Controlling the Genome

Duke Bioengineers Can Control What Controls Our Genes
May 18, 2015 
Genetics has not been just about genes in many years.
The genes that carry all of the necessary information to build an organism are only a small part of the genome. Other DNA sequences called promoters and enhancers tell cells when and to what degree certain genes should be expressed. A myriad number of proteins and small chemicals, known collectively as the epigenome, exert more control on when the genes, promoters and enhancers should work and when they should not.
These controls explain why brain cells and muscle cells have the same DNA but look and behave so differently.
Scientists have recently begun attempting to decipher these genetic controls: how the epigenome knows when to work and exactly which specific promoters and enhancers activate a particular gene. This can be a complicated process as enhancers are often located far away from the genes they activate.
Now Duke University bioengineers Charles Gersbach and Timothy Reddy have borrowed a technique from bacteria to activate specific promoter and enhancer sequences. Their method is the first that can target specific enhancers, opening the door for research into genetic disorders and new stem cell research.
Gersbach and Reddy’s technique borrows from a tool bacteria use to fight off viruses called CRISPR-Cas, which is short for clustered regularly interspaced short palindromic repeat-CRISPR associated protein. Despite the long name, its function is simple — find specific DNA sequences and cut them out.
Imagine DNA as a very long Word document, containing detailed instructions on how to build an organism. CRISPR is the “Find” tool. It carries around an RNA sequence to match the specific DNA sequence it wants to find. Bacteria keep CRISPR on hand to find viral DNA or RNA that infiltrate it. 
Cas is the “Cut” tool. It is an enzyme attached to the CRISPR RNA segment whose sole job is to cut out the pieces of DNA that CRISPR is sent to find. Bacteria use CRISPR-Cas to recognize and destroy virus DNA before it can destroy the bacteria.
Recently genetic engineers have modified CRISPR-Cas to serve a “Find and Paste” function to implant genes into bacteria and even make antibiotics.
Reddy, whose primary research has been locating enhancer sequences, partnered with Gersbach, a CRISPR-Cas expert, to see whether CRISPR’s ability to recognize specific DNA sequences could be used to activate specific enhancers.
So Gersbach, Reddy and their colleagues created a modified CRISPR-Cas system that would carry an enzyme called acetyltransferase to the enhancer sequence. Acetyltransferase would then attach a small molecule to the epigenetic proteins near the enhancer, thereby turning the enhancer on. You can think of it as a “Find and Bold” function.
They tested their modified CRISPR-Cas system on a few specific places they already knew were strongly associated with gene activation and found not only did their method activate genes, but it did a better job activating genes than current methods do.
Gersbach and Reddy’s method is also the first to activate specific enhancers. This could be very important for genetic disorders as the underlying issue is often associated with mechanisms like promoters and enhancers that control the genes as opposed to the genes themselves.
So if a researcher has a hypothesis that malfunctioning enhancer X is causing problem Y with gene Z, he can use this method to trigger enhancer X to see exactly what enhancer X is supposed to do and compare that to how a faulty enhancer X is behaving.
This method can also be useful in stem cell research. Stem cells become the more than 200 different types of cells in the body by expressing different genes. Muscle cells are different from bone cells which are different from skin cells, etc. 
By selectively activating specific promoters and enhancers with CRISPR-Cas, scientists may be able to more efficiently grow functional cells from stem cells.
The work appears in the journal, Nature Biotechnology.
— Daniel Lane
Daniel Lane covers science, engineering, medicine and the environment in North Carolina.