![]() ![]() ![]() This diagram illustrates some of the methods used by the ENCODE researchers to identify biologically functional parts of the genome: transcript sequencing (RNA-seq and RT-PCR) to identify transcribed regions), chromatin immunoprecipitation sequencing (ChIP-seq to identify sequences bound by proteins that are involved in controlling transcription), DNase digestion (DNase-seq to identify open chromatin), computational predictions (for finding genes and identifying highly conserved sequences), and expression reporter assays (e.g. Figure 2: Unpacking the genome: zooming in on a chromosome to double-stranded DNA. The consortium was supported by the National Human Genome Research Institute in the USA and led by the European Bioinformatics Institute (EBI see box ) in the UK. The ENCODE pilot phase ran from 2003 to 2007 and allowed a global network of researchers to test, compare and optimise experimental and computational methods for identifying the active parts in a 1% portion of the genome – essentially sifting through some of the genomic ‘junk’. In 2003, the ENCODE consortium was formed to characterise the non-coding but functional elements of the human genome. Once the human genome was sequenced, it was time to find out whether these sequences really were junk. As a result, it was often referred to as ‘junk’ DNA. After accounting for additional bits of the genome such as non-coding RNAs, parts involved in controlling the activity of genes and introns (the sections of a gene’s sequence that are removed before the messenger RNA molecule is translated), a common view was that the rest of the genome had no biological function. One of the big surprises of the human genome was that only 2% of the genome contains genes, the instructions to make proteins. Then, perhaps, we can apply this knowledge to biomedical research and healthcare. Deciphering how this sequence is interpreted by our cells is essential to understanding how the genome works. The Human Genome Project – the sequencing of the human genome – was a major achievement of the past decade: it laid bare the human genetic blueprint, all three billion bases, but the story doesn’t stop there. What does the majority of our DNA do? Hundreds of scientists have spent years examining these ‘junk’ sequences, which may hold the key to serious diseases – and much more. ![]()
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