Skip to main content
SpringerLink
Log in

Methods Used for Noncoding RNAs Analysis

  • Chapter
  • First Online:
Molecular Pathology in Cancer Research

  • 1070 Accesses

Abstract

Noncoding RNAs are RNA species that do not encode for proteins, and the majority of the human transcriptome is dominated by ncRNA. Recent extensive genomic and transcriptomic analyses have identified many different classes and sizes of ncRNA. They are now understood to be critical to the overall functioning, growth, development, and differentiation of cells. Differential expression and tissue specificity of many ncRNAs have been reported in normal development and disease states including cancer. Lack of functional ncRNAs may also lead to cancer progression. Therefore noncoding transcripts as biomarkers may be used in either predictive or prognostic ways. As such, over the past 15 years they have emerged as key biomarkers in cancer pathology, relating to both early detection and molecular subtyping. Due to important functional roles of ncRNAs in various cancers, the requirement for technologies used in the field is rapidly increasing. This chapter classifies ncRNAs based on their sizes, and describes methods applied for the identification and characterization of ncRNAs. It outlines key methods used for the purification of good quality RNA, various detection methods, analysis of gene expression as well as techniques that can applied for functional characterization of ncRNA. It also highlights critical steps and options to provide a general guide for ncRNA analysis.

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 89.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 119.99
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. Esteller M (2011) Non coding RNAs in human disease. Nat Rev Genet 12(12):861–874

    Google Scholar 

  2. Mattick J (2005) The functional genomics of Non coding RNA. Science 309(5740):1527–1528

    Google Scholar 

  3. Mattick J, Makunin IV (2006) Non coding RNA. Hum Mol Genet 15 Spec No 1:R17–R29

    Google Scholar 

  4. Prensner J, Chinnaiyan AM (2011) The emergence of lncRNAs in cancer biology. Cancer Discov 1(5):391–407

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  5. Zhang H, Chen Z, Wang X, Huang Z, He Z, Chen Y (2013) Long Non coding RNA: a new player in cancer. J Hematol Oncol 6(1):37

    Google Scholar 

  6. Guttman M, Rinn JL (2012) Modular regulatory principles of large Non coding RNAs. Nature 482(7385):339–346

    Google Scholar 

  7. Kim E, Sung S (2012) Long Non coding RNA: unveiling hidden layer of gene regulatory networks. Trends Plant Sci 17(1):16–21

    Google Scholar 

  8. Lee R, Feinbaum RL, Ambros V (1993) The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 75(5):843–854

    Article  CAS  PubMed  Google Scholar 

  9. Aravin A, Naumova NM, Tulin AV, Vagin VV, Rozovsky YM, Gvozdev VA (2011) Double-stranded RNA-mediated silencing of genomic tandem repeats and transposable elements in the D. melanogaster germline. Curr Biol 11(13):1017–1027

    Article  Google Scholar 

  10. Bachellerie J, Cavaille J, Huttenhofer A (2002) The expanding snoRNA world. Biochimie 84(8):775–790

    Article  CAS  PubMed  Google Scholar 

  11. Gerard M, Myslinski E, Chylak N, Baudrey S, Krol A, Carbon P (2010) The scaRNA2 is produced by an independent transcription unit and its processing is directed by the encoding region. Nucleic Acids Res 38(2):370–381

    Article  CAS  PubMed  Google Scholar 

  12. Mendell J (2005) MicroRNAs: critical regulators of development, cellular physiology and malignancy. Cell Cycle 4(9):1179–1184

    Article  CAS  PubMed  Google Scholar 

  13. Bernstein B, Birney E, Dunham I, Green ED, Gunter C, Snyder M (2012) An integrated encyclopedia of DNA elements in the human genome. Nature 489(7414):57–74

    Article  Google Scholar 

  14. Carninci P, Kasukawa T, Katayama S, Gough J, Frith MC, Maeda N, Oyama R et al (2005) The transcriptional landscape of the mammalian genome. Science 311(5740):1559–1563

