Skip to main content Accessibility help
×
Hostname: page-component-8448b6f56d-qsmjn Total loading time: 0 Render date: 2024-04-23T08:56:42.777Z Has data issue: false hasContentIssue false

4 - Don’t Kill the Messenger: Employing Genome Editing to Study Regulatory RNA Interactions

from Part I - Biology of Endonucleases (Zinc-Finger Nuclease, TALENs and CRISPRs) and Regulatory Networks

Published online by Cambridge University Press:  30 July 2018

Krishnarao Appasani
Affiliation:
GeneExpression Systems, Inc.
Get access

Summary

Image of the first page of this content. For PDF version, please use the ‘Save PDF’ preceeding this image.'
Type
Chapter
Information
Genome Editing and Engineering
From TALENs, ZFNs and CRISPRs to Molecular Surgery
, pp. 52 - 68
Publisher: Cambridge University Press
Print publication year: 2018

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

Abudayyeh, OO, Gootenberg, JS, Konermann, S, et al. 2016. C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector. Science 353(6299): aaf5573CrossRefGoogle ScholarPubMed
Ala, U, Karreth, FA, Bosia, C, et al. 2013. Integrated transcriptional and competitive endogenous RNA networks are cross-regulated in permissive molecular environments. Proc Natl Acad Sci USA 110: 71547159.CrossRefGoogle ScholarPubMed
Armstrong, GA, Liao, M, You, Z, et al. 2016. Homology directed knockin of point mutations in the zebrafish tardbp and fus genes in ALS using the CRISPR/Cas9 system. PLoS One 11: e0150188.CrossRefGoogle ScholarPubMed
Bartel, DP. 2004. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116: 281297.CrossRefGoogle ScholarPubMed
Bartel, DP, Chen, CZ. 2004. Micromanagers of gene expression: the potentially widespread influence of metazoan microRNAs. Nat Rev Genet 5: 396400.CrossRefGoogle ScholarPubMed
Bibikova, M, Carroll, D, Segal, DJ, et al. 2001. Stimulation of homologous recombination through targeted cleavage by chimeric nucleases. Mol Cell Biol 21: 289297.CrossRefGoogle ScholarPubMed
Bikard, D, Jiang, W, Samai, P, et al. 2013. Programmable repression and activation of bacterial gene expression using an engineered CRISPR-Cas system. Nucleic Acids Res 41: 74297437.CrossRefGoogle ScholarPubMed
Bitinaite, J, Wah, DA, Aggarwal, AK, Schildkraut, I. 1998. FokI dimerization is required for DNA cleavage. Proc Natl Acad Sci USA 95: 1057010575.CrossRefGoogle ScholarPubMed
Boch, J. 2011. TALEs of genome targeting. Nat Biotechnol 29: 135136.CrossRefGoogle ScholarPubMed
Boch, J, Scholze, H, Schornack, S, et al. 2009. Breaking the code of DNA binding specificity of TAL-type III effectors. Science 326: 15091512.CrossRefGoogle ScholarPubMed
Bosson, AD, Zamudio, JR, Sharp, PA. 2014. Endogenous miRNA and target concentrations determine susceptibility to potential ceRNA competition. Mol Cell 56: 347359.CrossRefGoogle ScholarPubMed
Cade, L, Reyon, D, Hwang, WY, et al. 2012. Highly efficient generation of heritable zebrafish gene mutations using homo- and heterodimeric TALENs. Nucleic Acids Res 40: 80018010.CrossRefGoogle ScholarPubMed
Calin, GA, Croce, CM. 2006. MicroRNA signatures in human cancers. Nat Rev Cancer 6: 857866.CrossRefGoogle ScholarPubMed
Calin, GA, Dumitru, CD, Shimizu, M, et al. 2002. Frequent deletions and down-regulation of micro-RNA genes miR15 and miR16 at 13q14 in chronic lymphocytic leukemia. Proc Natl Acad Sci USA 99: 1552415529.CrossRefGoogle ScholarPubMed
Carlson, DF, Tan, W, Lillico, SG, et al. 2012. Efficient TALEN-mediated gene knockout in livestock. Proc Natl Acad Sci USA 109: 1738217387.CrossRefGoogle ScholarPubMed
Carninci, P, Kasukawa, T, Katayama, S, et al. 2005. The transcriptional landscape of the mammalian genome. Science 309: 15591563.CrossRefGoogle ScholarPubMed
