Skip to main content
SpringerLink
Log in

Methods to Study Long Noncoding RNA Biology in Cancer

  • Chapter
  • First Online:
Book cover The Long and Short Non-coding RNAs in Cancer Biology

Part of the book series: Advances in Experimental Medicine and Biology ((AEMB,volume 927))

Abstract

Thousands of long noncoding RNAs (lncRNAs) have been discovered in recent years. The functions of lncRNAs range broadly from regulating chromatin structure and gene expression in the nucleus to controlling messenger RNA (mRNA) processing, mRNA posttranscriptional regulation, cellular signaling, and protein activity in the cytoplasm. Experimental and computational techniques have been developed to characterize lncRNAs in high-throughput scale, to study the lncRNA function in vitro and in vivo, to map lncRNA binding sites on the genome, and to capture lncRNA–protein interactions with the identification of lncRNA-binding partners, binding sites, and interaction determinants. In this chapter, we will discuss these technologies and their applications in decoding the functions of lncRNAs. Understanding these techniques including their advantages and disadvantages and developing them in the future will be essential to elaborate the roles of lncRNAs in cancer and other diseases.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 129.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 169.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  1. Quek XC, Thomson DW, Maag J-LV, et al. LncRNAdb v2.0: expanding the reference database for functional long non-coding RNAs. Nucleic Acids Res. 2015;43(Database issue):D168–73.

    Article  PubMed  Google Scholar 

  2. Bu D, Yu KT, Sun SL, et al. NONCODE v3.0: integrative annotation of long non-coding RNAs. Nucleic Acids Res. 2012;40(Database issue):D210–5.

    Article  CAS  PubMed  Google Scholar 

  3. Volders PJ, Verheggen K, Menschaert G, et al. An update on LNCipedia: a database for annotated human lncRNA sequences. Nucleic Acids Res. 2015;43(Database issue):D174–80.

    Article  PubMed  Google Scholar 

  4. RNAcentral Consortium. RNAcentral: an international database of ncRNA sequences. Nucleic Acids Res. 2015;43(Database issue):D123–9.

    Article  Google Scholar 

  5. Fatica A, Bozzoni I. Long non-coding RNAs: new players in cell differentiation and development. Nat Rev Genet. 2014;15(1):7–21.

    Article  CAS  PubMed  Google Scholar 

  6. Derrien T, Johnson R, Bussotti G, et al. The GENCODE v7 catalog of human long non-coding RNAs: analysis of their gene structure, evolution, and expression. Genome Res. 2012;22(9):1775–89.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  7. Marguerat S, Bahler J. RNA-seq: from technology to biology. Cell Mol Life Sci. 2010;67(4):569–79.

    Article  CAS  PubMed  Google Scholar 

  8. Ozsolak F, Milos PM. RNA sequencing: advances, challenges and opportunities. Nat Rev Genet. 2011;12(2):87–98.

    Article  CAS  PubMed  Google Scholar 

  9. Wang Z, Gerstein M, Snyder M. RNA-seq: a revolutionary tool for transcriptomics. Nat Rev Genet. 2009;10(1):57–63.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Atkinson SR, Marguerat S, Bahler J. Exploring long non-coding RNAs through sequencing. Semin Cell Dev Biol. 2012;23(2):200–5.

    Article  CAS  PubMed  Google Scholar 

  11. Heyer EE, Ozadam H, Ricci EP, et al. An optimized kit-free method for making strand-specific deep sequencing libraries from RNA fragments. Nucleic Acids Res. 2015;43(1):e2.

