Cited by 3,910Cancer-related molecular mechanisms researchMicroRNA in disease regulationRNA Research and Splicing

The multilayered complexity of ceRNA crosstalk and competition

Open access
Tay, Yvonne, Rinn, John, Pandolfi, Pier Paolo·2014·Nature

Abstract

Recent reports have described an intricate interplay among diverse RNA species, including protein-coding messenger RNAs and non-coding RNAs such as long non-coding RNAs, pseudogenes and circular RNAs. These RNA transcripts act as competing endogenous RNAs (ceRNAs) or natural microRNA sponges - they communicate with and co-regulate each other by competing for binding to shared microRNAs, a family of small non-coding RNAs that are important post-transcriptional regulators of gene expression. Understanding this novel RNA crosstalk will lead to significant insight into gene regulatory networks and have implications in human development and disease.

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1038/nature12986

Cites

4 of 4 references verified0 citation errors · 0 not checkable

Statistics

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Cites

Flagged first, then by citations

Research works printed but not linked: 96

  1. [1]Volders PJ LNCipedia: a database for annotated human lncRNA transcript sequences and structures Nucleic Acids Res 41 D246 D251 2013 23042674 PMC3531107
  2. [2]Dunham I An integrated encyclopedia of DNA elements in the human genome Nature 489 57 74 2012 22955616 PMC3439153
  3. [3]Nagano T Fraser P No-nonsense functions for long noncoding RNAs Cell 145 178 181 2011 21496640
  4. [4]Brockdorff N The product of the mouse Xist gene is a 15 kb inactive X-specific transcript containing no conserved ORF and located in the nucleus Cell 71 515 526 1992 1423610
  5. [5]Shabalina SA Spiridonov NA The mammalian transcriptome and the function of non-coding DNA sequences Genome Biol 5 105 2004 15059247 PMC395773
  6. [6]Gutschner T Diederichs S The hallmarks of cancer: a long non-coding RNA point of view RNA Biol 9 703 719 2012 22664915 PMC3495743
  7. [7]Mattick JS Non-coding RNAs: the architects of eukaryotic complexity EMBO Rep 2 986 991 2001 11713189 PMC1084129
  8. [8]Mattick JS Gagen MJ The evolution of controlled multitasked gene networks: the role of introns and other noncoding RNAs in the development of complex organisms Mol Biol Evol 18 1611 1630 2001 11504843
  9. [9]Guttman M Rinn JL Modular regulatory principles of large non-coding RNAs Nature 482 339 346 2012 22337053 PMC4197003
  10. [10]Ebert MS Sharp PA Emerging roles for natural microRNA sponges Curr Biol 20 R858 R861 2010 20937476 PMC4070712
  11. [11]Salmena L A ceRNA hypothesis: the Rosetta Stone of a hidden RNA language? Cell 146 353 358 2011 This essay proposes that all types of RNA transcripts may crosstalk and be co-regulated through a predictable ‘ceRNA language’ of RNA, and summarizes the experimental evidence in support of the ceRNA hypothesis at the time 21802130 PMC3235919
  12. [12]Seitz H Redefining microRNA targets Curr Biol 19 870 873 2009 19375315
  13. [13]Wee LM Flores-Jasso CF Salomon WE Zamore PD Argonaute divides its RNA guide into domains with distinct functions and RNA-binding properties Cell 151 1055 1067 2012 This work investigates the effect of miRNA and sponge transcript abundance on the efficacy of miRNA target repression and proposes that the ceRNA hypothesis may only apply to a subset of moderate or low abundance miRNAs 23178124 PMC3595543
  14. [14]Cazalla D Yario T Steitz JA Down-regulation of a host microRNA by a Herpesvirus saimiri noncoding RNA Science 328 1563 1566 2010 This work extends ceRNA crosstalk to viruses and shows that a viral non-coding RNA sequesters and promotes the degradation of a miRNA in infected host cells 20558719 PMC3075239
  15. [15]Franco-Zorrilla JM Target mimicry provides a new mechanism for regulation of microRNA activity Nature Genet 39 1033 1037 2007 This study in plants, which demonstrates effective sequestration of miR-399 by the non-coding transcript IPS1, was the first to describe a role for non-coding RNAs as natural microRNA sponges in eukaryotic cells 17643101
  16. [16]Poliseno L A coding-independent function of gene and pseudogene mRNAs regulates tumour biology Nature 465 1033 1038 2010 This work focusing on the PTEN pseudogene was the first to define a functional role for expressed pseudogenes in cancer as well as attribute a ceRNA function to pseudogene and protein-coding mRNAs 20577206 PMC3206313