Cech, TR, Steitz, JA. 2014. The noncoding RNA revolution-trashing old rules to forge new ones. Cell 157: 7794.CrossRefGoogle ScholarPubMed
Chen, B, Chen, X, Wu, X, et al. 2015. Disruption of microRNA-21 by TALEN leads to diminished cell transformation and increased expression of cell-environment interaction genes. Cancer Lett 356: 506516.CrossRefGoogle ScholarPubMed
Chiu, HS, Llobet-Navas, D, Yang, X, et al. 2015. Cupid: simultaneous reconstruction of microRNA-target and ceRNA networks. Genome Res 25: 257267.CrossRefGoogle ScholarPubMed
Christian, M, Cermak, T, Doyle, EL, et al. 2010. Targeting DNA double-strand breaks with TAL effector nucleases. Genetics 186: 757761.CrossRefGoogle ScholarPubMed
Cong, L, Ran, FA, Cox, D, et al. 2013. Multiplex genome engineering using CRISPR/Cas systems. Science 339: 819823.CrossRefGoogle ScholarPubMed
Djebali, S, Davis, CA, Merkel, A, et al. 2012. Landscape of transcription in human cells. Nature 489: 101108.CrossRefGoogle ScholarPubMed
Fedorov, Y, Anderson, EM, Birmingham, A, et al. 2006. Off-target effects by siRNA can induce toxic phenotype. RNA 12: 11881196.CrossRefGoogle ScholarPubMed
Fire, A, Xu, S, Montgomery, MK, et al. 1998. Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 391: 806811.CrossRefGoogle ScholarPubMed
Gilbert, LA, Larson, MH, Morsut, L, et al. 2013. CRISPR-mediated modular RNA-guided regulation of transcription in eukaryotes. Cell 154: 442451.CrossRefGoogle ScholarPubMed
Gupta, A, Christensen, RG, Rayla, AL, et al. 2012. An optimized two-finger archive for ZFN-mediated gene targeting. Nat Methods 9: 588590.CrossRefGoogle ScholarPubMed
Gutschner, T, Baas, M, Diederichs, S. 2011. Noncoding RNA gene silencing through genomic integration of RNA destabilizing elements using zinc finger nucleases. Genome Res 21: 19441954.CrossRefGoogle ScholarPubMed
Ha, M, Kim, VN. 2014. Regulation of microRNA biogenesis. Nat Rev Mol Cell Biol 15: 509524.CrossRefGoogle ScholarPubMed
Hansen, TB, Jensen, TI, Clausen, BH, et al. 2013. Natural RNA circles function as efficient microRNA sponges. Nature 495: 384388.CrossRefGoogle ScholarPubMed
Hausser, J, Syed, AP, Bilen, B, Zavolan, M. 2013. Analysis of CDS-located miRNA target sites suggests that they can effectively inhibit translation. Genome Res 23: 604615.CrossRefGoogle ScholarPubMed
Heintze, J, Luft, C, Ketteler, R. 2013. A CRISPR CASe for high-throughput silencing. Front Genet 4: 193.CrossRefGoogle ScholarPubMed
Hu, R, Wallace, J, Dahlem, TJ, Grunwald, DJ, O’Connell, RM. 2013. Targeting human microRNA genes using engineered Tal-effector nucleases (TALENs). PLoS One 8: e63074.CrossRefGoogle ScholarPubMed
Inui, M, Miyado, M, Igarashi, M, et al. 2014. Rapid generation of mouse models with defined point mutations by the CRISPR/Cas9 system. Sci Rep 4: 5396.CrossRefGoogle ScholarPubMed
Jinek, M, Chylinski, K, Fonfara, I, et al. 2012. A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science 337: 816821.CrossRefGoogle ScholarPubMed
Karreth, FA, Reschke, M, Ruocco, A, et al. 2015. The BRAF pseudogene functions as a competitive endogenous RNA and induces lymphoma in vivo. Cell 161: 319332.CrossRefGoogle Scholar
Karreth, FA, Tay, Y, Perna, D, et al. 2011. In vivo identification of tumor-suppressive PTEN ceRNAs in an oncogenic BRAF-induced mouse model of melanoma. Cell 147: 382395.CrossRefGoogle Scholar
Khan, AA, Betel, D, Miller, ML, et al. 2009. Transfection of small RNAs globally perturbs gene regulation by endogenous microRNAs. Nat Biotechnol 27: 549555.CrossRefGoogle ScholarPubMed
Kim, H, Kim, JS. 2014. A guide to genome engineering with programmable nucleases. Nat Rev Genet 15: 321334.CrossRefGoogle ScholarPubMed
