Disease-Associated Circular RNAs: From Biology to Computational Identification.
Journal
BioMed research international
ISSN: 2314-6141
Titre abrégé: Biomed Res Int
Pays: United States
ID NLM: 101600173
Informations de publication
Date de publication:
2020
2020
Historique:
received:
03
06
2020
accepted:
10
07
2020
entrez:
10
9
2020
pubmed:
11
9
2020
medline:
28
4
2021
Statut:
epublish
Résumé
Circular RNAs (circRNAs) are endogenous RNAs with a covalently closed continuous loop, generated through various backsplicing events of pre-mRNA. An accumulating number of studies have shown that circRNAs are potential biomarkers for major human diseases such as cancer and Alzheimer's disease. Thus, identification and prediction of human disease-associated circRNAs are of significant importance. To this end, a computational analysis-assisted strategy is indispensable to detect, verify, and quantify circRNAs for downstream applications. In this review, we briefly introduce the biology of circRNAs, including the biogenesis, characteristics, and biological functions. In addition, we outline about 30 recent bioinformatic analysis tools that are publicly available for circRNA study. Principles for applying these computational strategies and considerations will be briefly discussed. Lastly, we give a complete survey on more than 20 key computational databases that are frequently used. To our knowledge, this is the most complete and updated summary on publicly available circRNA resources. In conclusion, this review summarizes key aspects of circRNA biology and outlines key computational strategies that will facilitate the genome-wide identification and prediction of circRNAs.
Identifiants
pubmed: 32908906
doi: 10.1155/2020/6798590
pmc: PMC7450300
doi:
Substances chimiques
RNA, Circular
0
Types de publication
Journal Article
Review
Langues
eng
Sous-ensembles de citation
IM
Pagination
6798590Informations de copyright
Copyright © 2020 Min Tang et al.
Déclaration de conflit d'intérêts
The authors declare that they have no conflicts of interest.
Références
Biochem Biophys Res Commun. 2017 Nov 25;493(3):1260-1266
pubmed: 28958934
Cell Physiol Biochem. 2018;51(5):2324-2340
pubmed: 30537738
Adv Exp Med Biol. 2018;1087:239-243
pubmed: 30259371
Cell Rep. 2015 Jan 13;10(2):170-7
pubmed: 25558066
J Neurotrauma. 2018 Jul 15;35(14):1659-1666
pubmed: 29357736
Sci Rep. 2016 Oct 11;6:34985
pubmed: 27725737
Brief Bioinform. 2017 Jul 1;18(4):547-557
pubmed: 27255916
Front Immunol. 2018 Oct 30;9:2407
pubmed: 30425709
RNA Biol. 2015;12(4):381-8
pubmed: 25746834
Nat Struct Mol Biol. 2015 Mar;22(3):256-64
