Skip to main content Accessibility help

We use cookies to distinguish you from other users and to provide you with a better experience on our websites. Close this message to accept cookies or find out how to manage your cookie settings.

Close cookie message
×
Hostname: page-component-76fb5796d-45l2p Total loading time: 0 Render date: 2024-04-26T19:46:32.669Z Has data issue: false hasContentIssue false

24 - Manipulation of Long Non-coding RNAs in Cardiovascular Disease Using Genome Editing Technology

from Part V - Genome Editing in Disease Biology

Published online by Cambridge University Press:  30 July 2018

By
Stefan Haemmig  and
Mark W. Feinberg
Edited by
Krishnarao Appasani
Foreword by
George M. Church
Krishnarao Appasani
Affiliation:
GeneExpression Systems, Inc.
Get access

Summary

A summary is not available for this content so a preview has been provided. Please use the Get access link above for information on how to access this content.
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. 371 - 388
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

Anderson, DM, Anderson, KM, Chang, CL, et al. 2015. A micropeptide encoded by a putative long noncoding RNA regulates muscle performance. Cell 160(4): 595–606.CrossRefGoogle ScholarPubMed
Andrews, SJ, Rothnagel, JA. 2014. Emerging evidence for functional peptides encoded by short open reading frames. Nat Rev Genet 15(3): 193–204.CrossRefGoogle ScholarPubMed
Aparicio-Prat, E, Arnan, C, Sala, I, et al. 2015. DECKO: single-oligo, dual-CRISPR deletion of genomic elements including long non-coding RNAs. BMC Genomics 16(1): 846.CrossRefGoogle ScholarPubMed
Bartel, DP. 2004. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116(2): 281–297.CrossRefGoogle ScholarPubMed
Bassett, AR, Akhtar, A, Barlow, DP, et al. 2014. Considerations when investigating lncRNA function in vivo. eLife 3: e03058.CrossRefGoogle ScholarPubMed
Bond, AM, Vangompel, MJ, Sametsky, EA, et al. 2009. Balanced gene regulation by an embryonic brain ncRNA is critical for adult hippocampal GABA circuitry. Nat Neurosci 12(8): 1020–1027.CrossRefGoogle ScholarPubMed
Bondue, A, Lapouge, G, Paulissen, C, et al. 2008. Mesp1 acts as a master regulator of multipotent cardiovascular progenitor specification. Cell Stem Cell 3(1): 69–84.CrossRefGoogle ScholarPubMed
Bu, D, Yu, K, Sun, S, et al. 2012. NONCODE v3.0: integrative annotation of long noncoding RNAs. Nucleic Acids Res 40(Database issue): D210–D215.CrossRefGoogle ScholarPubMed
Canver, MC, Bauer, DE, Dass, A, et al. 2014. Characterization of genomic deletion efficiency mediated by clustered regularly interspaced palindromic repeats (CRISPR)/Cas9 nuclease system in mammalian cells. J Biol Chem 289(31): 21312–21324.CrossRefGoogle ScholarPubMed
Chu, C, Qu, K, Zhong, FL, Artandi, SE, Chang, HY. 2011. Genomic maps of long noncoding RNA occupancy reveal principles of RNA-chromatin interactions. Mol Cell 44(4): 667–678.CrossRefGoogle ScholarPubMed
Congrains, A, Kamide, K, Oguro, R, et al. 2012. Genetic variants at the 9p21 locus contribute to atherosclerosis through modulation of ANRIL and CDKN2A/B. Atherosclerosis 220(2): 449–455.CrossRefGoogle ScholarPubMed
da Rocha, ST, Edwards, CA, Ito, M, Ogata, T, Ferguson-Smith, AC. 2008. Genomic imprinting at the mammalian Dlk1-Dio3 domain. Trends Genet 24(6): 306–316.CrossRefGoogle ScholarPubMed
