Transcriptome analysis of clock disrupted cancer cells reveals differential alternative splicing of cancer hallmarks genes.
Journal
NPJ systems biology and applications
ISSN: 2056-7189
Titre abrégé: NPJ Syst Biol Appl
Pays: England
ID NLM: 101677786
Informations de publication
Date de publication:
12 05 2022
12 05 2022
Historique:
received:
08
11
2021
accepted:
04
04
2022
entrez:
13
5
2022
pubmed:
14
5
2022
medline:
18
5
2022
Statut:
epublish
Résumé
Emerging evidence points towards a regulatory role of the circadian clock in alternative splicing (AS). Whether alterations in core-clock components may contribute to differential AS events is largely unknown. To address this, we carried out a computational analysis on recently generated time-series RNA-seq datasets from three core-clock knockout (KO) genes (ARNTL, NR1D1, PER2) and WT of a colorectal cancer (CRC) cell line, and time-series RNA-seq datasets for additional CRC and Hodgkin's lymphoma (HL) cells, murine WT, Arntl KO, and Nr1d1/2 KO, and murine SCN WT tissue. The deletion of individual core-clock genes resulted in the loss of circadian expression in crucial spliceosome components such as SF3A1 (in ARNTL
Identifiants
pubmed: 35552415
doi: 10.1038/s41540-022-00225-w
pii: 10.1038/s41540-022-00225-w
pmc: PMC9098426
doi:
Substances chimiques
ARNTL Transcription Factors
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
17Informations de copyright
© 2022. The Author(s).
Références
Bioessays. 2006 Apr;28(4):378-86
pubmed: 16547952
RNA. 2021 Dec;27(12):1557-1576
pubmed: 34544891
Oncol Rep. 2013 Sep;30(3):1137-42
pubmed: 23835524
Nat Rev Genet. 2021 Mar;22(3):185-198
pubmed: 33235359
Oncogene. 2020 May;39(22):4390-4403
pubmed: 32332923
J Nutr. 2015 May;145(5):841-6
pubmed: 25761502
Sci Rep. 2019 Jul 30;9(1):11062
pubmed: 31363108
Mol Cancer Ther. 2012 Sep;11(9):2010-20
pubmed: 22778155
Science. 2010 Jan 22;327(5964):463-6
pubmed: 20093473
Cell. 2000 Dec 22;103(7):1009-17
pubmed: 11163178
Nat Rev Mol Cell Biol. 2017 Jul;18(7):437-451
pubmed: 28488700
Cell Stem Cell. 2014 Mar 6;14(3):342-56
pubmed: 24607406
Protein Sci. 2022 Jan;31(1):47-53
pubmed: 34423492
Sci Rep. 2021 Jan 11;11(1):390
pubmed: 33431968
Proc Natl Acad Sci U S A. 2021 Jan 19;118(3):
pubmed: 33452134
Nucleic Acids Res. 2000 Sep 15;28(18):3442-4
pubmed: 10982861
Signal Transduct Target Ther. 2021 Feb 24;6(1):78
pubmed: 33623018
Front Oncol. 2019 Jan 04;8:655
pubmed: 30662872
Elife. 2017 Jun 08;6:
pubmed: 28594322
Hum Mutat. 2012 Jan;33(1):81-5
pubmed: 21922594
Hum Mol Genet. 2010 Aug 1;19(15):3011-20
pubmed: 20484225
BMC Genomics. 2012 Aug 17;13:405
pubmed: 22900683
Histol Histopathol. 2020 Aug;35(8):887-892
pubmed: 32073129
J Neuroendocrinol. 2003 Oct;15(10):991-1002
pubmed: 12969245
Bioinformatics. 2016 Sep 15;32(18):2800-8
pubmed: 27207944