pubmed: 25664725
Biomolecules. 2019 Aug 30;9(9):
pubmed: 31480381
Cell Physiol Biochem. 2016;39(1):205-16
pubmed: 27336675
RNA Biol. 2017 Aug 3;14(8):1064-1074
pubmed: 27982734
RNA. 2014 Nov;20(11):1666-70
pubmed: 25234927
Database (Oxford). 2019 Jan 1;2019:
pubmed: 31058278
Nat Rev Mol Cell Biol. 2016 Apr;17(4):205-11
pubmed: 26908011
Science. 2017 Sep 22;357(6357):
pubmed: 28798046
Int J Cardiol. 2019 Dec 1;296:136-140
pubmed: 31466885
BMC Bioinformatics. 2016 Jan 13;17:31
pubmed: 26758031
PLoS One. 2012;7(2):e30733
pubmed: 22319583
Mol Cancer. 2018 Sep 20;17(1):138
pubmed: 30236141
Bioinformatics. 2018 May 1;34(9):1580-1582
pubmed: 29280994
Nucleic Acids Res. 2016 May 19;44(9):e87
pubmed: 26873924
Genes Dev. 2014 Oct 15;28(20):2233-47
pubmed: 25281217
Carcinogenesis. 2018 Jul 30;39(8):981-992
pubmed: 29726904
Genomics Proteomics Bioinformatics. 2018 Aug;16(4):226-233
pubmed: 30172046
Mol Cell. 2017 Apr 6;66(1):22-37.e9
pubmed: 28344082
J Cell Biochem. 2019 Mar;120(3):3428-3437
pubmed: 30246481
Nat Neurosci. 2015 Apr;18(4):603-610
pubmed: 25714049
Curr Mol Med. 2020;20(7):516-526
pubmed: 31995005
Bioinformatics. 2020 Jan 15;36(2):539-545
pubmed: 31373611
Mol Cell. 2017 Apr 6;66(1):1-2
pubmed: 28388436
Trends Neurosci. 2016 Sep;39(9):597-604
pubmed: 27445124
Bioinformatics. 2017 Jul 15;33(14):2131-2139
pubmed: 28334396
Brief Bioinform. 2020 Jan 30;:
pubmed: 31998941
Int J Mol Med. 2019 Apr;43(4):1699-1708
pubmed: 30816430
Aging (Albany NY). 2018 Sep 6;10(9):2266-2283
pubmed: 30187887
RNA Biol. 2020 Jun 18;:1-13
pubmed: 32506995
Nat Rev Cardiol. 2019 Aug;16(8):503-514
pubmed: 30952956
Int J Med Sci. 2018 May 14;15(7):703-712
pubmed: 29910675
Cancer Sci. 2019 Sep;110(9):2960-2972
pubmed: 31301086
Epigenomics. 2020 Mar;12(5):439-454
pubmed: 32043895
Cell Rep. 2020 Feb 18;30(7):2170-2179.e5
pubmed: 32075758
Genome Biol. 2015 Jun 16;16:126
pubmed: 26076956
Sci Rep. 2016 May 11;6:25749
pubmed: 27167008
Cell Death Dis. 2018 Apr 27;9(5):475
pubmed: 29700306
Biomed Res Int. 2019 Nov 7;2019:4128315
pubmed: 31815137
Cell Rep. 2017 Aug 29;20(9):2262-2276
pubmed: 28854373
Brief Bioinform. 2019 Nov 27;20(6):2327-2333
pubmed: 30184150
Bioinformatics. 2016 Apr 1;32(7):1094-6
pubmed: 26556385
Genome Biol. 2014 Feb 10;15(2):R34
pubmed: 24512684
Methods Mol Biol. 2019;1870:137-149
pubmed: 30539552
J Mol Histol. 2020 Jun;51(3):317-327
pubmed: 32409849
Cell. 2014 Sep 25;159(1):134-147
pubmed: 25242744
Nature. 1979 Jul 26;280(5720):339-40
pubmed: 460409
Nat Commun. 2016 Apr 06;7:11215
pubmed: 27050392
BMC Genomics. 2017 Oct 3;18(Suppl 6):680
pubmed: 28984197
J Cell Mol Med. 2018 Nov;22(11):5176-5187