Djebali, S, Davis, CA, Merkel, A, et al. 2012. Landscape of transcription in human cells. Nature 489(7414): 101–108.CrossRefGoogle ScholarPubMed
Engreitz, JM, Pandya-Jones, A, McDonel, P, et al. 2013. The Xist lncRNA exploits three-dimensional genome architecture to spread across the X chromosome. Science 341(6147): 1237973–1237973.CrossRefGoogle ScholarPubMed
Engreitz, JM, Sirokman, K, McDonel, P, et al. 2014. RNA-RNA interactions enable specific targeting of noncoding RNAs to nascent pre-mRNAs and chromatin sites. Cell 159(1): 188–199.CrossRefGoogle ScholarPubMed
Farazi, TA, Hoell, JI, Morozov, P, Tischl, T. 2013. MicroRNAs in human cancer. In MicroRNA Cancer Regulation, Schmitz, U, Wolkenhauer, O, Vera, J, eds., Dordrecht, the Netherlands: Springer, pp. 1–20.Google Scholar
Feng, Y, Hu, X, Zhang, Y, et al. 2014. Methods for the study of long noncoding RNA in cancer cell signaling. Methods Mol Biol 1165: 115–143.CrossRefGoogle Scholar
Gagnon, KT, Li, L, Chu, Y, et al. 2014. RNAi factors are present and active in human cell nuclei. Cell Rep 6(1): 211–221.CrossRefGoogle ScholarPubMed
Gilbert, C, Svejstrup, JQ. 2006. RNA immunoprecipitation for determining RNA-protein associations in vivo. Curr Protoc Mol Biology Chapter 27: Unit 27.4.CrossRefGoogle Scholar
Gilbert, LA, Larson, MH, Morsut, L, et al. 2013. CRISPR-mediated modular RNA-guided regulation of transcription in eukaryotes. Cell 154(2): 442–451.CrossRefGoogle ScholarPubMed
Goff, LA, Rinn, JL. 2015. Linking RNA biology to lncRNAs. Genome Res 25(10): 1456–1465.CrossRefGoogle ScholarPubMed
Grote, P, Wittler, L, Hendrix, D, et al. 2013. The tissue-specific lncRNA Fendrr is an essential regulator of heart and body wall development in the mouse. Dev Cell 24(2): 206–214.CrossRefGoogle ScholarPubMed
Gutschner, T. 2015. Silencing long noncoding RNAs with genome-editing tools. Methods Mol Biol 1239: 241–250.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(11): 1944–1954.CrossRefGoogle ScholarPubMed
Gutschner, T, Hämmerle, M, Eissmann, M, et al. 2013. The noncoding RNA MALAT1 is a critical regulator of the metastasis phenotype of lung cancer cells. Cancer Res 73(3): 1180–1189.CrossRefGoogle ScholarPubMed
Han, J, Zhang, J, Chen, L, et al. 2014a. Efficient in vivo deletion of a large imprinted lncRNA by CRISPR/Cas9. RNA Biol 11(7): 829–835.CrossRefGoogle ScholarPubMed
Han, P, Li, W, Lin, CH, et al. 2014b. A long noncoding RNA protects the heart from pathological hypertrophy. Nature 514(7520): 102–106.CrossRefGoogle ScholarPubMed
He, S, Liu, C, Skogerbø, G, et al. 2008. NONCODE v2.0: decoding the non-coding. Nucleic Acids Res 36(Database issue): D170–D172.CrossRefGoogle ScholarPubMed
Hill, JA, Olson, EN. 2008. Cardiac plasticity. N Engl J Med 358(13): 1370–1380.CrossRefGoogle ScholarPubMed
Ho, T-T, Zhou, N, Huang, J, et al. 2015. Targeting non-coding RNAs with the CRISPR/Cas9 system in human cell lines. Nucleic Acids Res 43(3): e17.CrossRefGoogle ScholarPubMed
Holdt, LM, Beutner, F, Scholz, M, et al. 2010. ANRIL expression is associated with atherosclerosis risk at chromosome 9p21. Arterioscl Thromb Vasc Biol 30(3): 620–627.CrossRefGoogle ScholarPubMed
Hwang, H-WH, Mendell, JTJ. 2006. MicroRNAs in cell proliferation, cell death, and tumorigenesis. Br J Cancer 94(6): 776–780.CrossRefGoogle ScholarPubMed
