메뉴 건너뛰기




Volumn 1402, Issue , 2016, Pages 271-286

Analyzing MiRNA–LncRNA interactions

Author keywords

Experimentally; HITS CLIP; In silico predictions; Interaction; lncRNA; microRNA; PAR CLIP; Sponge; Supported

Indexed keywords

LONG UNTRANSLATED RNA; MICRORNA;

EID: 84953276825     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-4939-3378-5_21     Document Type: Chapter
Times cited : (776)

References (55)
  • 1
    • 84865790047 scopus 로고    scopus 로고
    • An integrated encyclopedia of DNA elements in the human genome
    • ENCODE Project Consortium (2012) An integrated encyclopedia of DNA elements in the human genome. Nature 489(7414):57-74
    • (2012) Nature , vol.489 , Issue.7414 , pp. 57-74
  • 2
    • 78751477191 scopus 로고    scopus 로고
    • Gene silencing by microRNAs: Contributions of translational repression and mRNA decay
    • Huntzinger E, Izaurralde E (2011) Gene silencing by microRNAs: contributions of translational repression and mRNA decay. Nat Rev Genet 12(2):99-110
    • (2011) Nat Rev Genet , vol.12 , Issue.2 , pp. 99-110
    • Huntzinger, E.1    Izaurralde, E.2
  • 3
    • 77949621355 scopus 로고    scopus 로고
    • miRBase: MicroRNA sequences and annotation
    • Unit12.9.1-Unit 12.9.10
    • Griffiths-Jones S (2010) miRBase: microRNA sequences and annotation. Curr Protoc Bioinformatics Chapter 12:Unit12.9.1-Unit 12.9.10
    • (2010) Curr Protoc Bioinformatics Chapter , vol.12
    • Griffiths-Jones, S.1
  • 4
    • 79955586226 scopus 로고    scopus 로고
    • Long noncoding RNAs: The search for function
    • Baker M (2011) Long noncoding RNAs: the search for function. Nat Methods 8(5):379-383
    • (2011) Nat Methods , vol.8 , Issue.5 , pp. 379-383
    • Baker, M.1
  • 5
    • 80052978224 scopus 로고    scopus 로고
    • Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses
    • Cabili MN et al (2011) Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev 25(18):1915-1927
    • (2011) Genes Dev , vol.25 , Issue.18 , pp. 1915-1927
    • Cabili, M.N.1
  • 6
    • 84890852686 scopus 로고    scopus 로고
    • Evolutionary conservation of long non-coding RNAs; sequence, structure, function
    • Johnsson P et al (2014) Evolutionary conservation of long non-coding RNAs; sequence, structure, function. Biochim Biophys Acta 1840(3):1063-1071
    • (2014) Biochim Biophys Acta , vol.1840 , Issue.3 , pp. 1063-1071
    • Johnsson, P.1
  • 7
    • 84861904178 scopus 로고    scopus 로고
    • Genome regulation by long noncoding RNAs
    • Rinn JL, Chang HY (2012) Genome regulation by long noncoding RNAs. Annu Rev Biochem 81:145-166
    • (2012) Annu Rev Biochem , vol.81 , pp. 145-166
    • Rinn, J.L.1    Chang, H.Y.2
  • 8
    • 84863495094 scopus 로고    scopus 로고
    • The hallmarks of cancer: A long non-coding RNA point of view
    • Gutschner T, Diederichs S (2012) The hallmarks of cancer: a long non-coding RNA point of view. RNA Biol 9(6):703-719
    • (2012) RNA Biol , vol.9 , Issue.6 , pp. 703-719
    • Gutschner, T.1    Diederichs, S.2
  • 9
    • 77956542998 scopus 로고    scopus 로고
    • CREB up-regulates long non-coding RNA, HULC expression through interaction with microRNA-372 in liver cancer
    • Wang J et al (2010) CREB up-regulates long non-coding RNA, HULC expression through interaction with microRNA-372 in liver cancer. Nucleic Acids Res 38(16):5366-5383
    • (2010) Nucleic Acids Res , vol.38 , Issue.16 , pp. 5366-5383
    • Wang, J.1
  • 10
    • 73649116987 scopus 로고    scopus 로고
    • The DLEU2/miR- 15a/16-1 cluster controls B cell proliferation and its deletion leads to chronic lymphocytic leukemia
    • Klein U et al (2010) The DLEU2/miR- 15a/16-1 cluster controls B cell proliferation and its deletion leads to chronic lymphocytic leukemia. Cancer Cell 17(1):28-40
    • (2010) Cancer Cell , vol.17 , Issue.1 , pp. 28-40
    • Klein, U.1
  • 11
    • 33847271696 scopus 로고    scopus 로고
    • The imprinted H19 noncoding RNA is a primary microRNA precursor
    • Cai X, Cullen BR (2007) The imprinted H19 noncoding RNA is a primary microRNA precursor. RNA 13(3):313-316
    • (2007) RNA , vol.13 , Issue.3 , pp. 313-316
    • Cai, X.1    Cullen, B.R.2
  • 12
    • 79961170994 scopus 로고    scopus 로고
    • A ceRNA hypothesis: The Rosetta Stone of a hidden RNA language?