  17. [17]Tay Y Coding-independent regulation of the tumor suppressor PTEN by competing endogenous mRNAs Cell 147 344 357 2011 This study presents a combined computational and experimental approach that can be used as a framework to predict and validate ceRNA interactions 22000013 PMC3235920
  18. [18]Karreth FA In vivo identification of tumor-suppressive PTEN ceRNAs in an oncogenic BRAF-induced mouse model of melanoma Cell 147 382 395 2011 This work used a Sleeping Beauty insertional mutagenesis screen to identify and validate ceRNAs in vivo 22000016 PMC3236086
  19. [19]Sanchez-Diaz P Penalva LO Post-transcription meets post-genomic: the saga of RNA binding proteins in a new era RNA Biol 3 101 109 2006 17114948
  20. [20]Lal A Concurrent versus individual binding of HuR and AUF1 to common labile target mRNAs EMBO J 23 3092 3102 2004 15257295 PMC514922
  21. [21]Barker A Sequence requirements for RNA binding by HuR and AUF1 J Biochem 151 423 437 2012 22368252
  22. [22]Al-Ahmadi W Alternative polyadenylation variants of the RNA binding protein, HuR: abundance, role of AU-rich elements and auto-regulation Nucleic Acids Res 37 3612 3624 2009 19359363 PMC2699509
  23. [23]Yoo S A HuD-ZBP1 ribonucleoprotein complex localizes GAP-43 mRNA into axons through its 3′ untranslated region AU-rich regulatory element J Neurochem 126 792 804 2013 23586486 PMC3766383
  24. [24]Cesana M A long noncoding RNA controls muscle differentiation by functioning as a competing endogenous RNA Cell 147 358 369 2011 22000014 PMC3234495
  25. [25]Wang J CREB up-regulates long non-coding RNA, HULC expression through interaction with microRNA-372 in liver cancer Nucleic Acids Res 38 5366 5383 2010 20423907 PMC2938198
  26. [26]Sumazin P An extensive microRNA-mediated network of RNA-RNA interactions regulates established oncogenic pathways in glioblastoma Cell 147 370 381 2011 This work in glioblastoma demonstrates that ceRNA interactions between approximately 7,000 transcripts are part of a surprisingly extensive post-transcriptional regulatory layer 22000015 PMC3214599
  27. [27]Lee DY A 3′-untranslated region (3′UTR) induces organ adhesion by regulating miR-199a* functions PLoS ONE 4 e4527 2009 19223980 PMC2638016
  28. [28]Brown BD Endogenous microRNA can be broadly exploited to regulate transgene expression according to tissue, lineage and differentiation state Nature Biotechnol 25 1457 1467 2007 18026085
  29. [29]Carè A MicroRNA-133 controls cardiac hypertrophy Nature Med 13 613 618 2007 17468766
  30. [30]Ebert MS Neilson JR Sharp PA MicroRNA sponges: competitive inhibitors of small RNAs in mammalian cells Nature Methods 4 721 726 2007 This study is the first to describe the use of an experimental miRNA sponge to inhibit miRNA function 17694064 PMC3857099
  31. [31]Ebert MS Sharp PA MicroRNA sponges: progress and possibilities RNA 16 2043 2050 2010 20855538 PMC2957044
  32. [32]Kluiver J Generation of miRNA sponge constructs Methods 58 113 117 2012 22836127
  33. [33]Gentner B Stable knockdown of microRNA in vivo by lentiviral vectors Nature Methods 6 63 66 2009 19043411
  34. [34]Valastyan S A pleiotropically acting microRNA, miR-31, inhibits breast cancer metastasis Cell 137 1032 1046 2009 19524507 PMC2766609
  35. [35]Brown BD Naldini L Exploiting and antagonizing microRNA regulation for therapeutic and experimental applications Nature Rev Genet 10 578 585 2009 19609263
  36. [37]Johnsson P A pseudogene long-noncoding-RNA network regulates PTEN transcription and translation in human cells Nature Struct Mol Biol 20 440 446 2013 23435381 PMC3618526
  37. [38]Mitrovich QM Anderson P mRNA surveillance of expressed pseudogenes in C. elegans Curr Biol 15 963 967 2005 15916954
  38. [39]Marques AC Evidence for conserved post-transcriptional roles of unitary pseudogenes and for frequent bifunctionality of mRNAs Genome Biol 13 R102 2012 23153069 PMC3580494
  39. [40]Yoon JH LincRNA-p21 suppresses target mRNA translation Mol Cell 47 648 655 2012 22841487 PMC3509343
  40. [41]Fan M A long non-coding RNA, PTCSC3, as a tumor suppressor and a target of miRNAs in thyroid cancer cells Exp Ther Med 5 1143 1146 2013 23599737 PMC3628718
