Witnessing the Transition from Gene-tic to Genome Engineering.
I am lucky to be involved in biological sciences in the 21st century.
Cloning and genetic engineering have enabled researchers to follow protein expression and gene regulation dynamics for several years now. Such engineering approaches in biology enable an experimentalist to try building a system from the ground up and in doing so, allows him to explore fundamental biological questions.
Often times, imaginations of scientists/innovators can go wild. While ventures as huge in scale as that of that of our favorite Jack Hammond from Jurassic Park is still viewed as a far-fetched idea, the establishment of protocols to i) synthesize long strands of DNA [1], ii) to transfect a microbial cell with a complete synthetic genome [1] and iii) to engineer /induce evolution in a genome in intelligent ways [2], have made whole genome engineering seem possible. At least in microbes, reconstructing entire genomes may not be very distant in the future.
In [2], researchers have prudently re-engineered the entire right arm of chromosome 9 in yeast. (They have also meddled a bit with chromosome 6.) I stress prudent re-engineering because the scientists did not merely synthesize a long strand of DNA without any major concern on the genes they are trying to pack. While i)they wanted their modified chromosomes to result in a (near) wild-type phenotype and fitness, they also made sure that ii) their newly synthesized chromosome arm lacked tRNA genes/transposons -- elements that are known to cause instabilities and also iii) hosted an evolutionary switch network based on the LoxP system that when turned on can result in a wide array of structural variations in the genomes (and hence phenotypes), which will be useful for future studies.
To check for constraint (i), the researchers observe the morphology and compare the transcript profiles between the wild type and the transformants. The Cre-LoxP system offers a general recombination toolkit that several experimental labs extensively exploit. In this work, the researchers, by integrating LoxP sites downstream of several non-essential genes, have used an inducible Cre-LoxP system to generate genomic structural variants. (They call this process "SCRaMbLE" :-D!).
If you are intrigued by the following question: "how does one selectively eliminate the right arm and incorporate the synthesized chromosome arm in its place?", I will not answer it here -- I will leave it for you to find out.
The authors' design constraints are intelligent. They have re-engineered ~92 MB of genomic sequence. A truly remarkable work!
~150 years ago, Mendel had the keenness to study heredity, associated "factors" as reasons behind his hybrid counts and genetics was born. Now, every undergraduate student in biology knows these factors are his principal toys. ~45 years ago, when restriction enzymes and DNA ligases were discovered, who would have envisioned a major work like this?
We are indeed witnessing a major transition in biotechnology - we will see large scale genome engineering projects soon. Such an advancement will transform biological studies fundamentally. It is truly invigorating to be involved in biological research in the 21st century!
References:
1. Gibson DG et al. (2010) Creation of a bacterial cell controlled by a chemically synthesized genome. Science 329:52-56. 2. Dymond JS et al. (2011) Synthetic chromosome arms function in yeast and generate phenotypic diversity by design. Nature 477:471-476.