The Power of Cas

Precise engineering of the genomes of higher eukaryotes can enable a variety of biological and medical applications. Targeted gene disruption, editing, and insertion can translate into the much desired freedom to generate cells or organisms bearing a desired genetic change. Recent developments in the stem cell field have created even more excitement for genetically modifying genomes because it enables delivering more beneficial stem cell-derived therapeutic cells to patients. For instance, by correcting a gene mutation known to be critical to Parkinson’s disease, LRRK2 G2019S, in patient-specific iPSCs (induced pluripotent stem cells), researchers were able to rescue neurodegenerative phenotypes [1].

Cumbersome reagent development and high costs have been major barriers to targeted genome modification using the current technologies, which include the zinc finger nuclease (ZFN) and transcription activator-like effector nuclease (TALEN). Unlike the ZFN and TALEN systems, CRISPR/cas does not require assembly of DNA pieces that encode the functional proteins every time a new sequence is to be targeted. Instead, it uses a guide RNA to direct the traffic of a nuclease complex. Five recent publications of modifying eukaryotic chromosomes showed the importance of the CRISPR/cas system [2-6], they also hinted at the ease of adapting this system in eukaryotes given that the functions of cas and the small guide RNA were described in bacteria merely few months ago [7].

The concern that the bacterial CRISPR/cas system would not access the chromatin structures of eukaryotic genome was muted as a result of recent publications; it also seems that the cas9 protein is as powerful an enzyme as one could have hoped in an endonuclease. As a matter of fact, cas9 from S. pyogenes contains 2 different single-stranded DNAse domains independent of each other, and can be mutated to change from a double-stranded DNA endonuclease to a single-strand cutter, or a non-cutting block. That’s not all, a more recent Nature publication further showed that cas9 (from another species, F. novicida), can bind to yet another small RNA and, instead of cutting chromosomal DNA, it degrades RNA, apparently through a direct cas9/RNA binding mechanism [8]. It may be chromosomal modification and RNAi rolled in one (cas9 from different genera are quite different though). One has to admire the powerful cas!

1. Reinhardt, P., et al., Genetic Correction of a LRRK2 Mutation in Human iPSCs Links Parkinsonian Neurodegeneration to ERK-Dependent Changes in Gene Expression. Cell Stem Cell, 2013. 12(3): p. 354-67.
2. Qi, L.S., et al., Repurposing CRISPR as an RNA-Guided Platform for Sequence-Specific Control of Gene Expression. Cell, 2013. 152(5): p. 1173-83.
3. Mali, P., et al., RNA-guided human genome engineering via Cas9. Science, 2013. 339(6121): p. 823-6.
4. Cong, L., et al., Multiplex genome engineering using CRISPR/Cas systems. Science, 2013. 339(6121): p. 819-23.
5. Cho, S.W., S. Kim, J.M. Kim, and J.S. Kim, Targeted genome engineering in human cells with the Cas9 RNA-guided endonuclease. Nat Biotechnol, 2013. 31(3): p. 230-2.
6. Hwang, W.Y., et al., Efficient genome editing in zebrafish using a CRISPR-Cas system. Nat Biotechnol, 2013. 31(3): p. 227-9.
7. Jinek, M., et al., A Programmable Dual-RNA-Guided DNA Endonuclease in Adaptive Bacterial Immunity. Science, 2012.
8. Sampson, T.R., et al., A CRISPR/Cas system mediates bacterial innate immune evasion and virulence. Nature, 2013.

Tags: cas9, choromsome modification, CRISPR/cas, F. novicida, genome engineering, nuclease, RNA interference, RNAi, S. pyogenes, TALE, TALEN, ZFN

Making Transfection-Grade mRNA by IVT (In Vitro Transcription)

RNases are an often feared in molecular biology labs because of their high stability and ominous presence in virtually all living systems. Consequently, people who work with RNA are trained to exercise extreme caution to avoid RNA degradation: change gloves often because human hands ooze RNases; use only sterilized labware as microbes may be sources of RNases; for surfaces that can’t be autoclaved, use sprays like “RNase Zap” (SDS- or guanidine-containing solutions). Such cautionary steps are especially necessary when dealing with low abundance RNA samples.