Kapranov, P, Cheng, J, Dike, S, et al. 2007. RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science 316(5830): 1484–1488.CrossRefGoogle Scholar
Katayama, S, Tomaru, Y, Kasukawa, T, et al. 2005. Antisense transcription in the mammalian transcriptome. Science 309(5740): 1564–1566.CrossRefGoogle ScholarPubMed
Khalil, AM, Guttman, M, Huarte, M, et al. 2009. Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc Natl Acad Sci USA 106(28): 11667–11672.CrossRefGoogle ScholarPubMed
Klattenhoff, CA, Scheuermann, JC, Surface, LE, et al. 2013. Braveheart, a long noncoding RNA required for cardiovascular lineage commitment. Cell 152(3): 570–583.CrossRefGoogle ScholarPubMed
Kotzin, JJ, Spencer, SP, McCright, SJ, et al. 2016. The long non-coding RNA Morrbid regulates Bim and short-lived myeloid cell lifespan. Nature 537(7619): 239–243.CrossRefGoogle Scholar
Latos, PA, Pauler, FM, Koerner, MV, et al. 2012. Airn transcriptional overlap, but not its lncRNA products, induces imprinted Igf2 r silencing. Science 338(6113): 1469–1472.CrossRefGoogle ScholarPubMed
Lee, S, Kopp, F, Chang, TC, et al. 2016. Noncoding RNA NORAD regulates genomic stability by sequestering PUMILIO proteins. Cell 164(1–2): 69–80.CrossRefGoogle ScholarPubMed
Leucci, E, Vendramin, R, Spinazzi, M, et al. 2016. Melanoma addiction to the long non-coding RNA SAMMSON. Nature 531(7595): 518–522.CrossRefGoogle Scholar
Libby, P, Ridker, PM, Hansson, GK. 2011. Progress and challenges in translating the biology of atherosclerosis. Nature 473(7347): 317–325.CrossRefGoogle ScholarPubMed
Liu, C, Bai, B, Skogerbø, G, et al. 2005. NONCODE: an integrated knowledge database of non-coding RNAs. Nucleic Acids Res 33(Database issue): D112–D115.CrossRefGoogle ScholarPubMed
Maeder, ML, Linder, SJ, Cascio, VM, et al. 2013. CRISPR RNA-guided activation of endogenous human genes. Nat Methods 10(10): 977–979.CrossRefGoogle ScholarPubMed
Michalik, KM, You, X, Manavski, Y, et al. 2014. Long noncoding RNA MALAT1 regulates endothelial cell function and vessel growth. Circ Res 114(9): 1389–1397.CrossRefGoogle ScholarPubMed
Moore, CB, Guthrie, EH, Huang, MT, Taxman, DJ. 2010. Short hairpin RNA (shRNA): design, delivery, and assessment of gene knockdown. Methods Mol Biol 629: 141–158.Google ScholarPubMed
Okazaki, Y, Furuno, M, Kasukawa, T, et al. 2002. Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature 420(6915): 563–573.Google Scholar
Ounzain, S, Micheletti, R, Arnan, C, et al. 2015. CARMEN, a human super enhancer-associated long noncoding RNA controlling cardiac specification, differentiation and homeostasis. J Mol Cell Cardiol 89(Pt A): 98–112.CrossRefGoogle Scholar
Palmer, AC, Egan, JB, Shearwin, KE. 2011. Transcriptional interference by RNA polymerase pausing and dislodgement of transcription factors. Transcription 2(1): 9–14.CrossRefGoogle ScholarPubMed
Perez-Pinera, P, Kocak, DD, Vockley, CM, et al. 2013. RNA-guided gene activation by CRISPR-Cas9-based transcription factors. Nat Methods 10(10): 973–976.CrossRefGoogle ScholarPubMed
Quinn, JJ, Ilik, IA, Qu, K, et al. 2014. Revealing long noncoding RNA architecture and functions using domain-specific chromatin isolation by RNA purification. Nat Biotechnol 32(9): 933–940.CrossRefGoogle ScholarPubMed