pubmed: 30277664
Front Genet. 2013 Dec 10;4:283
pubmed: 24339831
Cell Discov. 2018 Sep 18;4:48
pubmed: 30245844
Cancer Med. 2018 Jun;7(6):2783-2791
pubmed: 29722168
Int J Biochem Cell Biol. 2020 Jun;123:105747
pubmed: 32315771
Stroke. 2017 Sep;48(9):2541-2548
pubmed: 28701578
J Neurochem. 2016 Nov;139(3):485-496
pubmed: 27470294
Biomolecules. 2020 Jan 25;10(2):
pubmed: 31991759
Database (Oxford). 2020 Jan 1;2020:
pubmed: 32219412
J Neurosci Res. 2020 Jan;98(1):87-97
pubmed: 30575990
Brief Bioinform. 2020 Apr 29;:
pubmed: 32349124
PeerJ. 2017 Feb 28;5:e2934
pubmed: 28265491
Bioinformatics. 2019 Jul 1;35(13):2326-2328
pubmed: 30462173
Genomics. 2019 Jul;111(4):753-758
pubmed: 29709512
Biol Psychiatry. 2017 Feb 1;81(3):252-264
pubmed: 27113499
Metabolism. 2018 Aug;85:192-204
pubmed: 29634953
Nat Commun. 2020 Jan 3;11(1):90
pubmed: 31900416
Cell Physiol Biochem. 2018;46(6):2284-2296
pubmed: 29734191
Hepatobiliary Pancreat Dis Int. 2019 Dec;18(6):580-586
pubmed: 30898507
PLoS One. 2018 Feb 9;13(2):e0192613
pubmed: 29425247
Acta Neuropathol. 2019 Jan;137(1):123-137
pubmed: 30267146
Int J Oncol. 2017 Dec;51(6):1625-1638
pubmed: 29039477
Genome Med. 2019 Jan 19;11(1):2
pubmed: 30660194
J Vis Exp. 2019 Nov 14;(153):
pubmed: 31789321
RNA. 2014 Dec;20(12):1829-42
pubmed: 25404635
Int J Mol Med. 2018 Sep;42(3):1353-1366
pubmed: 29956720
Cell. 2015 Mar 12;160(6):1125-34
pubmed: 25768908
Nucleic Acids Res. 2016 Feb 18;44(3):e29
pubmed: 26442529
Mol Ther. 2017 Sep 6;25(9):2053-2061
pubmed: 28669840
Exp Neurol. 2019 Mar;313:37-48
pubmed: 30529438
Wiley Interdiscip Rev RNA. 2020 Jan;11(1):e1566
pubmed: 31489773
Nat Commun. 2018 Jul 6;9(1):2629
pubmed: 29980667
Trends Genet. 2018 May;34(5):389-400
pubmed: 29338875
Mol Ther Nucleic Acids. 2018 Dec 7;13:651-664
pubmed: 30497055
Aging (Albany NY). 2018 Apr 30;10(4):833-852
pubmed: 29723158
Adv Exp Med Biol. 2018;1087:35-38
pubmed: 30259355
Bioinformatics. 2019 Nov 1;35(22):4760-4763
pubmed: 31150052
Cell Tissue Res. 2018 Apr;372(1):33-40
pubmed: 29294205
Clin Cancer Res. 2017 Jul 15;23(14):3918-3928
pubmed: 28174233
Front Genet. 2019 Oct 10;10:981
pubmed: 31649739
Clin Chim Acta. 2015 Apr 15;444:132-6
pubmed: 25689795
Hypertens Res. 2019 Nov;42(11):1824-1825
pubmed: 31316171
Nucleic Acids Res. 2018 Jan 4;46(D1):D106-D112
pubmed: 30053265
J Cell Mol Med. 2018 Jun;22(6):3097-3107
pubmed: 29532994
Front Genet. 2020 Mar 10;11:212
pubmed: 32211036
Cancer Cell. 2020 Jan 13;37(1):55-70.e15
pubmed: 31935372
Brief Bioinform. 2018 Jul 20;19(4):622-626
pubmed: 28096075
Cell. 2019 Feb 7;176(4):869-881.e13
pubmed: 30735636
