.org/wiki/Human_genome. About twice as much is still repetitive “junk”, some of which may also have function. Plus, even though introns are important, much of the sequence within an intron is still probably “junk” in the sense that it can be removed and/or substituted quite happily. I would bet that substantial changes could be made to introns without upsetting the regulation described in this paper. (You only have to look at intron variability within and between species to see this.)

    Finally, there is a big cause and effect question here. Clearly, cell regulation etc. has to take care of the introns that are there and will use the existing features when it does so but that is very different from those introns and/or their precise nature being there *for* that regulation. I use my Google account to sign in here but that is not why Google exists. If I were a Creationist, I would not be waving any flags about this one!