Abstract
The ability to predict phenotype from genotype has been an elusive goal for the biological sciences for several decades. Progress decoding genotype–phenotype relationships has been hampered by the challenge of introducing precise genetic changes to specific genomic locations. Here we provide a comparative review of the major techniques that have been historically used to make genetic changes in cells as well as the development of the CRISPR technology which enabled the ability to make marker-free disruptions in endogenous genomic locations. We also discuss how the achievement of truly scarless genome editing has required further adjustments of the original CRISPR method. We conclude by examining recently developed genome editing methods which are not reliant on the induction of a DNA double strand break and discuss the future of both genome engineering and the study of genotype–phenotype relationships.
Similar content being viewed by others
References
Andrianantoandro E, Basu S, Karig DK, Weiss R (2006) Synthetic biology: new engineering rules for an emerging discipline. Mol Syst Biol 2:0028, https://doi.org/10.1038/msb4100073 (2006)
Arnold FH (1993) Engineering proteins for nonnatural environments. FASEB J 7:744–749
Barbieri EM, Muir P, Akhuetie-Oni BO, Yellman CM, Isaacs FJ (2017) Precise editing at DNA replication forks enables multiplex genome engineering in Eukaryotes. Cell 171(e1413):1453–1467. https://doi.org/10.1016/j.cell.2017.10.034
Barrangou R et al (2007) CRISPR provides acquired resistance against viruses in prokaryotes. Science 315:1709–1712. https://doi.org/10.1126/science.1138140
Benoist C, Chambon P (1981) In vivo sequence requirements of the SV40 early promotor region. Nature 290:304–310
Bibikova M, Beumer K, Trautman JK, Carroll D (2003) Enhancing gene targeting with designed zinc finger nucleases. Science 300:764. https://doi.org/10.1126/science.1079512
Boeke JD, Trueheart J, Natsoulis G, Fink GR (1987) 5-Fluoroorotic acid as a selective agent in yeast molecular genetics. Methods Enzymol 154:164–175
BRAM RJ, KORNBERG RD (1985) Specific protein binding to far upstream activating sequences in polymerase II promoters. Proc Natl Acad Sci USA 82:43–47
Brouns SJ et al (2008) Small CRISPR RNAs guide antiviral defense in prokaryotes. Science 321:960–964. https://doi.org/10.1126/science.1159689
Bush WS, Oetjens MT, Crawford DC (2016) Unravelling the human genome-phenome relationship using phenome-wide association studies. Nat Rev Genet 17:129–145. https://doi.org/10.1038/nrg.2015.36
Carey LB, van Dijk D, Sloot PM, Kaandorp JA, Segal E (2013) Promoter sequence determines the relationship between expression level and noise. PLoS Biol 11:e1001528. https://doi.org/10.1371/journal.pbio.1001528
Christian, M et al (2010) Targeting DNA double-strand breaks with TAL effector nucleases. Genetics 186:757–761. https://doi.org/10.1534/genetics.110.120717
Collinge DB, Lund OS, Thordal-Christensen H (2008) What are the prospects for genetically engineered, disease resistant plants? Eur J Plant Pathol 121:217–231. https://doi.org/10.1007/s10658-007-9229-2
DiCarlo JE et al (2013) Genome engineering in Saccharomyces cerevisiae using CRISPR-Cas systems. Nucleic Acids Res 41:4336–4343. https://doi.org/10.1093/nar/gkt135
Dill KA, MacCallum JL (2012) The protein-folding problem, 50 years on. Science 338:1042–1046
DOUGLAS HC, CONDIE F (1954) The genetic control of galactose utilization in Saccharomyces. J Bacteriol 68:662–670
Elison GL, Song R, Acar MA (2017) Precise genome editing method reveals insights into the activity of eukaryotic promoters. Cell Rep 18:275–286. https://doi.org/10.1016/j.celrep.2016.12.014
Elledge SJ, Davis RW (1988) A family of versatile centromeric vectors designed for use in the sectoring-shuffle mutagenesis assay in Saccharomyces cerevisiae. Gene 70:303–312
Fraser PD, Enfissi EM, Bramley PM (2009) Genetic engineering of carotenoid formation in tomato fruit and the potential application of systems and synthetic biology approaches. Arch Biochem Biophys 483:196–204. https://doi.org/10.1016/j.abb.2008.10.009
Fridman Y et al (2010) Subtle alterations in PCNA-partner interactions severely impair DNA replication and repair. PLoS Biol 8:e1000507. https://doi.org/10.1371/journal.pbio.1000507
Friedmann T, Roblin R (1972) Gene therapy for human genetic disease? Science 175:949–955