    Article  PubMed  Google Scholar 

  12. Mili S, Steitz JA. Evidence for reassociation of RNA-binding proteins after cell lysis: implications for the interpretation of immunoprecipitation analyses. RNA. 2004;10(11):1692–4.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  13. Zhao J, Ohsumi TK, Kung JT, et al. Genome-wide identification of polycomb-associated RNAs by RIP-seq. Mol Cell. 2010;40(6):939–53.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  14. Zhang C, Darnell RB. Mapping in vivo protein-RNA interactions at single-nucleotide resolution from HITS-CLIP data. Nat Biotechnol. 2011;29(7):607–14.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  15. Olivarius S, Plessy C, Carninci P. High-throughput verification of transcriptional starting sites by Deep-RACE. Biotechniques. 2009;46(2):130–2.

    Article  CAS  PubMed  Google Scholar 

  16. Pastori C, Peschansky VJ, Barbouth D, et al. Comprehensive analysis of the transcriptional landscape of the human FMR1 gene reveals two new long non-coding RNAs differentially expressed in Fragile X syndrome and Fragile X-associated tremor/ataxia syndrome. Hum Genet. 2014;133(1):59–67.

    Article  CAS  PubMed  Google Scholar 

  17. Wheeler DL, Church DM, Federhen S, et al. Database resources of the National Center for Biotechnology. Nucleic Acids Res. 2003;31(1):28–33.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Lin MF, Jungreis I, Kellis M. PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions. Bioinformatics. 2011;27(13):i275–82.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  19. Kong L, Zhang Y, Ye ZQ, et al. CPC: assess the protein-coding potential of transcripts using sequence features and support vector machine. Nucleic Acids Res. 2007;35(Web Server issue):W345–9.

    Article  Google Scholar 

  20. Wang L, Park HJ, Dasari S, et al. CPAT: Coding-Potential Assessment Tool using an alignment-free logistic regression model. Nucleic Acids Res. 2013;41(6):e74.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  21. Sun L, Luo H, Bu D, et al. Utilizing sequence intrinsic composition to classify protein-coding and long non-coding transcripts. Nucleic Acids Res. 2013;41(17):e166.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Ingolia NT. Ribosome profiling: new views of translation, from single codons to genome scale. Nat Rev Genet. 2014;15(3):205–13.

    Article  CAS  PubMed  Google Scholar 

  23. Ingolia NT, Ghaemmaghami S, Newman JR, et al. Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science. 2009;324(5924):218–23.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Ingolia NT, Lareau LF, Weissman JS. Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes. Cell. 2011;147(4):789–802.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Guttman M, Russell P, Ingolia NT, et al. Ribosome profiling provides evidence that large non-coding RNAs do not encode proteins. Cell. 2013;154(1):240–51.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Zhang K, Shi ZM, Chang YN, et al. The ways of action of long non-coding RNAs in cytoplasm and nucleus. Gene. 2014;547(1):1–9.

    Article  CAS  PubMed  Google Scholar 

  27. Cabili MN, Dunagin MC, McClanahan PD, et al. Localization and abundance analysis of human lncRNAs at single-cell and single-molecule resolution. Genome Biol. 2015;16:20.

    Article  PubMed  PubMed Central  Google Scholar 

  28. Pinaud R, Mello CV, Velho TA, et al. Detection of two mRNA species at single-cell resolution by double-fluorescence in situ hybridization. Nat Protoc. 2008;3(8):1370–9.

    Article  CAS  PubMed  Google Scholar 

  29. Dunagin M, Cabili MN, Rinn J, et al. Visualization of lncRNA by single-molecule fluorescence in situ hybridization. Methods Mol Biol. 2015;1262:3–19.

    Article  CAS  PubMed  Google Scholar 

  30. Streit S, Michalski CW, Erkan M, et al. Northern blot analysis for detection and quantification of RNA in pancreatic cancer cells and tissues. Nat Protoc. 2009;4(1):37–43.

    Article  CAS  PubMed  Google Scholar 

  31. Nolan T, Hands RE, Bustin SA. Quantification of mRNA using real-time RT-PCR. Nat Protoc. 2006;1(3):1559–82.

    Article  CAS  PubMed  Google Scholar 

  32. Schmittgen TD, Livak KJ. Analyzing real-time PCR data by the comparative C(T) method. Nat Protoc. 2008;3(6):1101–8.

    Article  CAS  PubMed  Google Scholar 

  33. Rosner M, Siegel I, Fuchs C, et al. Efficient siRNA-mediated prolonged gene silencing in human amniotic fluid stem cells. Nat Protoc. 2010;5(6):1081–95.

    Article  CAS  PubMed  Google Scholar 

  34. Schaniel C, Li F, Schafer XL, et al. Delivery of short hairpin RNAs – triggers of gene silencing – into mouse embryonic stem cells. Nat Methods. 2006;3(5):397–400.

    Article  CAS  PubMed  Google Scholar 

  35. Moore CB, Guthrie EH, Huang MT, et al. Short hairpin RNA (shRNA): design, delivery, and assessment of gene knockdown. Methods Mol Biol. 2010;629:141–58.

    PubMed  PubMed Central  Google Scholar 

  36. Teplova M, et al. Crystal structure and improved antisense properties of 2′-O-(2-methoxyethyl)-RNA. Nat Struct Biol. 1999;6(6):535–9.

    Article  CAS  PubMed  Google Scholar 

  37. Obernosterer G, Martinez J, Alenius M. Locked nucleic acid-based in situ detection of microRNAs in mouse tissue sections. Nat Protoc. 2007;2(6):1508–14.

    Article  CAS  PubMed  Google Scholar 

  38. Grunweller A, Hartmann RK. Locked nucleic acid oligonucleotides: the next generation of antisense agents? BioDrugs. 2007;21(4):235–43.

    Article  PubMed  Google Scholar 

  39. Lennox KA, Behlke MA. Cellular localization of long non-coding RNAs affects silencing by RNAi more than by antisense oligonucleotides. Nucleic Acids Res. 2016;44(2):863–77. doi:10.1093/nar/gkv1206.

    Article  PubMed  Google Scholar 

  40. Boettcher M, McManus MT. Choosing the right tool for the job: RNAi, TALEN, or CRISPR. Mol Cell. 2015;58(4):575–85.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Cong L, Ran FA, Cox D, et al. Multiplex genome engineering using CRISPR/Cas systems. Science. 2013;339(6121):819–23.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Mali P, Esvelt KM, Church GM. Cas9 as a versatile tool for engineering biology. Nat Methods. 2013;10(10):957–63.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  43. Esvelt KM, Smidler AL, Catteruccia F, et al. Concerning RNA-guided gene drives for the alteration of wild populations. Elife. 2014;3(1), e03401. doi:10.7554/eLife.03401.

    PubMed Central  Google Scholar 

  44. Ho TT, Zhou N, Huang J, et al. Targeting non-coding RNAs with the CRISPR/Cas9 system in human cell lines. Nucleic Acids Res. 2015;43(3):e17.

    Article  PubMed  Google Scholar 

  45. Han J, Zhang J, Chen L, et al. Efficient in vivo deletion of a large imprinted lncRNA by CRISPR/Cas9. RNA Biol. 2014;11(7):829–35.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  46. Maeder ML, Linder SJ, Reyon D, et al. Robust, synergistic regulation of human gene expression using TALE activators. Nat Methods. 2013;10(3):243–5.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  47. Perez-Pinera P, Ousterout DG, Brunger JM, et al. Synergistic and tunable human gene activation by combinations of synthetic transcription factors. Nat Methods. 2013;10(3):239–42.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  48. Konermann S, Brigham MD, Trevino AE, et al. Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex. Nature. 2015;517(7536):583–8.

    Article  CAS  PubMed  Google Scholar 

  49. Chu C, Qu K, Zhong FL, et al. Genomic maps of long non-coding RNA occupancy reveal principles of RNA-chromatin interactions. Mol Cell. 2011;44(4):667–78.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  50. Chu C, Quinn J, Chang HY. Chromatin isolation by RNA purification (ChIRP). J Vis Exp. 2012;61:3912. doi:10.3791/3912.