    Google Scholar 

  15. Carninci P (2007) Constructing the landscape of the mammalian transcriptome. J Exp Biol 210:1497–1506

    Article  CAS  PubMed  Google Scholar 

  16. Djebali S, Davis CA, Merkel A, Dobin A, Lassmann T, Mortazavi A, Tanzer A, Lagarde J et al (2012) Landscape of transcription in human cells. Nature 489(7414):101–108

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  17. Dinger M, Pang KC, Mercer TR, Mattick JS (2008) Differentiating protein-coding and Non coding RNA: challenges and ambiguities. PLoS Comput Biol 4, e1000176

    Google Scholar 

  18. Ponting C, Oliver PL, Reik W (2009) Evolution and functions of long Non coding RNAs. Cell 136(4):629–641

    Google Scholar 

  19. Feng J, Bi C, Clark BS, Mady R, Shah P, Kohtz JD (2006) The Evf-2 Non coding RNA is transcribed from the Dlx-5/6 ultraconserved region and functions as a Dlx-2 transcriptional coactivator. Genes Dev 20:1470–1484

    Google Scholar 

  20. Shamovsky I, Ivannikov M, Kandel ES, Gershon D, Nudler E (2006) RNA-mediated response to heat shock in mammalian cells. Nature 440(7083):556–560

    Article  CAS  PubMed  Google Scholar 

  21. Wang X, Arai S, Song X, Reichart D, Du K, Pascual G, Tempst P, Rosenfeld MG, Glass CK, Kurokawa R (2008) Induced ncRNAs allosterically modify RNA-binding proteins in cis to inhibit transcription. Nature 454(7200):126–130

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  22. Clemson C, Hutchinson JN, Sara SA, Ensminger AW, Fox AH, Chess A, Lawrence JB (2009) An architectural role for a nuclear Non coding RNA: NEAT1 RNA is essential for the structure of paraspeckles. Mol Cell 33(6):717–726

    Google Scholar 

  23. Sunwoo H, Dinger ME, Wilusz JE, Amaral PP, Mattick JS, Spector DL (2009) MEN epsilon/beta nuclear-retained Non coding RNAs are up-regulated upon muscle differentiation and are essential components of paraspeckles. Genome Res 19(3):347–359

    Google Scholar 

  24. Dieci G, Preti M, Montanini B (2009) Eukaryotic snoRNAs: a paradigm for gene expression flexibility. Genomics 94(2):83–88

    Article  CAS  PubMed  Google Scholar 

  25. Cai X, Hagedorn CH, Cullen BR (2004) Human microRNAs are processed from capped, polyadenylated transcripts that can also function as mRNAs. RNA 10(12):1957–1966

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  26. Lee Y, Kim M, Han J, Yeom KH, Lee S, Baek SH, Kim VN (2004) MicroRNA genes are transcribed by RNA polymerase II. EMBO J 23(20):4051–4060

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Ji P et al (2003) MALAT-1, a novel Non coding RNA, and thymosin beta4 predict metastasis and survival in early-stage non-small cell lung cancer. Oncogene 22(39):8031–8041

    Google Scholar 

  28. Gupta R, Shah N, Wang KC, Kim J, Horlings HM, Wong DJ, Tsai MC, Hung T, Argani P, Rinn JL, Wang Y, Brzoska P, Kong B, Li R, West RB, van de Vijver MJ, Sukumar S, Chang HY (2010) Long Non coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis. Nature 464(7291):1071–1076

    Google Scholar 

  29. Calin G, Croce CM (2006) MicroRNA signatures in human cancers. Nat Rev Cancer 6(11):857–866

    Article  CAS  PubMed  Google Scholar 

  30. Iorio M, Ferracin M, Liu CG, Veronese A, Spizzo R, Sabbioni S, Magri E, Pedriali M, Fabbri M et al (2005) MicroRNA gene expression deregulation in human breast cancer. Cancer Res 65(16):7065–7070