J Biol Rhythms. 2019 Dec;34(6):584-595
pubmed: 31389290
Biology (Basel). 2021 Nov 18;10(11):
pubmed: 34827197
Nat Commun. 2017 Oct 30;8(1):1189
pubmed: 29084942
Biomed Res Int. 2015;2015:150514
pubmed: 26273588
Adv Drug Deliv Rev. 2010 Jul 31;62(9-10):979-1001
pubmed: 20600409
OMICS. 2012 May;16(5):284-7
pubmed: 22455463
Nat Rev Cancer. 2018 Jun;18(6):341-358
pubmed: 29674709
Exp Mol Med. 2018 Dec 6;50(12):1-10
pubmed: 30523262
Mol Cell Endocrinol. 2014 Feb 15;382(2):888-98
pubmed: 24239982
Bioinformatics. 2014 Aug 1;30(15):2114-20
pubmed: 24695404
Nucleic Acids Res. 2006 Jan 1;34(Database issue):D535-9
pubmed: 16381927
Sleep Med Clin. 2015 Dec;10(4):413-21
pubmed: 26568119
Cell Cycle. 2014;13(6):984-91
pubmed: 24552823
Nat Rev Clin Oncol. 2020 Aug;17(8):457-474
pubmed: 32303702
Nucleic Acids Res. 2013 Jan;41(Database issue):D132-41
pubmed: 23118483
Sci Rep. 2019 Jul 15;9(1):10171
pubmed: 31308426
Hum Genet. 2017 Sep;136(9):1015-1042
pubmed: 28374191
Mol Cell. 2014 May 22;54(4):651-62
pubmed: 24837677
J Biol Rhythms. 2014 Dec;29(6):391-400
pubmed: 25326247
Nucleic Acids Res. 2009 Jan;37(Database issue):D767-72
pubmed: 18988627
Cell Rep. 2019 Nov 26;29(9):2672-2688.e7
pubmed: 31775037
World J Surg Oncol. 2014 Dec 02;12:367
pubmed: 25441176
J Environ Pathol Toxicol Oncol. 2017;36(2):99-105
pubmed: 29199590
World J Surg Oncol. 2017 Jan 6;15(1):9
pubmed: 28061901
Cell Rep. 2018 Apr 3;23(1):282-296.e4
pubmed: 29617667
Int J Mol Sci. 2019 Aug 15;20(16):
pubmed: 31443305
J Biol Chem. 2015 Jan 16;290(3):1804-17
pubmed: 25471370
Oncol Rep. 2013 Apr;29(4):1570-8
pubmed: 23404221
Nat Rev Neurosci. 2003 Aug;4(8):649-61
pubmed: 12894240
Annu Rev Pharmacol Toxicol. 2010;50:377-421
pubmed: 20055686
Nature. 2008 Nov 27;456(7221):470-6
pubmed: 18978772
Ann N Y Acad Sci. 2000 Jun;910:106-18; discussion 118-20
pubmed: 10911909
Int J Mol Sci. 2019 Mar 08;20(5):
pubmed: 30857150
Mol Cell. 2009 Mar 13;33(5):591-601
pubmed: 19285943
Cancer Res. 2004 Nov 1;64(21):7647-54
pubmed: 15520162
Bioessays. 2021 Apr;43(4):e2000205
pubmed: 33533033
Acta Pharm Sin B. 2015 Sep;5(5):378-89
pubmed: 26579469
Cancer Res. 2013 Aug 1;73(15):4732-43
pubmed: 23752693
Cancer. 2000 Aug 15;89(4):733-40
pubmed: 10951334
Int J Mol Sci. 2021 May 12;22(10):
pubmed: 34065983
F1000Res. 2015 Dec 30;4:1521
pubmed: 26925227
Cancer Lett. 2021 Mar 31;501:83-104
pubmed: 33309781
F1000Res. 2013 Sep 16;2:188
pubmed: 24555089
RNA. 2016 Sep;22(9):1285-301
pubmed: 27530828
PLoS Biol. 2021 Dec 30;19(12):e3001492
pubmed: 34968386
Genome Biol. 2018 Mar 23;19(1):40
pubmed: 29571299
Nucleic Acids Res. 2017 Feb 28;45(4):1848-1859
pubmed: 27924002
Cancer Res. 2019 Aug 1;79(15):3806-3814
pubmed: 31300477
Bioinformatics. 2010 Jan 1;26(1):139-40
pubmed: 19910308
Elife. 2015 Nov 02;4:
pubmed: 26523393
Nucleic Acids Res. 2019 Jun 4;47(10):5381-5394
