Sunday, April 19, 2009

Modified Bases in DNA

Adenine: from the Greek adenas "gland": first isolated from pancreatic glands (1885)

Cytosine: derived from cyto- from the Greek word for "receptacle," refering to cells (1894)

Guanine: originally isolated from "guano" or bird excrement (1850)

Thymine: first isolated from thymus glands (1894)

(source Horton et al. 2006)
Bacterial genomes contain a number of unusual bases in addition to the classic adenine (A), cytosine (C), guanine (G), and thymine (T). The most common of the unusual bases are 5-methylcytosine, N4-methylcytosine, and N6-methyladenine (Erlich et al. 1987).

Bacteriophage DNA, especially the DNA of bacteriophage T4 and its close relatives, can contain 5-hydroxymethylcytosine. The base is usually glycoslylated in normal phage. (A sugar group is attached to the hydroxymethyl group.)

Many of these modified bases serve to protect DNA from restriction endonucleases—enzymes that cleave foreign DNA at specific sites. The restriction endonucleases act on bacteriophage (virus) DNA preventing it from replicating inside the bacterial cell [see Restriction, Modification, and Epigenetics].

If bacteriophage modify their nucleotides at the site of cleavage, they will escape the defenses of the bacterial cell. Of course, bacteria that make restriction endonucleases have to protect their own DNA or else they will be committing suicide. That's why their genomes have modified nucleotides.

Many other modified bases have been found in DNA but they are quite rare. Examples are uracil, α-putrescinylthymine, and 5-dihydroxypentyluracil.

Eukaryotic DNA doesn't have as many modified bases. In fact, 5-methylcytosine is the only one that's common in all eukaryotes. N6-methyladenine is known to exist in protist and plant DNA and it is thought to exist at low levels in mammalian DNA as well (Ratel et al. 2006). The presence of hydroxymethycytosine has been reported in various animals as far back as 1972 (Penn et al. 1972).

Now Kriaucionis and Heintz (2009) have re-discovered hydroxymethylcytosine in mammalian DNA. Their paper appears in the latest issue of Science. Apparently the modified nucleotide is found in certain brain cells. Their result confirms the work done by Penn et al. (1972), a result that had not been confirmed in several other studies. This makes hydroxymethylcytosine the seventh modified base in eukaryotic DNA—unless there are some that I don't know about.

The problem with the press release is that it doesn't put the discovery in the proper context.
ScienceDaily (Apr. 17, 2009) — Anyone who studied a little genetics in high school has heard of adenine, thymine, guanine and cytosine – the A, T, G and C that make up the DNA code. But those are not the whole story. The rise of epigenetics in the past decade has drawn attention to a fifth nucleotide, 5-methylcytosine (5-mC), that sometimes replaces cytosine in the famous DNA double helix to regulate which genes are expressed. And now there's a sixth: 5-hydroxymethylcytosine.

In experiments to be published online April 16 by Science, researchers reveal an additional character in the mammalian DNA code, opening an entirely new front in epigenetic research.
We aren't told that the sixth nucleotide is actually N6-methhyladenine. We aren't told that many other modified bases have been discovered in bacteria, including hydroxylmethylcytosine. And we aren't told that the authors actually cite earlier work showing the presence of hydroxymethylcytosine in mammalian DNA.

That's a shame. The authors are quoted in the press release. They should have made more of an effort to ensure that it was scientifically accurate.

Ehrlich, M., Wilson, G.G., Kuo, K.C., and Gehrke. C.W. (1987) N4-methylcytosine as a minor base in bacterial DNA. J Bacteriol. 169:939-943. [Journal of Bacteriology]

Kriaucionis, S. and Heintz, N. (2009) The Nuclear DNA Base 5-Hydroxymethylcytosine Is Present in Purkinje Neurons and the Brain. Science Published Online April 16, 2009 [DOI: 10.1126/science.1169786]

Penn, N.W., Suwalski, R., O'Riley, C., Bojanowski, K. and Yura, R. (1972) The presence of 5-hydroxymethylcytosine in animal deoxyribonucleic acid. Biochem J. :781–790. [Biochem. J.]

Ratel, D., Ravanat, J.L., Berger, F., and Wion, D. (2006) N6-methyladenine: the other methylated base of DNA. Bioessays :309-15. [PubMed


  1. Thanks for getting to this. I saw the story a few days ago but thought there was something iffy about how overblown it was.

  2. DNA base J (-D-glucosylhydroxymethyluracil) in Trypanosomes.

  3. I heard about this a few weeks ago by word of mouth. I had no idea about the 1972 paper though, and it seems they find it in brain tissue there too. Still, it's an interesting discovery

  4. Uuhh, they forgot T4 phage, which has Hydroxymethyl C, as a site for glycosylation.

  5. You can't expect press releases to have good, or even complete, scientific information. It might not be the "6th base" but it's still damned interesting.

    Among the most interesting things about the 5-hydroxymethylcytosine are that 1) it is indistinguishable from MeC using bisulfite mapping, and 2) methyl-binding proteins like MeCP2 have a different affinity for the OHMeC compared to the MeC. This could be huge in that it may account for differential activation and repression of some genes by MeCP2, and some of the ambiguity around the actual role of methylation in gene expression...

  6. Great post, thank you for pointing this out. There are many inaccuracies in press releases, which makes one wonder, why is there no peer review for press articles? It should take only 5-10 minutes to read a press article, and often more people read this false info than the true article. We should implement peer review for press releases!

  7. Re: Ian Vitro, there is now a way to distinguish OHMeC from MeC: