he Human Genome Project, a proposal to sequence the entirety of the human genome and all of its nucleotides, was completed in April of 2003. While there are still scientific debates on whether it properly completed all of the genome, there remains another part of the project that one can say for certain is not completed and is not anywhere close to completion.
The purpose of the project was not just to complete a sequencing, but also a full functional understanding of what all the genes in the human genome do. Since, without that, knowing the genetic code itself isn’t exactly useful. Efforts can be made to one by one determine the function of each gene, but that would be a long and slow process.
MARGI, A Friend To DNA
Researchers at the University of California – San Diego decided to design a tool to help speed up this functionality hunt.
Meet MARGI, the Mapping RNA Genome Interactions tool.
It is a first of its kind tool that is capable of measuring all of the RNA involved with a desired segment of DNA and also all the interactions made between them. These types of RNA interact with and regulate chromatin in the cell.
How DNA Works
Chromatin is the 3-dimensional structure that DNA forms itself into within the genome. One example of this structure that you may be aware of is the 23 pairs of chromosomes that humans have, which are a very tightly super-coiled and condensed form of chromatin.
But it’s more than just the DNA, chromatin is also the proteins and RNA that interact and form the structure of that DNA. Histones, for example, are a type of protein that DNA wraps around in a bundling shape. These too are a part of what makes up chromatin.
Making A Map
Now then, back to the original RNA we were discussing, which have a special name due to their interactions with chromatin. It’s as apparent as you’d expect: chromatin-associated RNAs (caRNAs).
In associating with chromatin, these caRNAs control protein output and other production factors that involve the DNA in the chromatin. The MARGI tool is able to measure and record all of these interactions.
The first step is going to be to use MARGI to isolate the genes involved in making these caRNAs themselves as a way to record all the different types of RNAs that regulate the genome. This will also allow an understanding of which genes the caRNAs ultimately target and affect.
The thing that makes MARGI amazing is that all prior tools and methods could only measure a single RNA interacting with the genome at a time, which is largely useless for understanding a segment of DNA. MARGI, however, can measure hundreds, speeding up the necessary amount of time to only a few years to cover the entire human genome. Hopefully, at least.
The scientists are able to use MARGI to make RNA-genome interaction maps that connect all the different functionalities of each caRNA and the rest of the genome.
Still More Work To Be Done
Though it should be noted that this tool isn’t foolproof. MARGI still produces a false positive 2.2% of the time where it claims interactions that don’t actually occur. So the data still has to be double-checked, but this new tool remains a remarkably faster method to finish a functionality map of the genome than anything else out there.
With any luck, in a few years time, we’ll finally be able to understand the effects of each gene in the human genome. Combine that with the ability to actively manipulate the genome with CRISPR and the medical world may never be the same.
Even more so than the miraculous scientific time period we live in right now.
Photo CCs: Nucleosome1 from Wikimedia Commons