Kim, JS, Lee, HJ, Carroll, D. 2010. Genome editing with modularly assembled zinc-finger nucleases. Nat Methods 7: 91; author reply 9192.CrossRefGoogle ScholarPubMed
Kim, Y, Kweon, J, Kim, JS. 2013a. TALENs and ZFNs are associated with different mutation signatures. Nat Methods 10: 185.CrossRefGoogle ScholarPubMed
Kim, YK, Wee, G, Park, J, et al. 2013b. TALEN-based knockout library for human microRNAs. Nat Struct Mol Biol 20: 14581464.CrossRefGoogle ScholarPubMed
Lee, RC, Feinbaum, RL, Ambros, V. 1993. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 75: 843854.CrossRefGoogle Scholar
Liu, XH, Sun, M, Nie, FQ, et al. 2014. Lnc RNA HOTAIR functions as a competing endogenous RNA to regulate HER2 expression by sponging miR-331-3p in gastric cancer. Mol Cancer 13: 92.CrossRefGoogle ScholarPubMed
Lu, M, Zhang, Q, Deng, M, et al. 2008. An analysis of human microRNA and disease associations. PLoS One 3: e3420.CrossRefGoogle ScholarPubMed
Maeder, ML, Thibodeau-Beganny, S, Osiak, A, et al. 2008. Rapid “open-source” engineering of customized zinc-finger nucleases for highly efficient gene modification. Mol Cell 31: 294301.CrossRefGoogle ScholarPubMed
Memczak, S, Jens, M, Elefsinioti, A, et al. 2013. Circular RNAs are a large class of animal RNAs with regulatory potency. Nature 495: 333338.CrossRefGoogle ScholarPubMed
Miranda, KC, Huynh, T, Tay, Y, et al. (2006). A pattern-based method for the identification of microRNA binding sites and their corresponding heteroduplexes. Cell 126: 12031217.CrossRefGoogle ScholarPubMed
Moehle, EA, Rock, JM, Lee, YL, et al. 2007. Targeted gene addition into a specified location in the human genome using designed zinc finger nucleases. Proc Natl Acad Sci USA 104: 30553060.CrossRefGoogle ScholarPubMed
Mojica, FJ, Diez-Villasenor, C, Garcia-Martinez, J, Soria, E. 2005. Intervening sequences of regularly spaced prokaryotic repeats derive from foreign genetic elements. J Mol Evol 60: 174182.CrossRefGoogle ScholarPubMed
Nelles, DA, Fang, MY, O’Connell, MR, et al. 2016. Programmable RNA tracking in live cells with CRISPR/Cas9. Cell 165: 488496.CrossRefGoogle ScholarPubMed
O’Connell, MR, Oakes, BL, Sternberg, SH, et al. 2014. Programmable RNA recognition and cleavage by CRISPR/Cas9. Nature 516: 263266.CrossRefGoogle ScholarPubMed
Orlando, SJ, Santiago, Y, Dekelver, RC, et al. 2010. Zinc-finger nuclease-driven targeted integration into mammalian genomes using donors with limited chromosomal homology. Nucleic Acids Res 38: e152.CrossRefGoogle ScholarPubMed
Orom, UA, Nielsen, FC, Lund, AH. 2008. MicroRNA-10a binds the 5’UTR of ribosomal protein mRNAs and enhances their translation. Mol Cell 30: 460471.CrossRefGoogle Scholar
Plaisier, CL, Pan, M, Baliga, NS. 2012. A miRNA-regulatory network explains how dysregulated miRNAs perturb oncogenic processes across diverse cancers. Genome Res 22: 23022314.CrossRefGoogle ScholarPubMed
Poliseno, L, Salmena, L, Zhang, J, et al. 2010. A coding-independent function of gene and pseudogene mRNAs regulates tumour biology. Nature 465: 10331038.CrossRefGoogle ScholarPubMed
Qi, LS, Larson, MH, Gilbert, LA, et al. 2013. Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. Cell 152: 11731183.CrossRefGoogle ScholarPubMed
Reyon, D, Tsai, SQ, Khayter, C, et al. 2012. FLASH assembly of TALENs for high-throughput genome editing. Nat Biotechnol 30: 460465.CrossRefGoogle ScholarPubMed
Salmena, L, Poliseno, L, Tay, Y, Kats, L, Pandolfi, PP. 2011. A ceRNA hypothesis: the Rosetta Stone of a hidden RNA language? Cell 146: 353358.CrossRefGoogle ScholarPubMed