    Article  CAS  PubMed  Google Scholar 

  31. Hildebrandt E, Lee JR, Crosby JH, Ferris DG, Anderson MG (2003) Liquid based pap smears as a source of RNA for analysis of gene expression. Appl Immunohistochem Mol Morphol 11(4):345–351

    Article  CAS  PubMed  Google Scholar 

  32. Lodde M, Fradet Y (2008) The detection of genetic markers of bladder cancer in urine and serum. Curr Opin Urol 18(5):499–503

    Article  PubMed  Google Scholar 

  33. Menke T, Warnecke JM (2004) Improved conditions for isolation and quantification of RNA in urine specimens. Ann N Y Acad Sci 1022:185–189

    Article  CAS  PubMed  Google Scholar 

  34. Taback B, Hoon DS (2004) Circulating nucleic acids and proteomics of plasma/serum: clinical utility. Ann N Y Acad Sci 1022:1–8

    Article  CAS  PubMed  Google Scholar 

  35. Zhang L, Farrell JJ, Zhou H, Elashoff D, Akin D, Park NH, Chia D, Wong DT (2010) Salivary transcriptomic biomarkers for detection of resectable pancreatic cancer. Gastroenterology 138(3):949–57 e1–7

    Google Scholar 

  36. Thery C, Zitvogel L, Amigorena S (2002) Exosomes: composition, biogenesis and function. Nat Rev Immunol 2(8):569–579

    CAS  PubMed  Google Scholar 

  37. Lasser C, Alikhani VS, Ekstrom K, Eldh M, Paredes PT, Bossios A, Sjostrand M, Gabrielsson S, Lotvall J, Valadi H (2011) Human saliva, plasma and breast milk exosomes contain RNA: uptake by macrophages. J Transl Med 9:9

    Article  PubMed  PubMed Central  Google Scholar 

  38. Borgna S, Armellin M, di Gennaro A, Maestro R, Santarosa M (2012) Mesenchymal traits are selected along with stem features in breast cancer cells grown as mammospheres. Cell Cycle 11(22):4242–4251

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  39. Beaulieu Y, Kleinman CL, Landry-Voyer AM, Majewski J, Bachand F (2012) Polyadenylation-dependent control of long Non coding RNA expression by the poly(A)-binding protein nuclear 1. PLoS Genet 8(11):e1003078

    Google Scholar 

  40. Schmittgen T, Jiang J, Liu Q, Yang L (2004) A high-throughput method to monitor the expression of microRNA precursors. Nucleic Acids Res 32(4), e43

    Article  PubMed  PubMed Central  Google Scholar 

  41. Dave R, Dinger ME, Andrew M, Askarian-Amiri M, Hume DA, Kellie S (2013) Regulated expression of PTPRJ/CD148 and an antisense long Non coding RNA in macrophages by proinflammatory stimuli. PLoS One 8, e68306

    Google Scholar 

  42. Korbie D, Mattick J (2008) Touchdown PCR for increased specificity and sensitivity in PCR amplification. Nat Protoc 3(9):1452–1456

    Article  CAS  PubMed  Google Scholar 

  43. Paul N, Shum J, Le T (2010) Hot start PCR. Methods Mol Biol 630:301–318

    Article  CAS  PubMed  Google Scholar 

  44. Gibson U, Heid CA, Williams PM (1996) A novel method for real time quantitative RT-PCR. Genome Res 6(10):995–1001

    Article  CAS  PubMed  Google Scholar 

  45. Heid C, Stevens J, Livak KJ, Williams PM (1996) Real time quantitative PCR. Genome Res 6(10):986–994

    Google Scholar 

  46. Kim J, Krichevsky A, Grad Y, Hayes GD, Kosik KS, Church GM, Ruvkun G (2004) Identification of many microRNAs that copurify with polyribosomes in mammalian neurons. Proc Natl Acad Sci U S A 101(1):360–365

    Article  CAS  PubMed  Google Scholar 

  47. Chen C, Ridzon DA, Broomer AJ, Zhou Z, Lee DH, Nguyen JT, Barbisin M, Xu NL, Mahuvakar VR, Andersen MR, Lao KQ, Livak KJ, Guegler KJ (2005) Real-time quantification of microRNAs by stem-loop RT-PCR. Nucleic Acids Res 33(20), e179

    Article  PubMed  PubMed Central  Google Scholar 

  48. Gibb E, Brown CJ, Lam WL (2011) The functional role of long Non coding RNA in human carcinomas. Mol Cancer 10:38

    Google Scholar 

  49. Gutschner T, Diederichs S (2012) The hallmarks of cancer: a long Non coding RNA point of view. RNA Biol 9(6):703–719

    Google Scholar 

  50. Huarte M, Rinn JL (2010) Large Non coding RNAs: missing links in cancer? Hum Mol Genet 19((R2)):R152–R161

    Google Scholar 

  51. Sanada Y, Yoshida K, Ohara M, Oeda M, Konishi K, Tsutani Y (2006) Histopathologic evaluation of stepwise progression of pancreatic carcinoma with immunohistochemical analysis of gastric epithelial transcription factor SOX2: comparison of expression patterns between invasive components and cancerous or nonneoplastic intraductal components. Pancreas 32(2):164–170

    Article  CAS  PubMed  Google Scholar 

  52. Askarian-Amiri ME, Crawford J, French JD, Smith MA, Smart CE, Ru K, Mercer TR, Thompson ER, Lakhani SR, Vargas AC, Campbell IG, Brown MA, Dinger ME, Mattick JS (2011) SNORD-host RNA Znfx1-as is a regulator of mammary development and a potential marker for breast cancer. RNA 17:878–891

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  53. Engreitz J, Pandya-Jones A, McDonel P, Shishkin A, Sirokman K, Surka C, Kadri S, Xing J, Goren A, Lander ES, Plath K, Guttman M (2013) The Xist lncRNA exploits three-dimensional genome architecture to spread across the X chromosome. Science 341(6147):1237973

    Article  PubMed  PubMed Central  Google Scholar 

  54. Kwon S (2013) Single-molecule fluorescence in situ hybridiz: quantitative imaging of single RNA molecules. BMB Rep 46(2):65–72

    Article  PubMed  PubMed Central  Google Scholar 

  55. Gall J, Pardue ML (1969) Formation and detection of RNA-DNA hybrid molecules in cytological preparations. Proc Natl Acad Sci U S A 63(2):378–383

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  56. Raap A, van de Corput MP, Vervenne RA, van Gijlswijk RP, Tanke HJ, Wiegant J (1995) Ultra-sensitive FISH using peroxidase-mediated deposition of biotin- or fluorochrome tyramides. Hum Mol Genet 4(4):529–534

    Article  CAS  PubMed  Google Scholar 

  57. Bauman J, Wiegant J, Borst P, van Duijn P (1980) A new method for fluorescence microscopical localization of specific DNA sequences by in situ hybridization of fluorochromelabelled RNA. Exp Cell Res 128(2):485–490

    Article  CAS  PubMed  Google Scholar 

  58. Levsky J, Singer RH (2003) Fluorescence in situ hybridization: past, present and future. J Cell Sci 116(Pt 14):2833–2838

    Article  CAS  PubMed  Google Scholar 

  59. Femino A, Fay FS, Fogarty K, Singer RH (1998) Visualization of single RNA transcripts in situ. Science 280(5363):585–590

    Article  CAS  PubMed  Google Scholar 

  60. Raj A, van den Bogaard P, Rifkin SA, van Oudenaarden A, Tyagi S (2008) Imaging individual mRNA molecules using multiple singly labeled probes. Nat Methods 10:877–879

