The genomic landscape of 8-oxodG reveals enrichment at specific inherently fragile promoters.
8-Hydroxy-2'-Deoxyguanosine
/ metabolism
Base Composition
Cell Line
DNA
/ chemistry
DNA Breaks, Double-Stranded
DNA Glycosylases
/ metabolism
DNA Repair
DNA Replication
Genome, Human
Genomic Instability
Humans
Poly (ADP-Ribose) Polymerase-1
/ metabolism
Promoter Regions, Genetic
Transcription, Genetic
Journal
Nucleic acids research
ISSN: 1362-4962
Titre abrégé: Nucleic Acids Res
Pays: England
ID NLM: 0411011
Informations de publication
Date de publication:
07 05 2020
07 05 2020
Historique:
accepted:
11
03
2020
revised:
09
03
2020
received:
05
12
2019
pubmed:
22
3
2020
medline:
28
7
2020
entrez:
22
3
2020
Statut:
ppublish
Résumé
8-Oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodG) is the most common marker of oxidative stress and its accumulation within the genome has been associated with major human health issues such as cancer, aging, cardiovascular and neurodegenerative diseases. The characterization of the different genomic sites where 8-oxodG accumulates and the mechanisms underlying its formation are still poorly understood. Using OxiDIP-seq, we recently derived the genome-wide distribution of 8-oxodG in human non-tumorigenic epithelial breast cells (MCF10A). Here, we identify a subset of human promoters that accumulate 8-oxodG under steady-state condition. 8-oxodG nucleotides co-localize with double strand breaks (DSBs) at bidirectional and CG skewed promoters and their density correlate with RNA Polymerase II co-occupancy and transcription. Furthermore, by performing OxiDIP-seq in quiescent (G0) cells, we found a strong reduction of oxidatively-generated damage in the majority of 8-oxodG-positive promoters in the absence of DNA replication. Overall, our results suggest that the accumulation of 8-oxodG at gene promoters occurs through DNA replication-dependent or -independent mechanisms, with a possible contribution to the formation of cancer-associated translocation events.
Identifiants
pubmed: 32198884
pii: 5810856
doi: 10.1093/nar/gkaa175
pmc: PMC7192600
doi:
Substances chimiques
8-Hydroxy-2'-Deoxyguanosine
88847-89-6
DNA
9007-49-2
PARP1 protein, human
EC 2.4.2.30
Poly (ADP-Ribose) Polymerase-1
EC 2.4.2.30
DNA Glycosylases
EC 3.2.2.-
oxoguanine glycosylase 1, human
EC 3.2.2.-
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
4309-4324Informations de copyright
© The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research.
Références
Cell. 2014 Dec 18;159(7):1538-48
pubmed: 25483776
Cell. 2015 Apr 23;161(3):541-554
pubmed: 25910208
J Environ Sci Health C Environ Carcinog Ecotoxicol Rev. 2009 Apr;27(2):120-39
pubmed: 19412858
Proc Natl Acad Sci U S A. 2017 Mar 7;114(10):2604-2609
pubmed: 28143930
Mol Cell. 2011 Dec 23;44(6):966-77
pubmed: 22195969
Bioinformatics. 2015 Jan 15;31(2):166-9
pubmed: 25260700
Mol Cell. 2012 Mar 30;45(6):814-25
pubmed: 22387027
DNA Repair (Amst). 2004 Oct 5;3(10):1323-34
pubmed: 15336627
J Am Chem Soc. 2017 Feb 22;139(7):2569-2572
pubmed: 28150947
Mutat Res Genet Toxicol Environ Mutagen. 2014 Apr;764-765:58-63
pubmed: 24055867
J Cell Physiol. 2016 Jan;231(1):3-14
pubmed: 26040249
Mol Cell. 2012 Nov 9;48(3):365-74
pubmed: 23041286
Nucleic Acids Res. 2015 Apr 30;43(8):4028-38
pubmed: 25813046
Nucleic Acids Res. 2012 Sep;40(16):7907-15
pubmed: 22718977
Nature. 2000 Feb 24;403(6772):859-66
pubmed: 10706276
Genome Biol. 2009;10(3):R25
pubmed: 19261174
Prog Mol Biol Transl Sci. 2012;110:123-53
pubmed: 22749145
Nat Commun. 2013;4:1796
pubmed: 23653208
PLoS Genet. 2017 Sep 28;13(9):e1006761
pubmed: 28957321
Oncotarget. 2016 Jan 26;7(4):4949-60
