October 2012: “Junk DNA” is not junk

DNA is the abbreviation for deoxyribonucleic acid that is arranged into chromatins, in which the DNA is structurally compacted by proteins.  DNA carries genetic information of all known living organisms including humans. The flow of genetic information is that DNA is transcribed into RNA (transcription) driven by transcription factors and then translated into proteins (translation), which can be hormones, enzymes, structural components of cells, etc. Back in 2003, the National Human Genome Research Institute launched the ECODE (Encyclopedia of DNA Elements) project, which is a public research consortium. The goal of this project is to understand the functional elements in the human genome. A pilot study from the ENCODE project identified and characterised 1% of the human genome. With the success of the pilot study, the ENCODE project was scaled up to analyse the whole human genome.

“Junk DNA” are portions of a genome sequence for which no discernible function had been identified. Yet, last week I attended an immunology journal club and learned that “junk DNA” is not useless. The article presented was published by Nature (ENCODE project), which revealed these non-coding regions of DNA control gene transcription like the “ON/OFF” switch to the genes. The authors first mapped the sites that were most sensitive to be cleaved by an enzyme called DNase I. These DNase I hypersensitive sites (DHS) correlate with where factors to which regulation transcription would bind. Then, they demonstrated that these DHS are located far away from the coding regions. Instead of the dogma that chromatin accessibility and DNA methylation control accessibility of transcription factors, the authors suggested that transcription factors drive chromatin accessibility, which is inversely correlated with DNA methylation. After all, this paper has provided new insights of the non-coding regions of the human genome, which identified them to be regulatory regions.

The ENCODE project may facilitate the understanding of biological processes and disease states by providing insights into how proteins interact with DNA to regulate gene expression. I think this project has a long way to go as it is just the tip of the iceberg. I think the human genome has a lot more to be uncovered and scientists around the world are beginning to discover and reveal the function of the different regions of the human genome.

Reference: Nature 2012 489(7414):75-82

 

By Vicki Cheng