    Article  Google Scholar 

  61. Orjalo Jr A, Johansson HE, Ruth JL (2011) Stellaris[trade] fluorescence in situ hybridization (FISH) probes: a powerful tool for mRNA detection. Nat Methods 8

    Google Scholar 

  62. Kretz M, Siprashvili Z, Chu C, Webster DE, Zehnder A, Qu K, Lee CS, Flockhart RJ, Groff AF, Chow J, Johnston D, Kim GE, Spitale RC, Flynn RA, Zheng GX, Aiyer S, Raj A, Rinn JL, Chang HY, Khavari PA (2013) Control of somatic tissue differentiation by the long Non coding RNA TINCR. Nature 493(7431):231–235

    Google Scholar 

  63. Raj A, Tyagi S (2010) Chapter 17 – Detection of individual endogenous RNA transcripts in situ using multiple singly labeled probes. In: Nils GW (ed) Methods in enzymology. Academic Press, pp 365–386

    Google Scholar 

  64. Shih J, Waks Z, Kedersha N, Silver PA (2011) Visualization of single mRNAs reveals temporal association of proteins with microRNA-regulated mRNA. Nucleic Acids Res 39(17):7740–7749

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  65. de Planell-Saguer M, Rodicio MC, Mourelatos Z (2010) Rapid in situ codetection of Non coding RNAs and proteins in cells and formalin-fixed paraffin-embedded tissue sections without protease treatment. Nat Protoc 5(6):1061–1073

    Google Scholar 

  66. Gilbert C, Svejstrup JQ (2006) RNA immunoprecipitation for determining RNA-protein associations in vivo (Chapter 27, Unit 27.4). In: Ausubel FM et al (eds) Curr Protoc in Mol Biol. doi: 10.1002/0471142727.mb2704s75

    Google Scholar 

  67. Ule J, Jensen KB, Ruggiu M, Mele A, Ule A, Darnell RB (2003) CLIP identifies Nova-regulated RNA networks in the brain. Science 302(5648):1212–1215

    Article  CAS  PubMed  Google Scholar 

  68. Ule J, Jensen K, Mele A, Darnell RB (2005) CLIP: a method for identifying protein-RNA interaction sites in living cells. Methods 37(4):376–386

    Article  CAS  PubMed  Google Scholar 

  69. Cabianca D, Casa V, Bodega B, Xynos A, Ginelli E, Tanaka Y, Gabellini D (2012) A long ncRNA links copy number variation to a polycomb/trithorax epigenetic switch in FSHD muscular dystrophy. Cell 149(4):819–831

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  70. Orom UA, Derrien T, Beringer M, Gumireddy K, Gardini A, Bussotti G, Lai F, Zytnicki M, Notredame C, Huang Q, Guigo R, Shiekhattar R (2010) Long Non coding RNAs with enhancer-like function in human cells. Cell 143(1):46–58

    Google Scholar 

  71. Tsai M, Manor O, Wan Y, Mosammaparast N, Wang JK, Lan F, Shi Y, Segal E, Chang HY (2010) Long Non coding RNA as modular scaffold of histone modification complexes. Science 329(5992):689–693

    Google Scholar 

  72. Duca M, Vekhoff P, Oussedik K, Halby L, Arimondo PB (2008) The triple helix: 50 years later, the outcome. Nucleic Acids Res 36(16):5123–5138

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  73. Koziol MJ, Rinn JL (2010) RNA traffic control of chromatin complexes. Curr Opin Genet Dev 20(2):142–148

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  74. Pedace L, De Simone P, Castori M, Sperduti I, Silipo V, Eibenschutz L, De Bernardo C, Buccini P, Moscarella E, Panetta C, Ferrari A, Grammatico P, Catricala C (2011) Clinical features predicting identification of CDKN2A mutations in Italian patients with familial cutaneous melanoma. Cancer Epidemiol 35:e116–e120