pubmed: 30931476
Annu Rev Biochem. 2015;84:291-323
pubmed: 25784052
Oncogene. 2014 Nov 13;33(46):5311-8
pubmed: 24336324
Int J Oncol. 2016 Jun;48(6):2339-48
pubmed: 27082853
Cancer Res. 2003 Nov 1;63(21):7277-83
pubmed: 14612524
Oncol Lett. 2017 Jun;13(6):4245-4251
pubmed: 28599425
J Pathol. 2013 Mar;229(4):630-9
pubmed: 23132731
Cell. 2017 Apr 6;169(2):203-215.e13
pubmed: 28388406
Oncotarget. 2016 Oct 4;7(40):65589-65601
pubmed: 27564110
Bioinformatics. 2013 Jan 1;29(1):15-21
pubmed: 23104886
EBioMedicine. 2018 Jul;33:68-81
pubmed: 29936137
FASEB J. 2019 May;33(5):6226-6238
pubmed: 30794439
Oncol Rep. 2018 Sep;40(3):1275-1286
pubmed: 30015914
Int J Cell Biol. 2013;2013:153634
pubmed: 24159334
Theor Biol Med Model. 2014 Apr 11;11:16
pubmed: 24725531
Cell Rep. 2020 Sep 22;32(12):108184
pubmed: 32966782
Cell Rep. 2017 Aug 29;20(9):2215-2226
pubmed: 28854369
J Biol Chem. 2005 Feb 11;280(6):4779-84
pubmed: 15546866
Biochem Biophys Res Commun. 2011 Dec 9;416(1-2):86-91
pubmed: 22085718
Elife. 2019 Feb 05;8:
pubmed: 30720431
Br J Cancer. 1996 Aug;74(3):342-51
pubmed: 8695347
Bioinformatics. 2019 Nov 08;:
pubmed: 31702788
Nat Rev Cancer. 2008 Nov;8(11):880-7
pubmed: 18923433
Int J Biochem Cell Biol. 2002 Jul;34(7):718-21
pubmed: 11950588
Int J Cancer. 2017 Dec 1;141(11):2164-2173
pubmed: 28608439
Nature. 2013 Oct 17;502(7471):333-339
pubmed: 24132290
J Biol Chem. 2008 Jan 18;283(3):1229-33
pubmed: 18024428
Hum Pathol. 1998 Jun;29(6):627-35
pubmed: 9635685
Immunol Rev. 2017 May;277(1):76-89
pubmed: 28462525
Bioinformatics. 2015 Sep 1;31(17):2912-4
pubmed: 25964631
Trends Mol Med. 2016 May;22(5):430-445
pubmed: 27066876
Oncol Lett. 2019 Nov;18(5):5332-5340
pubmed: 31612043
Nat Methods. 2017 Apr;14(4):417-419
pubmed: 28263959
Biol Direct. 2015 Jan 29;10:4
pubmed: 25630343
Mol Pharmacol. 2002 Dec;62(6):1261-73
pubmed: 12435793
Biochim Biophys Acta. 2013 Jun-Jul;1829(6-7):680-8
pubmed: 23246978
Cell Death Differ. 2016 Dec;23(12):1919-1929
pubmed: 27689872
Carbohydr Polym. 2021 Jan 1;251:117103
pubmed: 33142641
Cell Commun Signal. 2013 Dec 20;11:97
pubmed: 24359404
Trends Cancer. 2020 Aug;6(8):631-644
pubmed: 32434734
Nat Rev Mol Cell Biol. 2009 Nov;10(11):741-54
pubmed: 19773805
J Clin Oncol. 2006 Aug 1;24(22):3562-9
pubmed: 16877722
Cancer Discov. 2013 Nov;3(11):1228-37
pubmed: 24145039
Nat Rev Genet. 2016 Jan;17(1):19-32
pubmed: 26593421
Biochem Pharmacol. 2018 May;151:188-200
pubmed: 29223352
Expert Opin Drug Metab Toxicol. 2015 May;11(5):673-89
pubmed: 25495223
Front Genet. 2020 Feb 05;11:29
pubmed: 32117445
Bioinformatics. 2015 Sep 15;31(18):3078-80
pubmed: 25979474
Lung Cancer. 2016 Sep;99:57-65
pubmed: 27565915
Clin Chim Acta. 2013 Feb 18;417:39-44
pubmed: 23266771
Mol Cell. 2013 Dec 12;52(5):720-33
pubmed: 24332178
Database (Oxford). 2011 Jul 23;2011:bar030
pubmed: 21785142