    PubMed  Google Scholar 

  51. Davis CP, West JA. Purification of specific chromatin regions using oligonucleotides: capture hybridization analysis of RNA targets (CHART). Methods Mol Biol. 2015;1262:167–82.

    Article  CAS  PubMed  Google Scholar 

  52. Simon MD. Capture hybridization analysis of RNA targets (CHART). Curr Protoc Mol Biol. 2013; Chapter 21:Unit 21 25. doi:10.1002/0471142727.mb2125s101.

  53. Engreitz JM, Pandya-Jones A, McDonel P, et al. The Xist lncRNA exploits three-dimensional genome architecture to spread across the X chromosome. Science. 2013;341(6147):1237973.

    Article  PubMed  PubMed Central  Google Scholar 

  54. Engreitz J, Lander ES, Guttman M. RNA antisense purification (RAP) for mapping RNA interactions with chromatin. Methods Mol Biol. 2015;1262:183–97.

    Article  CAS  PubMed  Google Scholar 

  55. Chu C, Spitale RC, Chang HY. Technologies to probe functions and mechanisms of long non-coding RNAs. Nat Struct Mol Biol. 2015;22(1):29–35.

    Article  CAS  PubMed  Google Scholar 

  56. Michlewski G, Caceres JF. RNase-assisted RNA chromatography. RNA. 2010;16(8):1673–8.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  57. Chu C, Zhang QC, da Rocha ST, et al. Systematic discovery of Xist RNA binding proteins. Cell. 2015;161(2):404–16.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  58. McHugh CA, Chen CK, Chow A, et al. The Xist lncRNA interacts directly with SHARP to silence transcription through HDAC3. Nature. 2015;521(7551):232–6.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  59. Bantscheff M, Schirle M, Sweetman G, et al. Quantitative mass spectrometry in proteomics: a critical review. Anal Bioanal Chem. 2007;389(4):1017–31.

    Article  CAS  PubMed  Google Scholar 

  60. McHugh CA, Russell P, Guttman M. Methods for comprehensive experimental identification of RNA-protein interactions. Genome Biol. 2014;15(1):203.

    Article  PubMed  PubMed Central  Google Scholar 

  61. Huarte M, Guttman M, Feldser D, et al. A large intergenic non-coding RNA induced by p53 mediates global gene repression in the p53 response. Cell. 2010;142(3):409–19.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  62. Bonifacino JS, Dell’Angelica ED, Springer TA. Immunoprecipitation. Curr Protoc Neurosci. 2006; Chapter 5:Unit 5 24.

    Google Scholar 

  63. Garner MM, Revzin A. A gel electrophoresis method for quantifying the binding of proteins to specific DNA regions: application to components of the Escherichia coli lactose operon regulatory system. Nucleic Acids Res. 1981;9(13):3047–60.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  64. Fried M, Crothers DM. Equilibria and kinetics of lac repressor-operator interactions by polyacrylamide gel electrophoresis. Nucleic Acids Res. 1981;9(23):6505–25.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  65. Wang K, Gao Y, Peng X, et al. Using FAM labeled DNA oligos to do RNA electrophoretic mobility shift assay. Mol Biol Rep. 2010;37(6):2871–5.

    Article  CAS  PubMed  Google Scholar 

  66. Zimmerman SG, Peters NC, Altaras AE, et al. Optimized RNA ISH, RNA FISH and protein-RNA double labeling (IF/FISH) in Drosophila ovaries. Nat Protoc. 2013;8(11):2158–79.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  67. Chaumeil J, Augui S, Chow JC, et al. Combined immunofluorescence, RNA fluorescent in situ hybridization, and DNA fluorescent in situ hybridization to study chromatin changes, transcriptional activity, nuclear organization, and X-chromosome inactivation. Methods Mol Biol. 2008;463:297–308.