Gasiunas G, Barrangou R, Horvath P, Siksnys V (2012) Cas9-crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria. Proc Natl Acad Sci USA 109:E2579-2586. https://doi.org/10.1073/pnas.1208507109
Hirschhorn JN, Lohmueller K, Byrne E, Hirschhorn K (2002) A comprehensive review of genetic association studies. Genet Med 4:45–61
Horwitz AA et al (2015) Efficient multiplexed integration of synergistic alleles and metabolic pathways in yeasts via CRISPR-Cas. Cell Syst 1:88–96. https://doi.org/10.1016/j.cels.2015.02.001
Hruscha A et al (2013) Efficient CRISPR/Cas9 genome editing with low off-target effects in zebrafish. Development 140:4982–4987. https://doi.org/10.1242/dev.099085
Jiang W, Bikard D, Cox D, Zhang F, Marraffini LA (2013) RNA-guided editing of bacterial genomes using CRISPR-Cas systems. Nat Biotechnol 31:233–239. https://doi.org/10.1038/nbt.2508
Jinek M et al (2012) A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 337:816–821. https://doi.org/10.1126/science.1225829
Johnston M, Davis RW (1984) Sequences that regulate the divergent GALJ-GALIO promoter in Saccharomyces cerevisiae. Mol Cell Biol 4:1440–1448
Joung JK, Sander JD (2013) TALENs: a widely applicable technology for targeted genome editing. Nat Rev Mol Cell Biol 14:49–55. https://doi.org/10.1038/nrm3486
Komor AC, Kim YB, Packer MS, Zuris JA, Liu DR (2016) Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage. Nature 533:420–424. https://doi.org/10.1038/nature17946
Li-En Jao SRW (2013) and Wenbiao Chen efficient multiplex biallelic zebrafish genome editing using a CRISPR nuclease system. Proc Natl Acad Sci USA 110:13904–13908
Mali P et al (2013) RNA-guided human genome engineering via Cas9. Science 339:823–826. https://doi.org/10.1126/science.1232033
Mans R et al (2015) CRISPR/Cas9: a molecular Swiss army knife for simultaneous introduction of multiple genetic modifications in Saccharomyces cerevisiae. FEMS Yeast Res 15:1–15. https://doi.org/10.1093/femsyr/fov004
Miller HI (2015) Germline gene therapy: we’re ready. Science 348:1325. https://doi.org/10.1126/science
Miller JC et al (2007) An improved zinc-finger nuclease architecture for highly specific genome editing. Nat Biotechnol 25:778–785. https://doi.org/10.1038/nbt1319
Mukherji S, van Oudenaarden A (2009) Synthetic biology: understanding biological design from synthetic circuits. Nat Rev Genet 10:859–871. https://doi.org/10.1038/nrg2697
Myers RM, Tilly K, Maniatis T (1986) Fine structure genetic analysis of a,I-G1obin promoter. Science 232:613–618
Myers RM, Lerman LS, Maniatis T (1985) A general method for saturation mutagenesis of cloned DNA fragments. Science 229:242–247
Naldini L (2015) Gene therapy returns to centre stage. Nature 526:351–360. https://doi.org/10.1038/nature15818
Packer MS, Liu DR (2015) Methods for the directed evolution of proteins. Nat Rev Genet 16:379–394. https://doi.org/10.1038/nrg3927
Purnick PE, Weiss R (2009) The second wave of synthetic biology: from modules to systems. Nat Rev Mol Cell Biol 10:410–422. https://doi.org/10.1038/nrm2698
Qi LS et al (2013) Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. Cell 152:1173–1183. https://doi.org/10.1016/j.cell.2013.02.022
Renata H, Wang ZJ, Arnold FH (2015) Expanding the enzyme universe: accessing non-natural reactions by mechanism-guided directed evolution. Angew Chem 54:3351–3367. https://doi.org/10.1002/anie.201409470
Ritchie MD, Holzinger ER, Li R, Pendergrass SA, Kim D (2015) Methods of integrating data to uncover genotype–phenotype interactions. Nat Rev Genet 16:85–97. https://doi.org/10.1038/nrg3868
Ryan OW et al (2014) Selection of chromosomal DNA libraries using a multiplex CRISPR system. eLife 3:e03703. https://doi.org/10.7554/eLife.03703
Ryan OW, Poddar S, Cate JH (2016) CRISPR-Cas9 genome engineering in Saccharomyces cerevisiae Cells. Cold Spring Harbor protocols 2016:525–533. https://doi.org/10.1101/pdb.prot086827
SCHERER S, DAVIS RW (1979) Replacement of chromosome segments with altered DNA sequences constructed in vitro. Proc Natl Acad Sci USA 76:4951–4955
Shao Z, Arnold FH (1996) Engineering new functions and altering existing functions. Curr Opin Struct Biol 6:513–518
Sharon E et al (2012) Inferring gene regulatory logic from high-throughput measurements of thousands of systematically designed promoters. Nat Biotechnol 30:521–530. https://doi.org/10.1038/nbt.2205
Sharon E et al (2014) Probing the effect of promoters on noise in gene expression using thousands of designed sequences. Genome Res 24:1698–1706. https://doi.org/10.1101/gr.168773.113