    • Salmena L et al (2011) A ceRNA hypothesis: the Rosetta Stone of a hidden RNA language? Cell 146(3):353-358
    • (2011) Cell , vol.146 , Issue.3 , pp. 353-358
    • Salmena, L.1
  • 13
    • 84876523096 scopus 로고    scopus 로고
    • DIANALncBase: Experimentally verified and computationally predicted microRNA targets on long non-coding RNAs
    • Paraskevopoulou MD et al (2013) DIANALncBase: experimentally verified and computationally predicted microRNA targets on long non-coding RNAs. Nucleic Acids Res 41 (Database issue):D239-D245
    • (2013) Nucleic Acids Res , vol.41 , Issue.Database issue , pp. D239-D245
    • Paraskevopoulou, M.D.1
  • 14
    • 84864464973 scopus 로고    scopus 로고
    • DIANA miRPath v. 2.0: Investigating the combinatorial effect of microRNAs in pathways
    • Vlachos IS et al (2012) DIANA miRPath v. 2.0: investigating the combinatorial effect of microRNAs in pathways. Nucleic Acids Res 40(Web Server issue):W498-W504
    • (2012) Nucleic Acids Res , vol.40 , Issue.Web Server issue , pp. W498-W504
    • Vlachos, I.S.1
  • 15
    • 84923263791 scopus 로고    scopus 로고
    • microTSS: Accurate microRNA transcription start site identification reveals a significant number of divergent pri- miRNAs
    • Georgakilas G et al (2014) microTSS: accurate microRNA transcription start site identification reveals a significant number of divergent pri- miRNAs. Nat Commun 5:5700
    • (2014) Nat Commun , vol.5 , pp. 5700
    • Georgakilas, G.1
  • 16
    • 80455143733 scopus 로고    scopus 로고
    • miRNA-dependent gene silencing involving Ago2-mediated cleavage of a circular antisense RNA
    • Hansen TB et al (2011) miRNA-dependent gene silencing involving Ago2-mediated cleavage of a circular antisense RNA. EMBO J 30(21): 4414-4422
    • (2011) EMBO J , vol.30 , Issue.21 , pp. 4414-4422
    • Hansen, T.B.1
  • 17
    • 84875369248 scopus 로고    scopus 로고
    • Circular RNAs are a large class of animal RNAs with regulatory potency
    • Memczak S et al (2013) Circular RNAs are a large class of animal RNAs with regulatory potency. Nature 495(7441):333-338
    • (2013) Nature , vol.495 , Issue.7441 , pp. 333-338
    • Memczak, S.1
  • 18
    • 84875372911 scopus 로고    scopus 로고
    • Natural RNA circles function as efficient microRNA sponges
    • Hansen TB et al (2013) Natural RNA circles function as efficient microRNA sponges. Nature 495(7441):384-388
    • (2013) Nature , vol.495 , Issue.7441 , pp. 384-388
    • Hansen, T.B.1
  • 19
    • 34548230885 scopus 로고    scopus 로고
    • Ultraconserved regions encoding ncRNAs are altered in human leukemias and carcinomas
    • Calin GA et al (2007) Ultraconserved regions encoding ncRNAs are altered in human leukemias and carcinomas. Cancer Cell 12(3):215-229
    • (2007) Cancer Cell , vol.12 , Issue.3 , pp. 215-229
    • Calin, G.A.1
  • 20
    • 77952698932 scopus 로고    scopus 로고
    • Evidence for natural antisense transcript-mediated inhibition of microRNA function
    • Faghihi MA et al (2010) Evidence for natural antisense transcript-mediated inhibition of microRNA function. Genome Biol 11(5):R56
    • (2010) Genome Biol , vol.11 , Issue.5
    • Faghihi, M.A.1