    Article  CAS  PubMed  Google Scholar 

  68. Turner DH, Sugimoto N, Freier SM. RNA structure prediction. Annu Rev Biophys Biophys Chem. 1988;17:167–92.

    Article  CAS  PubMed  Google Scholar 

  69. Zwieb C. The principles of RNA structure architecture. Methods Mol Biol. 2014;1097:33–43.

    Article  CAS  PubMed  Google Scholar 

  70. Giese MR, Betschart K, Dale T, et al. Stability of RNA hairpins closed by wobble base pairs. Biochemistry. 1998;37(4):1094–100.

    Article  CAS  PubMed  Google Scholar 

  71. Spitale RC, Flynn RA, Torre EA, et al. RNA structural analysis by evolving SHAPE chemistry. Wiley Interdiscip Rev RNA. 2014;5(6):867–81.

    Article  CAS  PubMed  Google Scholar 

  72. Zuker M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 2003;31(13):3406–15.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  73. Denman RB. Using RNAFOLD to predict the activity of small catalytic RNAs. Biotechniques. 1993;15(6):1090–5.

    CAS  PubMed  Google Scholar 

  74. Mathews DH. Using an RNA secondary structure partition function to determine confidence in base pairs predicted by free energy minimization. RNA. 2004;10(8):1178–90.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  75. Fourmy D, Yoshizawa S. Protein-RNA footprinting: an evolving tool. Wiley Interdiscip Rev RNA. 2012;3(4):557–66.

    Article  CAS  PubMed  Google Scholar 

  76. Peng Y, Soper TJ, Woodson SA. RNase footprinting of protein binding sites on an mRNA target of small RNAs. Methods Mol Biol. 2012;905:213–24.

    CAS  PubMed  Google Scholar 

  77. Weeks KM. Advances in RNA structure analysis by chemical probing. Curr Opin Struct Biol. 2010;20(3):295–304.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  78. Kertesz M, Wan Y, Mazor E, et al. Genome-wide measurement of RNA secondary structure in yeast. Nature. 2010;467(7311):103–7.

    Article  CAS  PubMed  Google Scholar 

  79. Wan Y, Qu K, Ouyang Z, et al. Genome-wide mapping of RNA structure using nuclease digestion and high-throughput sequencing. Nat Protoc. 2013;8(5):849–69.

    Article  CAS  PubMed  Google Scholar 

  80. Martin L, Meier M, Lyons SM, et al. Systematic reconstruction of RNA functional motifs with high-throughput microfluidics. Nat Methods. 2012;9(12):1192–4.

    Article  CAS  PubMed  Google Scholar 

  81. Rockel S, Geertz M, Maerkl SJ. MITOMI: a microfluidic platform for in vitro characterization of transcription factor-DNA interaction. Methods Mol Biol. 2012;786:97–114.

    Article  CAS  PubMed  Google Scholar 

  82. Quinn JJ, Ilik IA, Qu K, et al. Revealing long non-coding RNA architecture and functions using domain-specific chromatin isolation by RNA purification. Nat Biotechnol. 2014;32(9):933–40.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  83. Quinn JJ, Chang HY. In situ dissection of RNA functional subunits by domain-specific chromatin isolation by RNA purification (dChIRP). Methods Mol Biol. 2015;1262:199–213.

    Article  CAS  PubMed  Google Scholar 

  84. Carey MF, Peterson CL, Smale ST. The RNase protection assay. Cold Spring Harb Protoc. 2013;2013(3). doi:10.1101/pdb.prot071910.

    Google Scholar 

  85. Gunzl A, Palfi Z, Bindereif A. Analysis of RNA-protein complexes by oligonucleotide-targeted RNase H digestion. Methods. 2002;26(2):162–9.

