Epigenetics: the search for methylated nucleotides is put on the conveyor
A new technology for decoding "supra-genomic" information has been developed
Tape.<url> based on Nature News: Genomics goes beyond DNA sequenceScientists have developed a new technology for decoding epigenetic information – "superstructures" of chromosomal DNA, which are not determined by traditional methods, but have a significant impact on the implementation of the data recorded in DNA.
The work of researchers from Pacific Biosciences is published in the journal Nature Methods (Benjamin A Flusberg et al., Direct detection of DNA methylation during single-molecule, real-time sequencing).
The science of epigenetics began to develop actively at the end of the last century, when scientists began to understand that hereditary information is embedded not only in the DNA sequence itself, but also in certain modifications of individual "letters" – nucleotides. For example, the addition of a methyl group – CH 3 – often leads to the inactivation of a modified DNA site.
Until now, researchers have not had a "streaming" method of working with the epigenome – the modified nucleotides were actually found manually. The most common technology for searching for methyl groups, for example, was as follows: DNA samples were chemically modified so that unmethylated nucleotides (specifically cytosine) turned into another type of nucleotides – uracil. Normally, DNA does not contain uracil, so after determining the sequence, researchers could find out which cytosines contain a methyl group and which do not. However, this method has several serious drawbacks – firstly, it is very expensive and takes time, secondly, it does not allow to find methylated adenines (such modification is very common, for example, in bacteria), and thirdly, chemical treatment damages DNA and reduces the accuracy of decoding.
The authors of the new work proposed a fundamentally different way of searching for epigenetic modifications. It is based on the use of fluorescent labels – during the determination, the DNA polymerase enzyme creates a copy of the studied DNA chain from nucleotides in the reaction mixture, to which fluorescent "appendages" are attached. Each of the four nucleotides that make up DNA (adenine, cytosine, guanine and thymine) fluoresces with its own color, so scientists can determine the sequence of the newly synthesized DNA strand using a special scanner. Scientists judge the presence of methylated nucleotides by the change in the time of the next outbreak, which means that the enzyme has included another nucleotide in the chain.
The new technology allows you to very quickly determine which nucleotides in DNA carry a methyl group. However, so far, researchers have not been able to adapt the technique for all types of methylation, and, in addition, it does not allow to determine the presence of methylation on long stretches of DNA – the technology works best for fragments less than a thousand nucleotides long. In order to obtain a full-genome map of methylation, scientists need to have DNA segments from eight to ten thousand nucleotides long as the "starting material".
In the foreseeable future, experts intend to eliminate the shortcomings of their method. Nevertheless, Pacific Biosciences plans to start producing devices that determine the DNA sequence using the new technology as early as 2010, and in 2011, researchers expect to launch a line of devices that could detect the presence of methyl groups.
Currently, scientists involved in epigenetics have shown that the change of supra-genomic modifications is extremely important for the course of many important processes in the body, in particular in the development of cancer. In addition to DNA modifications, epigenetic changes affect proteins associated with nucleic acids.
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12.05.2010