  41. [42]Kallen AN The imprinted H19 lncRNA antagonizes Let-7 microRNAs Mol Cell 52 101 112 2013 24055342 PMC3843377
  42. [43]Wang Y Endogenous miRNA sponge lincRNA-RoR regulates Oct4, Nanog, and Sox2 in human embryonic stem cell self-renewal Dev Cell 25 69 80 2013 23541921
  43. [44]Capel B Circular transcripts of the testis-determining gene Sry in adult mouse testis Cell 73 1019 1030 1993 7684656
  44. [45]Hansen TB Natural RNA circles function as efficient microRNA sponges Nature 495 384 388 2013 This study was one of the first to functionalize circRNAs as a new class of highly stable and efficient natural miRNA ceRNAs 23446346
  45. [46]Memczak S Circular RNAs are a large class of animal RNAs with regulatory potency Nature 495 333 338 2013 23446348
  46. [48]Taulli R Loretelli C Pandolfi PP From pseudo-ceRNAs to circ-ceRNAs: a tale of cross-talk and competition Nature Struct Mol Biol 20 541 543 2013 23649362 PMC4141855
  47. [49]Wilusz JE Sharp PA Molecular biology. A circuitous route to noncoding RNA Science 340 440 441 2013 23620042 PMC4063205
  48. [50]Lee DY Expression of versican 3′-untranslated region modulates endogenous microRNA functions PLoS ONE 5 e13599 2010 21049042 PMC2963607
  49. [51]Fang L Versican 3′-untranslated region (3′-UTR) functions as a ceRNA in inducing the development of hepatocellular carcinoma by regulating miRNA activity FASEB J 27 907 919 2013 23180826
  50. [52]Jeyapalan Z Expression of CD44 3′-untranslated region regulates endogenous microRNA functions in tumorigenesis and angiogenesis Nucleic Acids Res 39 3026 3041 2011 21149267 PMC3082902
  51. [53]Rutnam ZJ Yang BB The non-coding 3′ UTR of CD44 induces metastasis by regulating extracellular matrix functions J Cell Sci 125 2075 2085 2012 22637644
  52. [54]Kumar MS Hmga2 functions as a competing endogenous RNA to promote lung cancer progression Nature http://dx.doi.org/10.1038/nature12785 2013 This study was the first to demonstrate that an abundant mRNA proteincoding transcript can act as ceRNA to out compete an abundant miRNA such as Let7 PMC3886898 24305048 · DOI
  53. [55]Libri V Murine cytomegalovirus encodes a miR-27 inhibitor disguised as a target Proc Natl Acad Sci USA 109 279 284 2012 22184245 PMC3252920
  54. [56]Marcinowski L Degradation of cellular mir-27 by a novel, highly abundant viral transcript is important for efficient virus replication in vivo PLoS Pathog 8 e1002510 2012 22346748 PMC3276556
  55. [57]Thomas M Lieberman J Lal A Desperately seeking microRNA targets Nature Struct Mol Biol 17 1169 1174 2010 20924405
  56. [58]Sarver AL Subramanian S Competing endogenous RNA database Bioinformation 8 731 733 2012 23055620 PMC3449376
  57. [59]Chi SW Zang JB Mele A Darnell RB Argonaute HITS-CLIP decodes microRNA-mRNA interaction maps Nature 460 479 486 2009 19536157 PMC2733940
  58. [60]Hafner M Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP Cell 141 129 141 2010 20371350 PMC2861495
  59. [61]Thomson DW Bracken CP Goodall GJ Experimental strategies for microRNA target identification Nucleic Acids Res 39 6845 6853 2011 21652644 PMC3167600
  60. [62]Schug J Dynamic recruitment of microRNAs to their mRNA targets in the regenerating liver BMC Genomics 14 264 2013 23597149 PMC3639193
  61. [63]Yoon JH Srikantan S Gorospe M MS2-TRAP (MS2-tagged RNA affinity purification): tagging RNA to identify associated miRNAs Methods 58 81 87 2012 22813890 PMC3493847
  62. [64]Mukherji S MicroRNAs can generate thresholds in target gene expression Nature Genet 43 854 859 2011 21857679 PMC3163764
  63. [65]Ala U Integrated transcriptional and competitive endogenous RNA networks are cross-regulated in permissive molecular environments Proc Natl Acad Sci USA 110 7154 7159 2013 23536298 PMC3645534
  64. [66]Figliuzzi M Marinari E De Martino A MicroRNAs as a selective channel of communication between competing RNAs: a steady-state theory Biophys J 104 1203 1213 2013 23473503 PMC3870798
  65. [67]Loinger A Competition between small RNAs: a quantitative view Biophys J 102 1712 1721 2012 22768926 PMC3328701
  66. [68]Srikantan S Tominaga K Gorospe M Functional interplay between RNA-binding protein HuR and microRNAs Curr Protein Pept Sci 13 372 379 2012 22708488 PMC3535178
  67. [69]Bhattacharyya SN Relief of microRNA-mediated translational repression in human cells subjected to stress Cell 125 1111 1124 2006 16777601
