Zebrafish Reverse Genetics

Zebrafish have proven to be a powerful genetic tool over the years, primarily through forward genetic screens where fish are mutagenized (typically with chemical agent) and screened for obvious defects. In recent years, our lab has seen this technique become a reality. Using targeted DNA disruption, we have made designer mutations in specific genes of interest. Here are some papers describing three different processes.

RNA guided nuclease (CRISPR)-/CRISPR-associted (Cas)

Hwang et al, Nat Biotech. 2013 Jan 29

Transcription activator-like effector nucleases (TALENs)

Cade et al, Nucleic Acids Res. 2012 Jun 7
Sander et al, Nat Biotechnol. 2011 Aug 5;29(8):697-8

Zinc-finger nucleases (ZFNs)

Sander et al, Nat Methods. 2011 Jan;8(1):67-9
Foley et al, PLoS One. 2009;4(2):e4348
Foley et al, Nat Protoc. 2009;4(12):1855-67





3-D Genetics 

The emergence of Next-Generation Sequencing technologies has significantly advanced our ability to read the information encoded in genomes. However, the chromatin in the nucleus is not simply a linear strand of DNA, but a tightly packed structure in 3-D space. The spatial folding of chromosomes in the nucleus has profound effects on its ability to control the dynamics of gene expression. In the Peterson lab, we are developing novel methods to map chromatin interactions in 3-D space and assess the functional impacts of such interactions using the latest genome engineering techniques.

Parvez S., J Am Chem Soc 2018


Optogenetics is a biological technique which involves the use of light to control cells, typically neurons, in living tissue that have been genetically engineered to express certain light-sensitive ion channels. It has become such a powerful and effective research tool because it enables specific and high-resolution optical control of neuronal activity. In the Peterson lab, we've identified a small molecule, known as Optovin, which enables repeated photo-activation of wild-type zebra fish. Miraculously, in animals with severed spinal cords, Optovin treatment activates neuronal pathways which enable control of motor activity in the paralyzed extremities by localized illumination.

Pui Ying Lam et al., Pub Med, 2017

Kokel et al., Nature Chemical Biology, 2013

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