  • 21
    • 84865379361 scopus 로고    scopus 로고
    • LincRNA-p21 suppresses target mRNA translation
    • Yoon JH et al (2012) LincRNA-p21 suppresses target mRNA translation. Mol Cell 47(4):648-655
    • (2012) Mol Cell , vol.47 , Issue.4 , pp. 648-655
    • Yoon, J.H.1
  • 22
    • 77953957633 scopus 로고    scopus 로고
    • A coding-independent function of gene and pseudogene mRNAs regulates tumour biology
    • Poliseno L et al (2010) A coding-independent function of gene and pseudogene mRNAs regulates tumour biology. Nature 465(7301): 1033-1038
    • (2010) Nature , vol.465 , Issue.7301 , pp. 1033-1038
    • Poliseno, L.1
  • 23
    • 80054715378 scopus 로고    scopus 로고
    • A long noncoding RNA controls muscle differentiation by functioning as a competing endogenous RNA
    • Cesana M et al (2011) A long noncoding RNA controls muscle differentiation by functioning as a competing endogenous RNA. Cell 147(2): 358-369
    • (2011) Cell , vol.147 , Issue.2 , pp. 358-369
    • Cesana, M.1
  • 24
    • 34547497309 scopus 로고    scopus 로고
    • Target mimicry provides a new mechanism for regulation of microRNA activity
    • Franco-Zorrilla JM et al (2007) Target mimicry provides a new mechanism for regulation of microRNA activity. Nat Genet 39(8):1033-1037
    • (2007) Nat Genet , vol.39 , Issue.8 , pp. 1033-1037
    • Franco-Zorrilla, J.M.1
  • 25
    • 84924579072 scopus 로고    scopus 로고
    • miR-CLIP capture of a miRNA targetome uncovers a lincRNA H19- miR- 106a interaction
    • Imig J et al (2015) miR-CLIP capture of a miRNA targetome uncovers a lincRNA H19- miR- 106a interaction. Nat Chem Biol 11(2): 107-114
    • (2015) Nat Chem Biol , vol.11 , Issue.2 , pp. 107-114
    • Imig, J.1
  • 26
    • 84885374473 scopus 로고    scopus 로고
    • The imprinted H19 lncRNA antagonizes let-7 microRNAs
    • Kallen AN et al (2013) The imprinted H19 lncRNA antagonizes let-7 microRNAs. Mol Cell 52(1):101-112
    • (2013) Mol Cell , vol.52 , Issue.1 , pp. 101-112
    • Kallen, A.N.1
  • 27
    • 84899630922 scopus 로고    scopus 로고
    • Linc-RNA-RoR acts as a "sponge" against mediation of the differentiation of endometrial cancer stem cells by micro RNA-145
    • Zhou X et al (2014) Linc-RNA-RoR acts as a "sponge" against mediation of the differentiation of endometrial cancer stem cells by micro RNA-145. Gynecol Oncol 133(2):333-339
    • (2014) Gynecol Oncol , vol.133 , Issue.2 , pp. 333-339
    • Zhou, X.1
  • 28
    • 84899912204 scopus 로고    scopus 로고
    • The long noncoding RNA CHRF regulates cardiac hypertrophy by targeting miR-489
    • Wang K et al (2014) The long noncoding RNA CHRF regulates cardiac hypertrophy by targeting miR-489. Circ Res 114(9):1377- 1388
    • (2014) Circ Res , vol.114 , Issue.9 , pp. 1377-1388
    • Wang, K.1
  • 29
    • 84922771430 scopus 로고    scopus 로고
    • Silencing of long noncoding RNA MALAT1 by miR-101 and miR- 217inhibits proliferation, migration and invasion of esophageal squamous cell carcinoma cells
    • Wang X et al (2015) Silencing of long noncoding RNA MALAT1 by miR-101 and miR- 217inhibits proliferation, migration and invasion of esophageal squamous cell carcinoma cells. J Biol Chem 290(7):3925-3935
    • (2015) J Biol Chem , vol.290 , Issue.7 , pp. 3925-3935
    • Wang, X.1
  • 30
    • 84893441632 scopus 로고    scopus 로고
    • MicroRNA-9 targets the long non-coding RNA MALAT1 for degradation in the nucleus
    • Leucci E et al (2013) MicroRNA-9 targets the long non-coding RNA MALAT1 for degradation in the nucleus. Sci Rep 3:2535
    • (2013) Sci Rep , vol.3 , pp. 2535
    • Leucci, E.1
  • 31
    • 84888003905 scopus 로고    scopus 로고
    • Hsa-miR-125b suppresses bladder cancer development by down- regulating oncogene SIRT7 and oncogenic long noncoding RNA MALAT1
    • Han Y et al (2013) Hsa-miR-125b suppresses bladder cancer development by down- regulating oncogene SIRT7 and oncogenic long noncoding RNA MALAT1. FEBS Lett
    • (2013) FEBS Lett
    • Han, Y.1
  • 32
    • 84922394216 scopus 로고    scopus 로고
    • Hsa-miR-1 downregulates long non-coding RNA urothelial cancer associated 1 in bladder cancer
    • Wang T et al (2014) Hsa-miR-1 downregulates long non-coding RNA urothelial cancer associated 1 in bladder cancer. Tumour Biol 35(10):10075-10084
    • (2014) Tumour Biol , vol.35 , Issue.10 , pp. 10075-10084
    • Wang, T.1
  • 33
    • 84921374786 scopus 로고    scopus 로고
    • The long non-coding RNA PCAT-1 promotes prostate cancer cell proliferation through cMyc
    • Prensner JR et al (2014) The long non-coding RNA PCAT-1 promotes prostate cancer cell proliferation through cMyc. Neoplasia 16(11): 900-908
    • (2014) Neoplasia , vol.16 , Issue.11 , pp. 900-908
    • Prensner, J.R.1
  • 34
    • 84918809202 scopus 로고    scopus 로고
    • Long non-coding RNA CASC2 suppresses malignancy in human gliomas by miR-21
    • Wang P et al (2015) Long non-coding RNA CASC2 suppresses malignancy in human gliomas by miR-21. Cell Signal 27(2):275-282
    • (2015) Cell Signal , vol.27 , Issue.2 , pp. 275-282
    • Wang, P.1
  • 35
    • 84905483304 scopus 로고    scopus 로고
    • MDRL lncRNA regulates the processing of miR-484 primary transcript by targeting miR-361
    • Wang K et al (2014) MDRL lncRNA regulates the processing of miR-484 primary transcript by targeting miR-361. PLoS Genet 10(7), e1004467
    • (2014) PLoS Genet , vol.10 , Issue.7
    • Wang, K.1
  • 36
    • 84922423166 scopus 로고    scopus 로고
    • LncRNA-HOST2 regulates cell biological behaviors in epithelial ovarian cancer through a mechanism involving microRNA let-7b
    • Gao Y et al (2015) LncRNA-HOST2 regulates cell biological behaviors in epithelial ovarian cancer through a mechanism involving microRNA let-7b. Hum Mol Genet 24(3):841-852
    • (2015) Hum Mol Genet , vol.24 , Issue.3 , pp. 841-852
    • Gao, Y.1
  • 37
    • 84881015477 scopus 로고    scopus 로고
    • Genistein inhibits prostate cancer cell growth by targeting miR- 34a and oncogenic HOTAIR
    • Chiyomaru T et al (2013) Genistein inhibits prostate cancer cell growth by targeting miR- 34a and oncogenic HOTAIR. PLoS One 8(8), e70372
    • (2013) PLoS One , vol.8 , Issue.8
    • Chiyomaru, T.1
  • 38
    • 84902760639 scopus 로고    scopus 로고
    • Long non-coding RNA HOTAIR, a c-Myc activated driver of malignancy, negatively regulates miRNA-130a in gallbladder cancer