Ran, FA, Hsu, PD, Lin, CY, et al. 2013. Double nicking by RNA-guided CRISPR Cas9 for enhanced genome editing specificity. Cell 154(6): 1380–1389.CrossRefGoogle ScholarPubMed
Rinn, JL, Chang, HY. 2012. Genome regulation by long noncoding RNAs. Annu Rev Biochem 81(1): 145–166.CrossRefGoogle ScholarPubMed
Royo, H, Cavaillé, J. 2008. Non-coding RNAs in imprinted gene clusters. Biol Cell 100(3): 149–166.CrossRefGoogle ScholarPubMed
Sallam, T, Jones, MC, Gilliland, T, et al. 2016. Feedback modulation of cholesterol metabolism by the lipid-responsive non-coding RNA LeXis. Nature 534(7605): 124–128.CrossRefGoogle ScholarPubMed
Samani, NJ, Erdmann, J, Hall, AS, et al. 2007. Genomewide association analysis of coronary artery disease. N Engl J Med 357(5): 443–453.CrossRefGoogle ScholarPubMed
Sander, JD, Joung, JK. 2014. CRISPR-Cas systems for editing, regulating and targeting genomes. Nat Biotechnol 32(4): 347–355.CrossRefGoogle ScholarPubMed
Sauvageau, M, Goff, LA, Lodato, S, et al. 2013. Multiple knockout mouse models reveal lincRNAs are required for life and brain development. eLife 2: e01749.CrossRefGoogle ScholarPubMed
Sleutels, F, Zwart, R, Barlow, DP. 2002. The non-coding Air RNA is required for silencing autosomal imprinted genes. Nature 415(6873): 810–813.CrossRefGoogle ScholarPubMed
Uchida, S, Dimmeler, S. 2015. Long noncoding RNAs in cardiovascular diseases. Circ Res 116(4): 737–750.CrossRefGoogle ScholarPubMed
Viereck, J, Kumarswamy, R, Foinquinos, A, et al. 2016. Long noncoding RNA Chast promotes cardiac remodeling. Sci Transl Medicine 8(326): 326ra22.CrossRefGoogle ScholarPubMed
Wang, K, Liu, F, Zhou, LY, et al. 2014. The long noncoding RNA CHRF regulates cardiac hypertrophy by targeting miR-489. Circ Res 114(9): 1377–1388.CrossRefGoogle Scholar
Wang, Z, Zhang, XJ, Ji, YX, et al. 2016. The long noncoding RNA Chaer defines an epigenetic checkpoint in cardiac hypertrophy. Nat Med 22(10): 1131–1139.CrossRefGoogle Scholar
Ward, LD, Kellis, M. 2012. HaploReg: a resource for exploring chromatin states, conservation, and regulatory motif alterations within sets of genetically linked variants. Nucleic Acids Res 40(Database issue): D930–D934.CrossRefGoogle ScholarPubMed
Washietl, S, Kellis, M, Garber, M. 2014. Evolutionary dynamics and tissue specificity of human long noncoding RNAs in six mammals. Genome Res 24(4): 616–628.CrossRefGoogle ScholarPubMed
Xie, C, Yuan, J, Li, H, et al. 2014. NONCODEv4: exploring the world of long non-coding RNA genes. Nucleic Acids Res 42(Database issue): D98–D103.CrossRefGoogle ScholarPubMed
Xue, Z, Hennelly, S, Doyle, B, et al. 2016. A G-rich motif in the lncRNA braveheart interacts with a zinc-finger transcription factor to specify the cardiovascular lineage. Mol Cell 64(1): 37–50.CrossRefGoogle ScholarPubMed
Zelcer, N, Tontonoz, P. 2006. Liver X receptors as integrators of metabolic and inflammatory signaling. J Clin Invest 116(3): 607–614.CrossRefGoogle ScholarPubMed
Zhang, B, Arun, G, Mao, YS, et al. 2012. The lncRNA Malat1 is dispensable for mouse development but its transcription plays a cis-regulatory role in the adult. Cell Rep 2(1): 111–123.CrossRefGoogle Scholar
Zhao, Y, Li, H, Fang, S, et al. 2016. NONCODE 2016: an informative and valuable data source of long non-coding RNAs. Nucleic Acids Res 44(D1): D203–D208.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
×