HI-NESS: a family of genetically encoded DNA labels based on a bacterial nucleoid-associated protein.
Journal
Nucleic acids research
ISSN: 1362-4962
Titre abrégé: Nucleic Acids Res
Pays: England
ID NLM: 0411011
Informations de publication
Date de publication:
25 01 2022
25 01 2022
Historique:
accepted:
08
10
2021
revised:
06
10
2021
received:
03
11
2020
pubmed:
5
11
2021
medline:
22
2
2022
entrez:
4
11
2021
Statut:
ppublish
Résumé
The interplay between three-dimensional chromosome organisation and genomic processes such as replication and transcription necessitates in vivo studies of chromosome dynamics. Fluorescent organic dyes are often used for chromosome labelling in vivo. The mode of binding of these dyes to DNA cause its distortion, elongation, and partial unwinding. The structural changes induce DNA damage and interfere with the binding dynamics of chromatin-associated proteins, consequently perturbing gene expression, genome replication, and cell cycle progression. We have developed a minimally-perturbing, genetically encoded fluorescent DNA label consisting of a (photo-switchable) fluorescent protein fused to the DNA-binding domain of H-NS - a bacterial nucleoid-associated protein. We show that this DNA label, abbreviated as HI-NESS (H-NS-based indicator for nucleic acid stainings), is minimally-perturbing to genomic processes and labels chromosomes in eukaryotic cells in culture, and in zebrafish embryos with preferential binding to AT-rich chromatin.
Identifiants
pubmed: 34734265
pii: 6414584
doi: 10.1093/nar/gkab993
pmc: PMC8789088
doi:
Substances chimiques
Bacterial Proteins
0
DNA, Bacterial
0
DNA-Binding Proteins
0
Fluorescent Dyes
0
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
e10Informations de copyright
© The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research.
Références
Data Brief. 2016 Jan 29;7:157-71
pubmed: 27054149
Sci Rep. 2017 Oct 3;7(1):12583
pubmed: 28974721
Nucleic Acids Res. 2010 Oct;38(19):6526-32
pubmed: 20511588
Neuron. 2003 Feb 20;37(4):597-609
pubmed: 12597858
Biochemistry. 1987 Apr 7;26(7):1987-95
pubmed: 3297137
Mol Biol Evol. 2021 Sep 27;38(10):4135-4148
pubmed: 34003286
Dev Dyn. 2005 Oct;234(2):244-54
pubmed: 16110506
Angew Chem Int Ed Engl. 2001 Jun 1;40(11):2004-2021
pubmed: 11433435
Methods. 2009 May;48(1):8-13
pubmed: 19245839
J Bacteriol. 1997 Mar;179(6):2060-4
pubmed: 9068655
BMC Bioinformatics. 2011 Aug 03;12:317
pubmed: 21812952
Biochim Biophys Acta. 2011 Jan;1813(1):27-38
pubmed: 21095207
Chem Commun (Camb). 2014 Jun 11;50(46):6149-52
pubmed: 24776726
Sci Rep. 2021 Feb 3;11(1):2910
pubmed: 33536448
J Bacteriol. 2016 May 27;198(12):1735-42
pubmed: 27044624
Plant Methods. 2010 Jan 28;6(1):5
pubmed: 20181034
Dev Biol. 2001 May 15;233(2):329-46
pubmed: 11336499
Open Biol. 2016 Jan;6(1):150172
pubmed: 26740587
Biol Pharm Bull. 2001 Jun;24(6):704-6
pubmed: 11411564
PLoS Genet. 2010 Nov 11;6(11):e1001207
pubmed: 21085634
J Mol Biol. 1992 May 20;225(2):445-56
pubmed: 1593629
Nucleic Acids Res. 1996 Mar 15;24(6):1080-90
pubmed: 8604342
Nat Protoc. 2012 Sep;7(9):1709-15
pubmed: 22918388
Nano Lett. 2011 Sep 14;11(9):4008-11
pubmed: 21838238
Nat Methods. 2009 Feb;6(2):131-3
pubmed: 19169260
Nucleus. 2015;6(4):314-25
pubmed: 26280391
Nucleic Acids Res. 2015 Aug 18;43(14):6919-33
pubmed: 26101254
Cytometry A. 2013 Nov;83(11):979-88
pubmed: 24115313
Glycoconj J. 2014 May;31(4):299-307
pubmed: 24748467
Annu Rev Cell Dev Biol. 2017 Oct 6;33:265-289
pubmed: 28783961