  68. [70]Srikantan S Translational control of TOP2A influences doxorubicin efficacy Mol Cell Biol 31 3790 3801 2011 21768308 PMC3165726
  69. [71]Tominaga K Competitive regulation of nucleolin expression by HuR and miR-494 Mol Cell Biol 31 4219 4231 2011 21859890 PMC3187287
  70. [72]Young LE The mRNA stability factor HuR inhibits microRNA-16 targeting of COX-2 Mol Cancer Res 10 167 180 2012 22049153 PMC3262080
  71. [73]Epis MR The RNA-binding protein HuR opposes the repression of ERBB-2 gene expression by microRNA miR-331–3p in prostate cancer cells J Biol Chem 286 41442 41454 2011 21971048 PMC3308856
  72. [74]Kim HH HuR recruits let-7/RISC to repress c-Myc expression Genes Dev 23 1743 1748 2009 19574298 PMC2720259
  73. [75]Glorian V HuR-dependent loading of miRNA RISC to the mRNA encoding the Ras-related small GTPase RhoB controls its translation during UV-induced apoptosis Cell Death Differ 18 1692 1701 2011 21527938 PMC3190107
  74. [76]Kedde M RNA-binding protein Dnd1 inhibits microRNA access to target mRNA Cell 131 1273 1286 2007 18155131
  75. [77]Ma F MicroRNA-466l upregulates IL-10 expression in TLR-triggered macrophages by antagonizing RNA-binding protein tristetraprolin-mediated IL-10 mRNA degradation J Immunol 184 6053 6059 2010 20410487
  76. [78]Nishikura K Editor meets silencer: crosstalk between RNA editing and RNA interference Nature Rev Mol Cell Biol 7 919 931 2006 17139332 PMC2953463
  77. [79]Maas S Posttranscriptional recoding by RNA editing Adv Protein Chem Struct Biol 86 193 224 2012 22243585
  78. [80]Kawahara Y Redirection of silencing targets by adenosine-to-inosine editing of miRNAs Science 315 1137 1140 2007 17322061 PMC2953418
  79. [81]Kawahara Y Frequency and fate of microRNA editing in human brain Nucleic Acids Res 36 5270 5280 2008 18684997 PMC2532740
  80. [82]Athanasiadis A Rich A Maas S Widespread A-to-I RNA editing of Alu-containing mRNAs in the human transcriptome PLoS Biol 2 e391 2004 15534692 PMC526178
  81. [83]Levanon EY Systematic identification of abundant A-to-I editing sites in the human transcriptome Nature Biotechnol 22 1001 1005 2004 15258596
  82. [85]Panzitt K Characterization of HULC, a novel gene with striking up-regulation in hepatocellular carcinoma, as noncoding RNA Gastroenterology 132 330 342 2007 17241883
  83. [87]Lembo A Di Cunto F Provero P Shortening of 3′UTRs correlates with poor prognosis in breast and lung cancer PLoS ONE 7 e31129 2012 22347440 PMC3275581
  84. [88]Pal S Gupta R Davuluri RV Alternative transcription and alternative splicing in cancer Pharmacol Ther 136 283 294 2012 22909788
  85. [89]Venables JP Cancer-associated regulation of alternative splicing Nature Struct Mol Biol 16 670 676 2009 19448617
  86. [90]Mallick B Ghosh Z A complex crosstalk between polymorphic microRNA target sites and AD prognosis RNA Biol 8 665 673 2011 21659796
  87. [91]Almeida MI Reis RM Calin GA Decoy activity through microRNAs: the therapeutic implications Expert Opin Biol Ther 12 1153 1159 2012 22650365 PMC3799811
  88. [92]Tollervey D Molecular biology: RNA lost in translation Nature 440 425 426 2006 16554791
  89. [93]Mercer TR Expression of distinct RNAs from 3′ untranslated regions Nucleic Acids Res 39 2393 2403 2011 21075793 PMC3064787
  90. [94]Khorshid M Hausser J Zavolan M van Nimwegen E A biophysical miRNA-mRNA interaction model infers canonical and noncanonical targets Nature Methods 10 253 255 2013 23334102
  91. [95]Helwak A Kudla G Dudnakova T Tollervey D Mapping the human miRNA interactome by CLASH reveals frequent noncanonical binding Cell 153 654 665 2013 23622248 PMC3650559
  92. [96]Tay Y MicroRNAs to Nanog, Oct4 and Sox2 coding regions modulate embryonic stem cell differentiation Nature 455 1124 1128 2008 18806776
  93. [97]Hausser J Syed AP Bilen B Zavolan M Analysis of CDS-located miRNA target sites suggests that they can effectively inhibit translation Genome Res 23 604 615 2013 23335364 PMC3613578
  94. [98]Vasudevan S Tong Y Steitz JA Switching from repression to activation: microRNAs can up-regulate translation Science 318 1931 1934 2007 18048652
  95. [99]Meijer HA Translational repression and eIF4A2 activity are critical for microRNA-mediated gene regulation Science 340 82 85 2013 23559250
  96. [100]Ibarra-Laclette E Architecture and evolution of a minute plant genome Nature 498 94 98 2013 23665961 PMC4972453