Int J Mol Med. 2018 Oct;42(4):1865-1874
pubmed: 30066828
Int J Med Sci. 2019 Jan 1;16(2):292-301
pubmed: 30745810
Genome Biol. 2020 Apr 28;21(1):101
pubmed: 32345360
Front Oncol. 2020 Apr 30;10:601
pubmed: 32426279
BMC Genomics. 2020 Mar 5;21(Suppl 1):749
pubmed: 32138643
Nat Rev Genet. 2016 May;17(5):272-83
pubmed: 27040487
Database (Oxford). 2019 Jan 1;2019:
pubmed: 30715276
Alcohol Clin Exp Res. 2020 Feb;44(2):415-422
pubmed: 31840820
Brief Bioinform. 2019 Jan 18;20(1):58-65
pubmed: 28968841
Nat Rev Genet. 2016 Oct 14;17(11):679-692
pubmed: 27739534
Database (Oxford). 2018 Jan 1;2018:
pubmed: 29741596
Cell Res. 2017 May;27(5):626-641
pubmed: 28281539
Circ Res. 2016 Oct 14;119(9):996-1003
pubmed: 27531932
Mol Cell. 2015 Jun 4;58(5):870-85
pubmed: 25921068
FEBS Lett. 2017 Jan;591(1):213-220
pubmed: 27878987
Gene. 2018 Nov 30;677:189-197
pubmed: 30025927
Arterioscler Thromb Vasc Biol. 2018 Sep;38(9):1986-1996
pubmed: 30354260
Sci Rep. 2016 Dec 13;6:38907
pubmed: 27958329
Life Sci Alliance. 2019 Apr 26;2(3):
pubmed: 31028096
Brief Bioinform. 2017 Nov 1;18(6):984-992
pubmed: 27543790
Genome Res. 2016 Sep;26(9):1277-87
pubmed: 27365365
Nature. 2013 Mar 21;495(7441):333-8
pubmed: 23446348
Nucleic Acids Res. 2016 Apr 7;44(6):e58
pubmed: 26657634
Cancer Res. 2017 May 1;77(9):2339-2350
pubmed: 28249903
FEBS J. 2017 Jul;284(14):2170-2182
pubmed: 28685964
J Cell Biochem. 2019 Oct;120(10):16658-16667
pubmed: 31106457
Cancer Biol Ther. 2019;20(1):73-80
pubmed: 30207835
Onco Targets Ther. 2020 Mar 09;13:2067-2092
pubmed: 32210574
Bioinformatics. 2016 Nov 15;32(22):3528-3529
pubmed: 27493192
J Neurosci. 2018 Jan 3;38(1):32-50
pubmed: 29114076
Mol Ther Nucleic Acids. 2019 Dec 6;18:1049-1062
pubmed: 31786335
Nucleic Acids Res. 2016 Jan 4;44(D1):D1005-10
pubmed: 26578591
Genome Biol. 2014 Jul 29;15(7):409
pubmed: 25070500
Sci Rep. 2018 Nov 16;8(1):16953
pubmed: 30446675
Front Genet. 2019 Feb 19;10:83
pubmed: 30838024
Biochem Biophys Res Commun. 2018 Apr 15;498(4):1009-1015
pubmed: 29550475
PLoS Comput Biol. 2017 Jun 8;13(6):e1005420
pubmed: 28594838
Proc Natl Acad Sci U S A. 2019 Feb 26;116(9):3646-3655
pubmed: 30808754
J Neurotrauma. 2019 Apr 1;36(7):1018-1028
pubmed: 30261810
Genome Biol. 2015 Jan 13;16:4
pubmed: 25583365
Nucleic Acids Res. 2016 Jan 4;44(D1):D196-202
pubmed: 26590255
Cell Death Dis. 2018 Aug 6;9(8):838
pubmed: 30082829
J Cell Physiol. 2020 Jul;235(7-8):5501-5510
pubmed: 31985056
J Cell Physiol. 2019 Nov;234(11):19895-19910
pubmed: 30963578
EBioMedicine. 2018 Aug;34:267-274
pubmed: 30078734
Cell Rep. 2014 Dec 11;9(5):1966-1980
pubmed: 25544350
Biochim Biophys Acta. 2016 Oct;1859(10):1245-51
