Devangshu Datta: What's in a genome

Devangshu Datta: What's in a genome The results of the Encode project may not be sensational but will clearly accelerate research in several key areas Devangshu Datta / New Delhi Sep 21, 2012, 00:55 IST

In early September, several teams working on the human genome published a flood of papers detailing their findings. The Encyclopaedia of DNA Elements Projects (Encode) has made great progress in detailing human genome functions.

This is the biggest set of breakthroughs since the human genome project (HGP) mapped the DNA sequence between 2000 and 2003. However, Encodes results have caused some controversy within the scientific community. The results are not being disputed. But several scientists have stated the press releases were misleading or misinterpreted.

Unusually, for a collaborative project of this scale, the papers were embargoed to ensure coordinated release. The raw data were made available for use, however. All data and papers are now freely available with a special search application on the portal, http://nature. com/encode/.

DNA (deoxyribonucleic acid) carries the information that offers inheritable characteristics. The HGP identified 20,000-plus DNA genes that carried protein-coded information unique to individuals. The coded sequences are responsible for most cell functions. If that set of protein-coded genes is replicated, it produces a clone, or identical twin.

But the coded DNA sequences are a very small proportion roughly 1 to 1.5 per cent of the entire genome. The genome contains many more DNA sequences that possess no protein-coding. It also has RNA (ribonucleic acid) sequences. RNA is required to copy and replicate DNA. RNA passes through the nuclear membrane of cells carrying selective DNA information to be replicated.

It was known that non-coded DNA sequences included switches that controlled and regulated the activity of coded sequences. However, many non-coded sequences also seem redundant. Some are broken bits of discarded genes and disabled viruses. Even some coded DNA is redundant. One hypothesis is that these bits of useless DNA are leftovers from evolutionary history.

Since functions of specific bits of non-coded DNA werent known and since some bits were apparently useless, these sections were misleadingly labelled junk. They are also referred to as dark matter.

Encode has figured out the biochemical activity in much of the junk and also confirms that there are many switches controlling the coded sections. The switches tell coded genes when to switch on and off and determine, for example, which cells become muscles, and which pancreas cells, or neurons.

Encode claims that at least 80 per cent of the junk is biochemically active. This is where confusion has arisen. It was reported that 80 per cent of junk was useful. But biochemically active doesnt necessarily translate to useful. Carrying a useless, disabled gene doesnt hurt the organism and most such sequences are biochemically active.

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Devangshu Datta: What's in a genome