RNAs can be produced by in vitro transcription (IVT), a simple reaction requiring only a DNA template (double-stranded or even single-stranded DNA as long as the promoter region is double-stranded), RNA polymerase (from T7, SP6, or T3 phage), NTPs, and a reaction buffer that provides appropriate salt and pH. Standard NTPs may be replaced with modified ones to either increase stability or to reduce immune-response when transfected into cultured cells. Additionally, a 5’ cap structure may be added during IVT for further stabilizing mRNAs inside the cells post transfection. Using a commercially assembled kit, one can routinely produce 40-50 µg of mRNA from 1 µg of DNA template in a single 20-50 µl reaction.

At such high concentrations, IVT mRNAs are not nearly as sensitive to RNase-mediated degradation as low-abundance samples. The mRNA can be easily observed on agarose gels that are regularly used for DNA, and their integrity can be monitored after transcription or storage. In most cases one distinct band of mRNA from an IVT reaction is obtained as long as a clean DNA template is used. Preparing a good, uniform IVT template is critical to prevent aberrant products. By using high quality templates, IVT mRNA produced in your own lab are often higher in quality than mRNAs purchased from current commercial sources (Figure in Blog shows mRNAs generated by IVT for R-iPSC). Sometimes there are minor bands created during IVT, but they normally do not interfere with the intended uses of the mRNA, and can be purified away with a purification kit (by using a discriminating purification scheme such as Allele Biotech’s Surface Bind RNA Purification, smaller species can be specifically removed, a separate topic for another blog).

Once produced, mRNAs can be stored at -20C for months, or -80C nearly indefinitely.

mRNAs generated by IVT for R-iPSC

Tags: fluorescent protein, iPS, IVT, luciferase, mRNA, nuclease, recombinase, RiPSCs, RNA degradation, RNase, TALEN

Legoland TALES of Binding DNA by Design

Imagine that you could have a protein that binds to a sequence in a chromosome where you want to activate transcription, nick or break DNA to target insertion or recombination, or create a DNA lesion for screening DNA repair pathway factors…imagine that you could build such proteins very much like putting together legos. Yes, it is possible based on findings about transcription activator-like effector (TALE) proteins. These are plant pathogen transcription factors naturally used to facilitate invasion of host species which have been rekindled to direct DNA binding in other species (1, 2).

Previously, zinc-finger nucleases (ZFNs) have been the focus of genomic modification tool development, but with only limited success. It is not easy to design or select a ZFN using available technologies. In comparison, TALEs have a modular 34 amino acid domain as a basic unit that recognizes a DNA base, with specificity mostly determined by residues 12 and 13. In other words, by using as few as 4 modules with dedicated diamino acids 12 and 13, one can create a protein that binds any DNA sequence.

However, it is not necessarily an easy construct to make because the highly repetitive sequence of TALEs causes plasmid instability during cloning. A team at Harvard recently published a method of minimizing repetitiveness and allowing step-wise ligation; (3). Other aspects of using TALEs involve the designing of an effector domain, e.g. DNAase or transcription activation domain, and packaging the “warhead” in a delivery vehicle such as a lentivirus. The unfolding of the TALEs is just starting, the future seems exciting.

1. J. Boch et al. Science 326, 1509 (2009); published online 29 October 2009
2. M. J. Moscou, and A. J. Bogdanove, Science 326, 1501 (2009)
3. Zhang, F. et al. Efficient construction of sequence-specific TAL effectors for modulating mammalian transcription. Nat. Biotechnol. 29, 149–153 (2011).

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Tags: DNA binding, DNA repari, homologues recombination, modular, nuclease, TALE, TALEs, transcription activator, ZFN, ZFNs