    Article  CAS  PubMed  Google Scholar 

  75. Tenenbaum S, Carson CC, Lager PJ, Keene JD (2000) Identifying mRNA subsets in messenger ribonucleoprotein complexes by using cDNA arrays. Proc Natl Acad Sci U S A 97(26):14085–14090

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  76. Tenenbaum S, Lager PJ, Carson CC, Keene JD (2002) Ribonomics: identifying mRNA subsets in mRNP complexes using antibodies to RNA-binding proteins and genomic arrays. Methods 26(2):191–198

    Article  CAS  PubMed  Google Scholar 

  77. Keene J, Komisarow JM, Friedersdorf MB (2006) RIP-Chip: the isolation and identification of mRNAs, microRNAs and protein components of ribonucleoprotein complexes from cell extracts. Nat Protoc 1(1):302–307

    Article  CAS  PubMed  Google Scholar 

  78. Kaneko S, Manley JL (2005) The mammalian RNA polymerase II C-terminal domain interacts with RNA to suppress transcription-coupled 3′ end formation. Mol Cell 20(1):91–103

    Article  CAS  PubMed  Google Scholar 

  79. Penalva L, Tenenbaum SA, Keene JD (2004) Gene expression analysis of messenger RNP complexes. Methods Mol Biol 257:125–134

    CAS  PubMed  Google Scholar 

  80. Kunitomo H, Uesugi H, Kohara Y, Iino Y (2005) Identification of ciliated sensory neuron-expressed genes in Caenorhabditis elegans using targeted pull-down of poly(A) tails. Genome Biol 6(2):R17

    Article  PubMed  PubMed Central  Google Scholar 

  81. Guil S, Soler M, Portela A, Carrere J, Fonalleras E, Gomez A, Villanueva A, Esteller M (2012) Intronic RNAs mediate EZH2 regulation of epigenetic targets. Nat Struct Mol Biol 19:664–670

    Article  CAS  PubMed  Google Scholar 

  82. Guttman M, Amit I, Garber M, French C, Lin MF, Feldser D, Huarte M, Zuk O, Carey BW, Cassady JP, Cabili MN, Jaenisch R, Mikkelsen TS, Jacks T, Hacohen N, Bernstein BE, Kellis M, Regev A, Rinn JL, Lander ES (2009) Chromatin signature reveals over a thousand highly conserved large Non coding RNAs in mammals. Nature 458(7235):223–227

    Google Scholar 

  83. Magistri M, Faghihi MA, St Laurent G 3rd, Wahlestedt C (2012) Regulation of chromatin structure by long Non coding RNAs: focus on natural antisense transcripts. Trends Genet 28:389–396

    Google Scholar 

  84. Mikkelsen T, Ku M, Jaffe DB, Issac B, Lieberman E, Giannoukos G, Alvarez P, Brockman W, Kim TK, Koche RP, Lee W, Mendenhall E, O'Donovan A, Presser A, Russ C, Xie X, Meissner A, Wernig M, Jaenisch R, Nusbaum C, Lander ES, Bernstein BE (2007) Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 448:553–560

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  85. Pandey R, Mondal T, Mohammad F, Enroth S, Redrup L, Komorowski J, Nagano T, Mancini-Dinardo D, Kanduri C (2008) Kcnq1ot1 antisense Non coding RNA mediates lineage-specific transcriptional silencing through chromatin-level regulation. Mol Cell 32(2):232–246

    Google Scholar 

  86. Dundr M, Hoffmann-Rohrer U, Hu Q, Grummt I, Rothblum LI, Phair RD, Misteli T (2002) A kinetic framework for a mammalian RNA polymerase in vivo. Science 298(5598):1623–1626

    Article  CAS  PubMed  Google Scholar 

  87. Cheutin T, McNairn AJ, Jenuwein T, Gilbert DM, Singh PB, Misteli T (2003) Maintenance of stable heterochromatin domains by dynamic HP1 binding. Science 299(5607):721–725