    • Ma MZ et al (2014) Long non-coding RNA HOTAIR, a c-Myc activated driver of malignancy, negatively regulates miRNA-130a in gallbladder cancer. Mol Cancer 13:156
    • (2014) Mol Cancer , vol.13 , pp. 156
    • Ma, M.Z.1
  • 39
    • 84921417537 scopus 로고    scopus 로고
    • The long intergenic noncoding RNA UFC1, a target of MicroRNA 34a, interacts with the mRNA stabilizing protein HuR to increase levels of beta-Catenin in HCC cells
    • Cao C et al (2015) The long intergenic noncoding RNA UFC1, a target of MicroRNA 34a, interacts with the mRNA stabilizing protein HuR to increase levels of beta-Catenin in HCC cells. Gastroenterology 148(2):415-26.e18
    • (2015) Gastroenterology , vol.148 , Issue.2 , pp. 415-26.e18
    • Cao, C.1
  • 40
    • 84885423196 scopus 로고    scopus 로고
    • Negative regulation of lncRNA GAS5 by miR-21
    • Zhang Z et al (2013) Negative regulation of lncRNA GAS5 by miR-21. Cell Death Differ 20(11):1558-1568
    • (2013) Cell Death Differ , vol.20 , Issue.11 , pp. 1558-1568
    • Zhang, Z.1
  • 41
    • 81855183267 scopus 로고    scopus 로고
    • microRNA-29 can regulate expression of the long non-coding RNA gene MEG3 in hepatocellular cancer
    • Braconi C et al (2011) microRNA-29 can regulate expression of the long non-coding RNA gene MEG3 in hepatocellular cancer. Oncogene 30(47):4750-4756
    • (2011) Oncogene , vol.30 , Issue.47 , pp. 4750-4756
    • Braconi, C.1
  • 42
    • 84874634893 scopus 로고    scopus 로고
    • A long non-coding RNA, PTCSC3, as a tumor suppressor and a target of miRNAs in thyroid cancer cells
    • Fan M et al (2013) A long non-coding RNA, PTCSC3, as a tumor suppressor and a target of miRNAs in thyroid cancer cells. Exp Ther Med 5(4):1143-1146
    • (2013) Exp Ther Med , vol.5 , Issue.4 , pp. 1143-1146
    • Fan, M.1
  • 43
    • 84941087952 scopus 로고    scopus 로고
    • DIANA-TarBase v7.0: Indexing more than half a million experimentally supported miRNA:MRNA interactions
    • Vlachos IS et al (2015) DIANA-TarBase v7.0: indexing more than half a million experimentally supported miRNA:mRNA interactions. Nucleic Acids Res 43(Database issue):D153-D159
    • (2015) Nucleic Acids Res , vol.43 , Issue.Database issue , pp. D153-D159
    • Vlachos, I.S.1
  • 44
    • 67749132423 scopus 로고    scopus 로고
    • Argonaute HITS-CLIP decodes microRNA-mRNA interaction maps
    • Chi SW et al (2009) Argonaute HITS-CLIP decodes microRNA-mRNA interaction maps. Nature 460(7254):479-486
    • (2009) Nature , vol.460 , Issue.7254 , pp. 479-486
    • Chi, S.W.1
  • 45
    • 77950920903 scopus 로고    scopus 로고
    • Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP
    • Hafner M et al (2010) Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP. Cell 141(1):129-141
    • (2010) Cell , vol.141 , Issue.1 , pp. 129-141
    • Hafner, M.1
  • 46
    • 84876935138 scopus 로고    scopus 로고
    • Mapping the human miRNA interactome by CLASH reveals frequent noncanonical binding
    • Helwak A et al (2013) Mapping the human miRNA interactome by CLASH reveals frequent noncanonical binding. Cell 153(3):654-665
    • (2013) Cell , vol.153 , Issue.3 , pp. 654-665