Sittig LJ et al (2016) Genetic background limits generalizability of genotype–phenotype relationships. Neuron 91:1253–1259. https://doi.org/10.1016/j.neuron.2016.08.013
Smith J et al (2000) Requirements for double-strand cleavage by chimeric restriction enzymes with zinc finger DNA-recognition domains. Nucleic Acids Res 28:3361–3369
Soreanu I, Hendler A, Dahan D, Dovrat D, Aharoni A (2018) Marker-free genetic manipulations in yeast using CRISPR/CAS9 system. Curr Genet. https://doi.org/10.1007/s00294-018-0831-y
Stemmer M, Thumberger T, Del Sol Keyer M, Wittbrodt J, Mateo JL, CCTop (2015) An intuitive, flexible and reliable CRISPR/Cas9 target prediction tool. PloS One 10:e0124633. https://doi.org/10.1371/journal.pone.0124633
Taft RJ, Pheasant M, Mattick JS (2007) The relationship between non-protein-coding DNA and eukaryotic complexity. BioEssays News Rev Mol Cell Dev Biol 29:288–299. https://doi.org/10.1002/bies.20544
Urnov FD, Rebar EJ, Holmes MC, Zhang HS, Gregory PD (2010) Genome editing with engineered zinc finger nucleases. Nat Rev Genet 11:636–646. https://doi.org/10.1038/nrg2842
Vaschetto LM (2018) Modulating signaling networks by CRISPR/Cas9-mediated transposable element insertion. Curr Genet 64:405–412. https://doi.org/10.1007/s00294-017-0765-9
Wang HH et al (2009) Programming cells by multiplex genome engineering and accelerated evolution. Nature 460:894–898. https://doi.org/10.1038/nature08187
Wang T, Wei JJ, Sabatini DM, Lander ES (2014) Genetic screens in human cells using the CRISPR-Cas9 system. Science 343:80–84. https://doi.org/10.1126/science.1246981
Weinhandl K, Winkler M, Glieder A, Camattari A (2014) Carbon source dependent promoters in yeasts. Microb Cell Fact 13:1–17
Funding
GLE was in part supported by the National Institute of Health T32 GM007499.
Author information
Authors and Affiliations
Corresponding author
Additional information
Communicated by M. Kupiec.
Glossary
- Directed Evolution
-
A process in which a specific DNA element (often an open reading frame or enzymatic binding site on a protein) is mutagenized to create a large library. This library is then put through a specific in vitro screening process, generally for multiple rounds, to identify mutations which give rise to a desired effect on the assayed activity or function
- DNA Binding Motif
-
A region of a protein which is capable of binding to a specific DNA sequence
- Donor Template
-
An (often) short piece of DNA containing desired DNA edits flanked by regions homologous to the region to be edited. Cells may use it as a repair template during homologous -recombination based DNA-repair mechanism
- Double Strand Break
-
A type of DNA damage in which both strands have been severed in close proximity to each other. This results in the creation of two distinct strands from the original
- Endogenous DNA
-
The native DNA of a cell
- Genome Editing
-
The process of intentionally altering (adding, removing, or changing) the genome of a cell
- Genome Scarring
-
The introduction of unwanted or unintended edits to cellular DNA during genome editing
- Genotype
-
The DNA composition of a genomic region or of the entire genome
- Homologous recombination based DNA repair
-
A type of DNA damage repair mechanism in which the cell uses a homologous region to the one which has been cut as a template to repair the cut strand. During natural repair, this template is generally the sister chromosome of the one being cut, but during genome editing this template is generally synthetic DNA introduced to the cell for this purpose
- Mutagenesis
-
The process of inducing random mutations to a piece of DNA or to an entire genome. Historically this has been done using radiation or mutagenic chemicals. A mutagenized stretch of DNA will contain a number of random mutations of all types
- Nuclease
-
A protein which is capable of inducing a DNA double strand break
- Phenotype
-
A behavior of a cell which is observable to a researcher
- Plasmid-based expression system
-
A means of gene expression in which the gene of interest is placed into a non-integrating plasmid and transformed into a cell
Rights and permissions
About this article
Cite this article
Elison, G.L., Acar, M. Scarless genome editing: progress towards understanding genotype–phenotype relationships. Curr Genet 64, 1229–1238 (2018). https://doi.org/10.1007/s00294-018-0850-8
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00294-018-0850-8