3Qs: New clues to unlocking the genome

Sep 19, 2012 by Angela Herring
Veronica Godoy-Carter’s research focuses on the genetic mechanisms guiding specialized DNA polymerases, a type of cellular machine important in DNA replication when cells are under stress. Credit: iStockphoto.

Last week, Nature Mag­a­zine, Genome Research and Genome Biology pub­lished 30 papers on break­through research that will change the face of genetics. After nearly a decade of searching, the Ency­clo­pedia of DNA Ele­ments (ENCODE) Con­sor­tium has assigned bio­chem­ical func­tions to 80 per­cent of the genome. Pre­vi­ously con­sid­ered "junk," the devel­op­ment adds sig­nif­i­cant insight into the impor­tance of the non­coding regions of DNA. We asked Veronica Godoy-​​Carter, assis­tant pro­fessor of biology, to explain.

What is noncoding DNA and why has it been called "junk"?

The genetic mate­rial present in all living organ­isms is DNA. It is under­stood that "coding" DNA can be "read" by the cel­lular machinery, as we read a page in a book, mostly as pro­teins (e.g., your hair and nails are made up of pro­teins). How­ever, there are sec­tions of the DNA in meta­zoans (e.g., humans) and in some uni­cel­lular organ­isms known to have no read­able code, that is, non­coding DNA. The word "junk" was used in the 14th cen­tury to denote an old or infe­rior rope. Today it is used to char­ac­terize use­less arti­cles or those of little value. Thus, when researchers started to deci­pher the linear sequence of the DNA, it became obvious that a large frac­tion of it is non­coding. There­fore, the word "junk" was used to describe such non­coding regions.

We've known for a while that noncoding DNA actually has very important physiological functions. How does this new research change or add to that understanding?

ENCODE has shown that, con­trary to pre­vious views, most of the of the are not use­less. Though it was pre­vi­ously known than non­coding regions were impor­tant for reg­u­la­tion, this project has demon­strated that non­coding sequences serve as a roadmap for reg­u­la­tory DNA binding pro­teins that effect expres­sion of coding regions. Pre­vious to this large-​​scale analysis, no one knew about the extent of reg­u­la­tory regions that existed in "junk" DNA, now referred to as "dark matter." For example, there are many sites that are specif­i­cally chem­i­cally mod­i­fied, per­mit­ting inhi­bi­tion or induc­tion of the DNA coding regions. Remark­ably, the reg­u­la­tion of expres­sion does not only occur in coding regions that are adja­cent to reg­u­la­tory ele­ments, as pre­vi­ously thought. In some cases, reg­u­la­tion is long range and seems to occur only when the reg­u­la­tory ele­ments are near coding regions in the three-​​dimensional space!

How will this new understanding of noncoding DNA change the face of genetic research?

The long-​​range reg­u­la­tion of coding regions in the DNA is such an exciting finding because it will permit us to start under­standing the effect of known changes in the DNA sequence (i.e., muta­tions) between, say, healthy and cancer tis­sues. As it turns out, many muta­tions asso­ci­ated with dis­ease are in non­coding regions, which pre­vi­ously made little sense. Now it will be pos­sible to map muta­tions on this and impor­tantly it will be pos­sible to under­stand how muta­tions far away in the linear change the reg­u­la­tory land­scape of cells.

Explore further: A touching story: The ancient conversation between plants, fungi and bacteria

add to favorites email to friend print save as pdf

Related Stories

Study: Junk DNA is critically important

Oct 19, 2005

A University of California-San Diego scientist says genetic material derisively called "junk" DNA is important to an organism's evolutionary survival.

Antifreeze fish make sense out of junk DNA

Apr 04, 2006

Scientists at the University of Illinois have discovered an antifreeze-protein gene in cod that has evolved from non-coding or 'junk' DNA. Since the creation of these antifreeze proteins is directly driven by polar glaciation, ...

3Qs: Hot, hot heat

Jun 28, 2012

A record-​​breaking heat wave hit the East Coast last week, fol­lowed by a spate of rain and thun­der­storms. Northeastern University news office asked Auroop Gan­guly, an asso­ciate pro­fessor ...

Recommended for you

Biotech firm's GM mosquitoes to fight dengue in Brazil

Aug 27, 2014

It's a dry winter day in southeast Brazil, but a steamy tropical summer reigns inside the labs at Oxitec, where workers are making an unusual product: genetically modified mosquitoes to fight dengue fever.

User comments : 0