    • Helwak, A.1
  • 47
    • 84905049901 scopus 로고    scopus 로고
    • Trimmomatic: A flexible trimmer for Illumina sequence data
    • Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30(15):2114- 2120
    • (2014) Bioinformatics , vol.30 , Issue.15 , pp. 2114-2120
    • Bolger, A.M.1    Lohse, M.2    Usadel, B.3
  • 48
    • 65449136284 scopus 로고    scopus 로고
    • TopHat: Discovering splice junctions with RNA-Seq
    • Trapnell C, Pachter L, Salzberg SL (2009) TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25(9):1105-1111
    • (2009) Bioinformatics , vol.25 , Issue.9 , pp. 1105-1111
    • Trapnell, C.1    Pachter, L.2    Salzberg, S.L.3
  • 49
    • 77951820899 scopus 로고    scopus 로고
    • Fast and SNP-tolerant detection of complex variants and splicing in short reads
    • Wu TD, Nacu S (2010) Fast and SNP-tolerant detection of complex variants and splicing in short reads. Bioinformatics 26(7):873-881
    • (2010) Bioinformatics , vol.26 , Issue.7 , pp. 873-881
    • Wu, T.D.1    Nacu, S.2
  • 50
    • 84883579190 scopus 로고    scopus 로고
    • DIANAmicroT web server v5.0: Service integration into miRNA functional analysis workflows
    • Paraskevopoulou MD et al (2013) DIANAmicroT web server v5.0: service integration into miRNA functional analysis workflows. Nucleic Acids Res 41(Web Server issue): W169-W173
    • (2013) Nucleic Acids Res , vol.41 , Issue.Web Server issue , pp. W169-W173
    • Paraskevopoulou, M.D.1
  • 51
    • 3242877996 scopus 로고    scopus 로고
    • Sfold web server for statistical folding and rational design of nucleic acids
    • Ding Y, Chan CY, Lawrence CE (2004) Sfold web server for statistical folding and rational design of nucleic acids. Nucleic Acids Res 32(Web Server issue):W135-W141
    • (2004) Nucleic Acids Res , vol.32 , Issue.Web Server issue , pp. W135-W141
    • Ding, Y.1    Chan, C.Y.2    Lawrence, C.E.3
  • 52
    • 4644237189 scopus 로고    scopus 로고
    • Fast and effective prediction of microRNA/target duplexes
    • Rehmsmeier M et al (2004) Fast and effective prediction of microRNA/target duplexes. RNA 10(10):1507-1517
    • (2004) RNA , vol.10 , Issue.10 , pp. 1507-1517
    • Rehmsmeier, M.1
  • 53
    • 74949092081 scopus 로고    scopus 로고
    • Detection of nonneutral substitution rates on mammalian phylogenies
    • Pollard KS et al (2010) Detection of nonneutral substitution rates on mammalian phylogenies. Genome Res 20(1):110-121
    • (2010) Genome Res , vol.20 , Issue.1 , pp. 110-121
    • Pollard, K.S.1
  • 54
    • 84860742355 scopus 로고    scopus 로고
    • NONCODE v3.0: Integrative annotation of long noncoding RNAs
    • Bu D et al (2012) NONCODE v3.0: integrative annotation of long noncoding RNAs. Nucleic Acids Res 40(Database issue): D210-D215
    • (2012) Nucleic Acids Res , vol.40 , Issue.Database issue , pp. D210-D215
    • Bu, D.1
  • 55
    • 84858221706 scopus 로고    scopus 로고
    • Ensembl 2012
    • Flicek P et al (2012) Ensembl 2012. Nucleic Acids Res 40(Database issue):D84-D90
    • (2012) Nucleic Acids Res , vol.40 , Issue.Database issue , pp. D84-D90
    • Flicek, P.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.