    Article  CAS  PubMed  Google Scholar 

  88. Koyanagi M, Baguet A, Martens J, Margueron R, Jenuwein T, Bix M (2005) EZH2 and histone 3 trimethyl lysine 27 associated with Il4 and Il13 gene silencing in Th1 cells. J Biol Chem 280(36):31470–31477

    Article  CAS  PubMed  Google Scholar 

  89. Metivier R, Penot G, Carmouche RP, Hubner MR, Reid G, Denger S, Manu D, Brand H, Kos M, Benes V, Gannon F (2004) Transcriptional complexes engaged by apo-estrogen receptor-alpha isoforms have divergent outcomes. EMBO J 23(18):3653–3666

    Google Scholar 

  90. Nelson J, Denisenko O, Bomsztyk K (2006) Protocol for the fast chromatin immunoprecipitation (ChIP) method. Nat Protoc 1(1):179–185

    Article  CAS  PubMed  Google Scholar 

  91. Nelson J, Denisenko O, Sova P, Bomsztyk K (2006) Fast chromatin immunoprecipitation assay. Nucleic Acids Res 34(1), e2

    Article  PubMed  PubMed Central  Google Scholar 

  92. Topisirovic I, Siddiqui N, Lapointe VL, Trost M, Thibault P, Bangeranye C, Pinol-Roma S, Borden KL (2009) Molecular dissection of the eukaryotic initiation factor 4E (eIF4E) export-competent RNP. EMBO J 28(8):1087–1098

    Google Scholar 

Download references

Acknowledgement

MEA-A is recipient of the Rodney and Elaine Davies Cancer Research Fellowship and funded by the Auckland Medical Research Foundation. Authors are greatly thankful to Professor Bruce Baguley for reading the manuscript and his critical comments. DJK is funded by the National Breast Cancer Foundation, Australia.

Author information

Author notes

    Authors and Affiliations

    1. Auckland Cancer Society Research Centre, University of Auckland, 85 Park Rd, Grafton, Auckland, 1023, New Zealand

      Marjan E. Askarian-Amiri, Debina Sarkar & Graeme Finlay

    2. Australian Institute of Bioengineering and Nanotechnology, University of Queensland, Corner of College and Coopers Roads, Building 75, St Lucia, QLD, 4067, Australia

      Darren J. Korbie

    Authors
    1. Marjan E. Askarian-Amiri
      View author publications

      You can also search for this author in PubMed Google Scholar

    2. Darren J. Korbie
      View author publications

      You can also search for this author in PubMed Google Scholar

    3. Debina Sarkar
      View author publications

      You can also search for this author in PubMed Google Scholar

    4. Graeme Finlay
      View author publications

      You can also search for this author in PubMed Google Scholar

    Corresponding author

    Correspondence to Marjan E. Askarian-Amiri .

    Editor information

    Editors and Affiliations

    1. UQ Centre for Clinical Research, The Royal Brisbane and Women’s Hospital, University of Queensland and Pathology Queensland, Brisbane, Queensland, Australia

      Sunil R. Lakhani

    2. Peter MacCallum Cancer Centre, University of Melbourne, Melbourne, Victoria, Australia

      Stephen B. Fox

    Rights and permissions

    Reprints and permissions

    Copyright information

    © 2016 Springer Science+Business Media LLC

    About this chapter

    Cite this chapter

    Askarian-Amiri, M.E., Korbie, D.J., Sarkar, D., Finlay, G. (2016). Methods Used for Noncoding RNAs Analysis. In: Lakhani, S., Fox, S. (eds) Molecular Pathology in Cancer Research. Springer, New York, NY. https://doi.org/10.1007/978-1-4939-6643-1_8

    Download citation

    Publish with us

    Policies and ethics

    Search

    Navigation