    Article  PubMed  Google Scholar 

  86. Kvaratskhelia M, Miller JT, Budihas SR, et al. Identification of specific HIV-1 reverse transcriptase contacts to the viral RNA: tRNA complex by mass spectrometry and a primary amine selective reagent. Proc Natl Acad Sci U S A. 2002;99(25):15988–93.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  87. Kvaratskhelia M, Grice SF. Structural analysis of protein-RNA interactions with mass spectrometry. Methods Mol Biol. 2008;488:213–9.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  88. Mendoza VL, Vachet RW. Probing protein structure by amino acid-specific covalent labeling and mass spectrometry. Mass Spectrom Rev. 2009;28(5):785–815.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  89. Li Y, Tollefsbol TO. DNA methylation detection: bisulfite genomic sequencing analysis. Methods Mol Biol. 2011;791:11–21.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  90. Frommer M, McDonald LE, Millar DS, et al. A genomic sequencing protocol that yields a positive display of 5-methylcytosine residues in individual DNA strands. Proc Natl Acad Sci U S A. 1992;89(5):1827–31.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  91. Furey TS. ChIP-seq and beyond: new and improved methodologies to detect and characterize protein-DNA interactions. Nat Rev Genet. 2012;13(12):840–52.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  92. Bhan A, Mandal SS. Estradiol-induced transcriptional regulation of long non-coding RNA, HOTAIR. Methods Mol Biol. 2016;1366:395–412.

    Article  PubMed  Google Scholar 

  93. Evertts AG, Zee BM, Garcia BA. Modern approaches for investigating epigenetic signaling pathways. J Appl Physiol (1985). 2010;109(3):927–33.

    Article  CAS  Google Scholar 

  94. Doyle A, McGarry MP, Lee NA, et al. The construction of transgenic and gene knockout/knockin mouse models of human disease. Transgenic Res. 2012;21(2):327–49.

    Article  CAS  PubMed  Google Scholar 

  95. Guo G, Kang Q, Zhu X, et al. A long non-coding RNA critically regulates Bcr-Abl-mediated cellular transformation by acting as a competitive endogenous RNA. Oncogene. 2015;34(14):768–79.

    Article  Google Scholar 

  96. Gomez JA, Wapinski OL, Yang YW, et al. The NeST long ncRNA controls microbial susceptibility and epigenetic activation of the interferon-gamma locus. Cell. 2013;152(4):743–54.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  97. Bassett AR, Akhtar A, Barlow DP, et al. Considerations when investigating lncRNA function in vivo. Elife. 2014;3:e03058.

    Article  PubMed  PubMed Central  Google Scholar 

  98. Eissmann M, Gutschner T, Hämmerle M, et al. Loss of the abundant nuclear non-coding RNA MALAT1 is compatible with life and development. RNA Biol. 2012;9(8):1076–87.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  99. Sauvageau M, Goff LA, Lodato S, et al. Multiple knockout mouse models reveal lincRNAs are required for life and brain development. Elife. 2013;2:e01749.

    Article  PubMed  PubMed Central  Google Scholar 

  100. Gupta RA, Shah N, Wang KC, et al. Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis. Nature. 2010;464(7291):1071–6.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  101. Liu B, Sun L, Liu Q, et al. A cytoplasmic NF-kappaB interacting long non-coding RNA blocks IkappaB phosphorylation and suppresses breast cancer metastasis. Cancer Cell. 2015;27(3):370–81.

    Article  CAS  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, 107 Yanjiang West Road, Guangzhou, 510120, China

    Man-Li Luo

Authors
  1. Man-Li Luo
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Man-Li Luo .

Editor information

Editors and Affiliations

  1. Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University, Guangzhou, China

    Erwei Song

Rights and permissions

Reprints and permissions

Copyright information

© 2016 Springer Science+Business Media Singapore

About this chapter

Cite this chapter

Luo, ML. (2016). Methods to Study Long Noncoding RNA Biology in Cancer. In: Song, E. (eds) The Long and Short Non-coding RNAs in Cancer Biology. Advances in Experimental Medicine and Biology, vol 927. Springer, Singapore. https://doi.org/10.1007/978-981-10-1498-7_3

Download citation

Publish with us

Policies and ethics

Search

Navigation