pubmed: 26700820
PLoS One. 2012;7(2):e30619
pubmed: 22312429
Proc Natl Acad Sci U S A. 2007 Aug 21;104(34):13535-6
pubmed: 17699620
Bioinformatics. 2010 Mar 1;26(5):589-95
pubmed: 20080505
Genome Res. 2015 Nov;25(11):1600-9
pubmed: 26275623
Redox Biol. 2018 Sep;18:43-53
pubmed: 29940424
Nucleic Acids Res. 2019 Jan 10;47(1):221-236
pubmed: 30462294
Bioinformatics. 2014 Aug 1;30(15):2114-20
pubmed: 24695404
Mol Cell. 2011 Jun 24;42(6):794-805
pubmed: 21700224
Annu Rev Biochem. 1994;63:915-48
pubmed: 7979257
Prostate. 2015 Jun 15;75(9):936-46
pubmed: 25728837
Science. 2008 Dec 19;322(5909):1845-8
pubmed: 19056941
Science. 2008 Jan 11;319(5860):202-6
pubmed: 18187655
Oncogene. 2010 Jun 24;29(25):3691-702
pubmed: 20418916
Nat Rev Genet. 2012 Feb 14;13(3):204-14
pubmed: 22330764
DNA Repair (Amst). 2006 Jan 5;5(1):43-51
pubmed: 16111924
Free Radic Biol Med. 2012 Jul 1;53(1):51-9
pubmed: 22583700
Mol Cell. 2016 May 5;62(3):327-334
pubmed: 27153532
ACS Chem Biol. 2017 Sep 15;12(9):2417-2426
pubmed: 28829124
Nat Biotechnol. 2015 Aug;33(8):877-81
pubmed: 26192317
Nat Struct Mol Biol. 2019 Jan;26(1):67-77
pubmed: 30598550
Mol Cell. 2014 Sep 18;55(6):829-842
pubmed: 25201414
Cell Mol Life Sci. 2009 Mar;66(6):981-93
pubmed: 19153658
Biochim Biophys Acta Rev Cancer. 2018 Jan;1869(1):29-41
pubmed: 29128527
Cell Cycle. 2010 Aug 1;9(15):3002-4
pubmed: 20714214
Genome Res. 2013 Jan;23(1):1-11
pubmed: 23187890
Genome Res. 2013 Oct;23(10):1590-600
pubmed: 23868195
Nat Commun. 2016 Oct 05;7:13049
pubmed: 27703167
Biochemistry. 2020 Jan 14;59(1):85-89
pubmed: 31618020
Mol Cell. 2012 Apr 27;46(2):115-24
pubmed: 22541554
Crit Rev Eukaryot Gene Expr. 2014;24(1):15-28
pubmed: 24579667
Stat Appl Genet Mol Biol. 2012 Mar 31;11(3):Article 9
pubmed: 22499706
Genome Biol. 2010;11(10):R106
pubmed: 20979621
Nucleic Acids Res. 2011 Jan;39(Database issue):D19-21
pubmed: 21062823
Trends Cell Biol. 2016 Jan;26(1):52-64
pubmed: 26437586
Nature. 2014 Oct 16;514(7522):389-93
pubmed: 25119026
Mol Cell. 2009 Jul 31;35(2):191-205
pubmed: 19647516
Genome Biol. 2008;9(9):R137
pubmed: 18798982
Proc Natl Acad Sci U S A. 2001 Jun 19;98(13):7426-30
pubmed: 11404468
Bioinformatics. 2013 Jan 1;29(1):15-21
pubmed: 23104886
Comput Struct Biotechnol J. 2020 Jan 07;18:207-219
pubmed: 31993111
Nucleic Acids Res. 2014 Jul;42(Web Server issue):W187-91
pubmed: 24799436
Cell Rep. 2016 Feb 9;14(5):1025-1031
pubmed: 26804908
J Immunol. 2014 Mar 1;192(5):2384-94
pubmed: 24489103
Genome Res. 2017 Mar;27(3):491-499
pubmed: 28100584
Nat Commun. 2017 May 12;8:15058
pubmed: 28497783
Nucleic Acids Res. 2014 Jun;42(11):7236-46
pubmed: 24829453
Annu Rev Genet. 2013;47:1-32
pubmed: 23909437
Bioinformatics. 2009 Aug 15;25(16):2078-9
pubmed: 19505943
Nucleic Acids Res. 2014;42(17):11040-55
pubmed: 25217584
Genome Biol. 2018 Dec 7;19(1):215
pubmed: 30526646
Bioinformatics. 2010 Mar 15;26(6):841-2
pubmed: 20110278
Nucleic Acids Res. 2019 Jun 4;47(10):5049-5060
pubmed: 30916339
Nat Genet. 2019 Jun;51(6):1011-1023
pubmed: 31110352
J Cell Biol. 1999 Sep 6;146(5):905-16
pubmed: 10477747
Antioxid Redox Signal. 2013 Jun 20;18(18):2429-43
pubmed: 23311711
DNA Repair (Amst). 2017 Aug;56:75-83
pubmed: 28629775
J Am Chem Soc. 2018 Aug 8;140(31):9783-9787
pubmed: 29944356
Arch Toxicol Suppl. 1987;11:84-8
pubmed: 3477203
Proc Natl Acad Sci U S A. 2015 May 5;112(18):5785-90
pubmed: 25902512
Nature. 2013 Sep 5;501(7465):58-62
pubmed: 23995680
Nucleic Acids Res. 2018 Apr 20;46(7):3446-3457
pubmed: 29447383
Oncogene. 2015 Sep 10;34(37):4845-54
pubmed: 25500544
FASEB J. 2003 Jul;17(10):1195-214
pubmed: 12832285
J Mol Biol. 1999 Jul 16;290(3):667-84
pubmed: 10395822