Tag Archives: ENCODE

A genome’s junk is a gene’s treasure

Research Profile Picture James Sleigh

By James Sleigh

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2012 was an eventful year.

We saw Queen Elizabeth II mark 60 years on the British throne, Team GB excel at the fantastic London Olympic and Paralympic Games, the re-election of US and Russian presidents, and Gangnam Style conquer the world, all while managing to survive the Mayan apocalypse.

The year will also be remembered for a number of considerable scientific achievements. But which is the most important?

The landing of the Curiosity Rover on the surface of Mars? The discovery of the Higgs boson at CERN? Or perhaps even Herr Baumgartner’s record-breaking skydive from 24 miles above the New Mexico desert?

Deciding is almost as tricky as picking last year’s BBC Sports Personality of the Year!

As the newest member of the PlayDNA team, I’ve decided to begin the year by highlighting the research from 2012 that I think has the greatest impact on our understanding of what makes us human.

The Human Dictionary

Spot the difference?

Spot the difference

You may think you’re quite different from a grasshopper, the mould growing on your week-old loaf, or your Mum’s cheese plant. And you would be quite right. But, despite the instructions to create each species being different, the pen with which they are written is the same.

That is, we all share a universal genetic code – the DNA (the instructions) of all organisms is made from long strings of consecutive molecules known as nucleotides, which come in one of four different flavours (A, C, T, or G). The order in which these nucleotides are arranged within DNA affects how the inherent information is read, and what creature is eventually produced.

This happens because relatively short, distinct stretches of DNA known as genes, are copied to produce intermediary molecules that are then used as a templates to create proteins, the fundamental components of all cells.

Original cartoon by Daniel Paz

Original cartoon by Daniel Paz

Thanks to the Human Genome Project (HGP), the entire instruction manual to build a human was mapped and published in 2003. This landmark scientific collaboration unravelled the sequence of all the letters in our DNA, and identified that each of us possesses a unique complement of about 3 billion nucleotides, including some 20,000 or so genes.

Incredible!

However, the term “genome” is perhaps somewhat of a misnomer, as unexpectedly genes were shown to account for only approximately 1% of the total DNA. The remaining 99% has since often been described as “junk” because it had not been linked to any particular function.

That is, until now.

The Human Encyclopaedia

ENCODE nature cover 1Picking up where the HGP left off, the Encyclopaedia of DNA Elements (ENCODE) project is a decade-long study, involving over 440 scientists in 32 laboratories, and costing in excess of £180 million. The primary results from this large international collaboration were published late last year across 30 scientific papers, and have earned the ENCODE project my pick for the breakthrough of 2012.

The main aim of the ENCODE project is to build upon the human lexicon described by the HGP, by improving our knowledge of the grammar that weaves the directory of words into meaningful sentences. That is, the ENCODE project is attempting to better our understanding of how our genome of 3 billion nucleotides fits together, how the genes are controlled, and what all that “junk” is actually for.

dnaUsing nearly 150 different cell types, the scientists studied on a very large scale many different properties of human DNA sequences. They looked at which regions were active, which were silent, and what sequences appeared to be important for driving the production of proteins.

Each type of cell uses different combinations and permutations of these DNA sequences to produce its own unique biology. By comparing these differences, we are able to better understand how the genome is put together, processed, and read.

The upshot from what is the most detailed analysis of the human genome to date is that approximately 80% of our DNA has now been assigned a biochemical function.

junk dna

Image credit: nytimes.com

It’s not junk!

Why should I care about that?!

Well, understanding what all the regions of the human genome are doing can help scientists to pinpoint certain genetic risk factors that predispose to different conditions. In the past, many studies looking at patient DNA sequences have found hotspots that appear to contribute in some way to particular diseases. Intriguingly, many of these regions were not found in genes but in the “junk,” making it hard to deduce how and why these seemingly unimportant parts of the genome were being correlated with certain diseases.

In light of the ENCODE results, it is highly likely that these regions are functionally impacting genes that at first glance did not appear to be involved in disease.

Just what the doctor ordered?

Just what the doctor ordered?

We are a long way from understanding the wealth of data that ENCODE has produced. And it’s not going to get any easier, as it is estimated that the project is only about 10% complete.

Nevertheless, by highlighting the importance of our genome’s “junk” for the function of our genes, this breakthrough project will undoubtedly lead to a deeper knowledge of diseases and how to treat them.

 
Dr James Sleigh is a published research scientist at the University of Oxford currently working on diseases that affect the nervous system. His interest in genetics and neuroscience was sparked while working in a lab at Harvard Medical School as an undergraduate, and he has never looked back! James is passionate about communicating science, and has even won awards for his science writing. He is the research correspondent for the SMA charity The Jennifer Trust and has recently joined PlayDNA as Chief Communications Officer – so no doubt you will be hearing plenty more from him!
 
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