Santiago, Y, Chan, E, Liu, PQ, et al. 2008. Targeted gene knockout in mammalian cells by using engineered zinc-finger nucleases. Proc Natl Acad Sci USA 105: 58095814.CrossRefGoogle ScholarPubMed
Shechner, DM, Hacisuleyman, E, Younger, ST, Rinn, JL. 2015. Multiplexable, locus-specific targeting of long RNAs with CRISPR-Display. Nat Methods 12: 664670.CrossRefGoogle ScholarPubMed
Sumazin, P, Yang, X, Chiu, HS, et al. 2011. An extensive microRNA-mediated network of RNA-RNA interactions regulates established oncogenic pathways in glioblastoma. Cell 147: 370381.CrossRefGoogle ScholarPubMed
Takada, S, Sato, T, Ito, Y, et al. 2013. Targeted gene deletion of miRNAs in mice by TALEN system. PLoS One 8: e76004.CrossRefGoogle ScholarPubMed
Tay, Y, Kats, L, Salmena, L, et al. 2011. Coding-independent regulation of the tumor suppressor PTEN by competing endogenous mRNAs. Cell 147: 344357.CrossRefGoogle ScholarPubMed
Tay, Y, Rinn, J, Pandolfi, PP. 2014. The multilayered complexity of ceRNA crosstalk and competition. Nature 505: 344352.CrossRefGoogle ScholarPubMed
Uhde-Stone, C, Sarkar, N, Antes, T, et al. 2014. A TALEN-based strategy for efficient bi-allelic miRNA ablation in human cells. RNA 20: 948955.CrossRefGoogle ScholarPubMed
Urnov, FD, Miller, JC, Lee, YL, et al. 2005. Highly efficient endogenous human gene correction using designed zinc-finger nucleases. Nature 435: 646651.CrossRefGoogle ScholarPubMed
Wang, J, Liu, X, Wu, H, et al. 2010. CREB up-regulates long non-coding RNA, HULC expression through interaction with microRNA-372 in liver cancer. Nucleic Acids Res 38: 53665383.CrossRefGoogle ScholarPubMed
Wightman, B, Ha, I, Ruvkun, G. 1993. Posttranscriptional regulation of the heterochronic gene lin-14 by lin-4 mediates temporal pattern formation in C. elegans. Cell 75: 855862.CrossRefGoogle ScholarPubMed
Wyman, C, Kanaar, R. 2006. DNA double-strand break repair: all’s well that ends well. Annu Rev Genet 40: 363383.CrossRefGoogle ScholarPubMed
Xiao, H, Tang, K, Liu, P, et al. 2015. LncRNA MALAT1 functions as a competing endogenous RNA to regulate ZEB2 expression by sponging miR-200s in clear cell kidney carcinoma. Oncotarget 6: 3800538015.CrossRefGoogle ScholarPubMed
Zalatan, JG, Lee, ME, Almeida, R, et al. 2015. Engineering complex synthetic transcriptional programs with CRISPR RNA scaffolds. Cell 160: 339350.CrossRefGoogle ScholarPubMed

Save book to Kindle

To save this book to your Kindle, first ensure coreplatform@cambridge.org is added to your Approved Personal Document E-mail List under your Personal Document Settings on the Manage Your Content and Devices page of your Amazon account. Then enter the ‘name’ part of your Kindle email address below. Find out more about saving to your Kindle.

Note you can select to save to either the @free.kindle.com or @kindle.com variations. ‘@free.kindle.com’ emails are free but can only be saved to your device when it is connected to wi-fi. ‘@kindle.com’ emails can be delivered even when you are not connected to wi-fi, but note that service fees apply.

Find out more about the Kindle Personal Document Service.

Available formats
×

Save book to Dropbox

To save content items to your account, please confirm that you agree to abide by our usage policies. If this is the first time you use this feature, you will be asked to authorise Cambridge Core to connect with your account. Find out more about saving content to Dropbox.

Available formats
×

Save book to Google Drive

To save content items to your account, please confirm that you agree to abide by our usage policies. If this is the first time you use this feature, you will be asked to authorise Cambridge Core to connect with your account. Find out more about saving content to Google Drive.

Available formats
×