Mol Imaging. 2003 Jan;2(1):37-49
pubmed: 12926236
Sci Rep. 2018 Oct 3;8(1):14768
pubmed: 30282984
Curr Biol. 1998 Mar 26;8(7):377-85
pubmed: 9545195
Nat Methods. 2012 Jun 28;9(7):676-82
pubmed: 22743772
Org Lett. 2010 Aug 6;12(15):3300-3
pubmed: 20597468
Curr Opin Cell Biol. 2016 Jun;40:60-65
pubmed: 26942688
Nature. 1992 Oct 29;359(6398):859-61
pubmed: 1436062
Cell. 2005 Dec 29;123(7):1213-26
pubmed: 16377563
Biotechniques. 2008 Jun;44(7):927-9
pubmed: 18533904
Mol Cell. 2012 Aug 10;47(3):383-95
pubmed: 22742833
Mol Cell. 2015 Aug 20;59(4):588-602
pubmed: 26295962
Nat Rev Genet. 2020 Apr;21(4):227-242
pubmed: 31767998
Genome Biol. 2007;8 Suppl 1:S7
pubmed: 18047699
Nucleic Acids Res. 1992 Jun 11;20(11):2803-12
pubmed: 1614866
J Struct Biol. 2012 Feb;177(2):344-8
pubmed: 22226957
Plant Cell. 2001 Mar;13(3):495-509
pubmed: 11251092
FEMS Microbiol Lett. 1990 Mar 15;56(3):341-6
pubmed: 2160398
Sci Rep. 2018 May 21;8(1):7898
pubmed: 29785044
Nucleic Acids Res. 1993 Aug 11;21(16):3705-9
pubmed: 7690125
Nat Commun. 2018 May 15;9(1):1911
pubmed: 29765029
Elife. 2017 Feb 27;6:
pubmed: 28240985
Cell Struct Funct. 1999 Oct;24(5):291-8
pubmed: 15216885
Nature. 2006 Nov 16;444(7117):387-90
pubmed: 17108966
Mol Pharmacol. 1989 Feb;35(2):177-82
pubmed: 2465485
J Struct Biol. 2014 Mar;185(3):243-9
pubmed: 24473063
Biochimie. 2001 Feb;83(2):193-200
pubmed: 11278069
Mol Microbiol. 2003 Aug;49(3):731-43
pubmed: 12864855
Cytometry. 1994 Oct 1;17(2):185-9
pubmed: 7530620
Nucleic Acids Res. 2010 Nov;38(21):7388-99
pubmed: 20663773
FEBS Lett. 1993 Feb 8;317(1-2):157-62
pubmed: 8381366
J Cell Sci. 2002 Aug 1;115(Pt 15):3061-72
pubmed: 12118062
Nat Methods. 2017 Jan;14(1):53-56
pubmed: 27869816
Biochemistry. 1995 Jul 11;34(27):8542-53
pubmed: 7612596
Nucleus. 2014 Jul-Aug;5(4):331-40
pubmed: 25482122
Nucleic Acids Res. 2017 May 5;45(8):e56
pubmed: 28082388
Nat Methods. 2012 May 13;9(7):727-9
pubmed: 22581370
J Bacteriol. 2012 Dec;194(23):6382-6
pubmed: 22904287
Anal Biochem. 2011 Oct 1;417(1):112-21
pubmed: 21683679
Chromosoma. 2018 Jun;127(2):235-245
pubmed: 29234867
Mol Microbiol. 2012 Dec;86(6):1318-33
pubmed: 23078205
Cell. 2013 May 9;153(4):882-95
pubmed: 23623305
J Cell Biol. 2001 Jun 25;153(7):1341-53
pubmed: 11425866
Chem Sci. 2018 Dec 12;10(7):1962-1970
pubmed: 30881625
Proc Natl Acad Sci U S A. 2008 Feb 19;105(7):2415-20
pubmed: 18272492
Anal Biochem. 2012 Jul 1;426(1):13-21
pubmed: 22484041
Nat Protoc. 2013 Jun;8(6):1114-24
pubmed: 23680983
Nat Commun. 2012 Mar 20;3:751
pubmed: 22434194
Nat Methods. 2012 Jul;9(7):671-5
pubmed: 22930834
Open Biol. 2019 Dec;9(12):190223
pubmed: 31795918
Nat Methods. 2016 Apr;13(4):359-65
pubmed: 26950745
Nat Methods. 2009 May;6(5):343-5
pubmed: 19363495
J Microsc. 2012 Apr;246(1):89-95
pubmed: 22288651
Methods Appl Fluoresc. 2015 Mar 09;3(1):014005
pubmed: 29148479
Cytometry A. 2013 May;83(5):441-51
pubmed: 23418106
Opt Nanoscopy. 2013;2(1):
pubmed: 27795878
J Biol Chem. 1998 Mar 6;273(10):5858-68
pubmed: 9488723
J Histochem Cytochem. 1982 Feb;30(2):111-6
pubmed: 7061816
J Biol Chem. 1996 Nov 1;271(44):27608-14
pubmed: 8910349
J Phys Chem B. 2008 Jan 24;112(3):1016-21
pubmed: 18171050
Genesis. 2005 Jul;42(3):162-71
pubmed: 15986455
Biochemistry. 1998 Dec 1;37(48):16863-76
pubmed: 9836579
Nat Commun. 2015 Oct 01;6:8497
pubmed: 26423723
J Bacteriol. 1995 Jul;177(14):4121-30
pubmed: 7608087
Biochemistry. 1994 Jun 14;33(23):7033-40
pubmed: 7516181
Cytometry A. 2005 Sep;67(1):45-52
pubmed: 16082711