Cited by

Sorted by citations

Authors
Tay, Y., Rinn, J., & Pandolfi, P. P.
Affiliations
  • Beth Israel Deaconess Medical Center (US)
  • Broad Institute (US)
Corresponding author
Pandolfi, Pier Paolo
Venue
Nature
Published
2014-01
Volume
505
Issue
7483
Pages
344-352
ISSN
  • 0028-0836 (ISSN-L)
  • 1476-4687
OpenAlex
W2130687298
Cited by
3,910
References
4
Citations by year
2026: 117 · 2025: 234 · 2024: 312 · 2023: 336 · 2022: 536 · 2021: 652 · 2020: 524 · 2019: 384 · 2018: 278 · 2017: 192 · 2016: 150 · 2015: 123 · 2014: 64 · 2013: 1
FWCI
17.51
Type
journal article
Language
en
Open access
Locations
  • Nature (publishedVersion)
  • PubMed (publishedVersion)
  • Europe PMC (PubMed Central) (acceptedVersion)
  • PubMed Central (acceptedVersion)
  • RePEc: Research Papers in Economics (submittedVersion)
Funders
National Cancer Institute (R01-CA-82328, R01CA170158, R01CA082328)
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Cancer-related molecular mechanisms research
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › MicroRNA in disease regulation
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
Keywords
competing endogenous RNA, microRNA sponge, long non-coding RNA, pseudogenes, circular RNA, microRNA competition, post-transcriptional regulation, gene regulatory networks, RNA-RNA interactions
MeSH terms
RNA, Circular, Animals, Binding, Competitive, Humans, Pseudogenes, RNA, RNA, Messenger, RNA-Binding Proteins, RNA Editing, MicroRNAs, Argonaute Proteins, RNA, Long Noncoding

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review