pubmed: 27449861
Cardiovasc Res. 2017 Mar 1;113(3):298-309
pubmed: 28082450
Bioinformatics. 2020 Jan 1;36(1):73-80
pubmed: 31268128
BMC Cardiovasc Disord. 2019 Oct 16;19(1):223
pubmed: 31619168
Cell. 2018 Jul 12;174(2):350-362.e17
pubmed: 29887379
Bioinformatics. 2017 Oct 15;33(20):3314-3316
pubmed: 29028266
FEBS Lett. 2019 Jun;593(11):1179-1189
pubmed: 31055837
J Neurotrauma. 2018 Sep 1;35(17):2056-2066
pubmed: 29409384
Cancer Lett. 2018 Apr 1;418:41-50
pubmed: 29330104
Nucleic Acids Res. 2010 Oct;38(18):e178
pubmed: 20802226
RNA. 2013 Feb;19(2):141-57
pubmed: 23249747
J Cardiovasc Pharmacol. 2020 Aug;76(2):128-137
pubmed: 32398477
J Cancer Res Clin Oncol. 2017 Jan;143(1):17-27
pubmed: 27614453
Acta Pharmacol Sin. 2019 Jan;40(1):55-63
pubmed: 30013032
Nature. 2013 Mar 21;495(7441):384-8
pubmed: 23446346
Front Bioeng Biotechnol. 2019 Sep 11;7:222
pubmed: 31572720
Brief Bioinform. 2018 Sep 28;19(5):803-810
pubmed: 28334140
Sci Rep. 2015 Jan 27;5:8057
pubmed: 25624062
Mol Cell. 2017 Apr 6;66(1):9-21.e7
pubmed: 28344080
Biomed Pharmacother. 2017 Dec;96:892-898
pubmed: 29223555
Nat Commun. 2016 Jun 28;7:12060
pubmed: 27350239
Nat Rev Genet. 2019 Nov;20(11):675-691
pubmed: 31395983
Nucleic Acids Res. 2016 Jan 4;44(D1):D209-15
pubmed: 26450965
FEBS J. 2017 Apr;284(7):1096-1109
pubmed: 28296235
Oncol Lett. 2018 Jul;16(1):1219-1225
pubmed: 29963195
Nat Commun. 2016 Aug 19;7:12429
pubmed: 27539542
Bioinformatics. 2020 Jun 1;36(12):3703-3711
pubmed: 32259207
Int J Clin Exp Pathol. 2017 Aug 01;10(8):8495-8502
pubmed: 31966702
RNA Biol. 2019 Jul;16(7):899-905
pubmed: 31023147
Int J Mol Sci. 2019 Dec 31;21(1):
pubmed: 31906249
Nucleic Acids Res. 2020 Jan 8;48(D1):D160-D165
pubmed: 31670377
Nat Biotechnol. 2014 May;32(5):453-61
pubmed: 24811520
J Cancer Res Clin Oncol. 2018 Apr;144(4):667-674
pubmed: 29372377
Genomics Proteomics Bioinformatics. 2019 Oct;17(5):511-521
pubmed: 31904419
Genom Data. 2015 Jul 21;5:385-7
pubmed: 26484292
Int J Mol Sci. 2020 Apr 24;21(8):
pubmed: 32344560
PeerJ. 2020 Mar 16;8:e8757
pubmed: 32211235
Anatol J Cardiol. 2019 Jan;21(1):2-10
pubmed: 30587718
Nucleic Acids Res. 2019 Jan 8;47(D1):D121-D127
pubmed: 30476305
Eur Heart J. 2016 Sep 01;37(33):2602-11
pubmed: 26802132
FASEB J. 1993 Jan;7(1):155-60
pubmed: 7678559
Neural Regen Res. 2019 Dec;14(12):2104-2111
pubmed: 31397348
Proc Natl Acad Sci U S A. 1976 Nov;73(11):3852-6
pubmed: 1069269
Mol Med Rep. 2019 Apr;19(4):2527-2536
pubmed: 30720076
Biosci Rep. 2017 Oct 24;37(5):
pubmed: 28928231
Mol Cancer. 2018 Sep 20;17(1):137
pubmed: 30236115
Mol Cell. 2013 Sep 26;51(6):792-806
pubmed: 24035497