Hidden DNA code cracked
Biophysicists from the FOM Foundation, Leiden University and Radboud University Nijmegen have discovered which pieces of DNA sequence provide instructions for the packaging of DNA around histone proteins. The position of these histones in the DNA are vital because they help to determine whether or not a gene can be read out. With the help of statistical mechanics the researchers have made a model with which they have demonstrated that a simple two-letter code in the DNA determines the positions of these histones. The discovery enables researchers to obtain far more information from DNA codes, not just about the sequences of the genes but also whether or not they are standardly programmed to be switched 'on' or 'off'. The results were published on 21 August 2012 in the Proceedings of the National Academy of Sciences (PNAS).
Gene activity
The human genome contains six billion base pairs in which about 25.000 genes are coded. Cells regulate the activity of all of these genes very accurately, for example by manipulating the accessibility of the DNA. A cell can do this by rolling up a specific piece of DNA around histones (little activity), or by ensuring it remains free (much activity). About 150 base pairs of DNA fit around a package of histone proteins. Such a unit is called a nucleosome. Allowing for some space between the nucleosomes this means that about 30 million nucleosomes are found in the genome. The exact positioning of each nucleosome is crucial: a shift of several base pairs can make a big difference for the binding of a transcription factor and consequently the activity of a gene.
Inside bend or outside bend
The 150 base pairs in a nucleosome form a chain about 50 nm long and 2 nm wide. The DNA must therefore be strongly bent to roll up into a barrel with a radius of 5 nm. Some DNA sequences are easier to bend than others. DNA is made up of the bases A (adenine), T (thymine), C (cytosine) and G (guanine) and specific combinations of two letters determine the bending preference. Two successive Ts, for example, have a tendency to take the inner bend and GC bases prefer to position themselves in the outer bend of the nucleosome. At the biophysics group in Leiden, John van Noort and Thijn van der Heijden used statistical mechanics to incorporate this knowledge into a model with which the bending preferences can be precisely calculated based on the DNA sequence.
Two-letter code
Although researchers can map the DNA sequence and the position of nucleosomes across the genome there is still a lot of discussion about how and to what extent the nucleosome positions are determined. In this study the researchers have shown that the position of the nucleosomes is largely determined by the DNA code. The two-letter code that has emerged can explain the exact position and affinity of histones if these are brought together in a test tube, even where unnatural DNA sequences are used. Yet more important still, the code accounts for about 67percent of the positions of nucleosomes in the cell. It is therefore clear that the hidden code in the DNA largely determines the positioning of the nucleosomes.
Model
The model forms the basis for a far more extensive study: researchers will now investigate the influence of the DNA sequence on the rate and mechanism of nucleosome translocation. They will also investigate how the DNA sequence influences the formation of larger structures in the cell nucleus. This must ultimately lead to a far better use of the information that emerges from the sequencing of the genome. Knowing just the 'genetic menu' is not enough. We also need to know exactly what 'dishes' are served.
The research was carried out by Thijn van der Heijden (Leiden University), Joke J.F.A. van Vugt (Leiden University), Colin Logie (Radboud University Nijmegen) and John van Noort (Leiden University), all of whom are involved in the FOM programme 'Physics of the genome'.
Further information
John van Noort +31 (0)71 527 5980
Physics of Life Processes
Cell Observatory, room 05.25
BF / LION, Leiden University
Niels Bohrweg 2, NL-2333 CA Leiden
Reference
Sequence-based prediction of single nucleosome positioning and genome-wide nucleosome occupancy.
Thijn van der Heijden, Joke J.F.A. van Vugt, Colin Logie and John van Noort.
PNAS, 21 Augustus 2012; 109 (34).