Light on Genome Function

RESEARCH HIGHLIGHTS SENSORS AND PROBES Light on genome function Optogenetic tools enable light-mediated the light-sensitive domain Cryptochrome 2 Inactive epiLITE Histone effector domain control over transcription and epigenetic (CRY-2). The second component includes CRY2PHR states in specific endogenous loci of the CRY-2’s interacting partner, CIB1, fused to mammalian genome. an effector protein. Upon illumination with CIB1 Studying the roles of specific genes or gene blue light, CIB1 binds CRY-2 at the genomic Ac networks in cells is fundamental to biol- locus where CRY2-TALE is bound, allowing TALE ogy research. Gene expression is dynamic the effector protein to then exert positive or and tightly regulated; to understand it, one negative control over the gene. needs approaches that enable fine control of Zhang’s team designed LITEs that acti- Active epiLITE the process. Recently, a variety of microbe- vate gene transcription in several different 466 nm Ac or plant-derived light-sensitive proteins genomic loci. They could augment the lev- have been engineered that allow precise els of certain target genes by tenfold within modulation of biochemical and electrical just a few hours of turning a blue light on. signaling pathways in cells by ‘optogenetics’. Controlling the light intensity and illumi- Optogenetic tools have also been built that nation cycle, they could define the level of LITE-mediated epigenetic modifications. Image allow control of transgene expression with gene expression desired and ensure that courtesy of the Zhang lab members. the ease of a light switch, but up until now, the cells were healthy and happy under the it had not been possible to use light to turn spotlight. memories” as Zhang puts it, by controlling on or off the expression of endogenous genes One way in which gene expression can be specific genetic programs. or manipulate the epigenetic regulatory land- turned off is by introducing epigenetic modi- After a lot of hard work spent optimiz- scape in the genome. fications at the gene’s genomic locus. Based ing the system, Zhang and his team are now Feng Zhang, who runs a laboratory at the on this idea, Zhang and his team engineered eager to get to work on those experiments. © 2013 Nature America, Inc. All rights reserved. America, Inc. © 2013 Nature Broad Institute of Massachusetts Institute of LITE-based systems in which they fused In the initial version of LITEs, the team Technology and Harvard, was in a unique repressive histone effectors, such as histone observed relatively high basal induction of position to tackle this technological chal- deacetylases, to the CRY-2 protein and could gene expression even in the absence of light lenge. Zhang previously worked in the lab of repress gene transcription. The approach, and had to painstakingly go through many npg Karl Deisseroth at Stanford University and called ‘epiLITE’, opens the possibility of test- rounds of protein engineering to optimize used light-sensitive proteins from green algae ing the role that epigenetic modifications the system and avoid these unwanted effects. and other microbes to develop a toolbox for have in gene regulation, something that has Zhang acknowledges that this was all thanks controlling the activity of neurons in living been hard to do with existing methods. to the efforts of Silvana Konermann and organisms with light. Now with his own Researchers in Zhang’s lab are primarily Mark Brigham, the two first authors of the lab, he sought to expand optogenetics to the interested in using these tools to understand paper, who are Zhang’s first graduate stu- realm of genome engineering. brain physiology and pathology. In this ini- dents. Zhang and his colleagues developed a new tial work, they showed that LITEs can acti- The team has also started to think of other set of tools called ‘LITEs’, for light-inducible vate the expression of specific genes in the methods for DNA targeting. Zhang is par- transcriptional effectors. The LITE system brain of freely behaving mice. The possibil- ticularly interested in using RNA-guided is composed of two parts: one part serves ity of controlling gene expression programs nucleolytically inactive mutants of Cas9 as an anchor that binds a specific place in in living animals while they are engaged in instead of TALEs. “Cas9 has much higher the genome upstream of a gene one wishes specific behaviors enables all sorts of interest- ability to be used to target multiple loci at to control, and the other part contains an ing experiments. Zhang would like to start by once,” he points out, “so we envision being ‘effector’ molecule that has the capacity to studying the genes involved in learning and able to activate networks of genes rather than control whether gene transcription turns on memory. “We would like to alter the expres- a single gene in the near future.” or not. Critically, the two components come sion profile of genes involved in changing Erika Pastrana together only when illuminated with certain synaptic plasticity, to find out which ones are RESEARCH PAPERS wavelengths of light. important for memory consolidation and Konermann, S. et al. Optical control of mammalian LITE uses transcriptional activator-like learning,” he says. Eventually, this may lead endogenous transcription and epigenetic states. effectors (TALEs) as DNA anchors fused to to ways in which researchers can “write new Nature doi:10.1038/nature12466 (23 July 2013). NATURE METHODS | VOL.10 NO.9 | SEPTEMBER 2013 | 817.

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