Interplay between DNA sequence and negative superhelicity drives R-loop structures.

Base Sequence DNA / chemistry DNA, Single-Stranded / chemistry DNA, Superhelical / chemistry Models, Genetic Nucleic Acid Conformation Nucleic Acid Hybridization Plasmids / chemistry RNA / chemistry Transcription, Genetic
DNA topology R-loop modeling transcription

Journal

Proceedings of the National Academy of Sciences of the United States of America
ISSN: 1091-6490
Titre abrégé: Proc Natl Acad Sci U S A
Pays: United States
ID NLM: 7505876

Informations de publication

Date de publication:
26 03 2019
Historique:
pubmed: 10 3 2019
medline: 21 5 2019
entrez: 10 3 2019
Statut: ppublish

Résumé

R-loops are abundant three-stranded nucleic-acid structures that form

Identifiants

DOI: 10.1073/pnas.1819476116 PMID: 30850542 PMC: PMC6442632
pubmed: 30850542
pii: 1819476116
doi: 10.1073/pnas.1819476116
pmc: PMC6442632
doi:

Substances chimiques

DNA, Single-Stranded 0
DNA, Superhelical 0
RNA 63231-63-0
DNA 9007-49-2

Types de publication

Journal Article Research Support, N.I.H., Extramural Research Support, U.S. Gov't, Non-P.H.S.

Langues

eng

Sous-ensembles de citation

IM

Pagination

6260-6269

Subventions

Organisme : NIGMS NIH HHS
ID : R01 GM120607
Pays : United States
Organisme : NIGMS NIH HHS
ID : T32 GM008799
Pays : United States

Informations de copyright

Copyright © 2019 the Author(s). Published by PNAS.

Déclaration de conflit d'intérêts

The authors declare no conflict of interest.

Références

J Biol Chem. 1999 Jun 4;274(23):16659-64
pubmed: 10347234
Nat Immunol. 2003 May;4(5):442-51
pubmed: 12679812
Science. 1992 Nov 27;258(5087):1463-6
pubmed: 1279808
Mol Microbiol. 1992 Feb;6(4):425-33
pubmed: 1313943
Proc Natl Acad Sci U S A. 1992 Dec 1;89(23):11461-5
pubmed: 1333610
Nucleic Acids Res. 2006 Jan 1;34(Database issue):D373-8
pubmed: 16381890
Proc Natl Acad Sci U S A. 2006 Mar 28;103(13):5030-5
pubmed: 16547142
Nature. 1990 Nov 22;348(6299):342-4
pubmed: 1701219
Front Biosci. 2007 May 01;12:4409-23
pubmed: 17485385
Mol Cell Biol. 2008 Jan;28(1):50-60
pubmed: 17954560
Nat Struct Mol Biol. 2008 Feb;15(2):146-54
pubmed: 18193062
PLoS Comput Biol. 2008 Jan;4(1):e17
pubmed: 18208321
Mol Biosyst. 2008 Jun;4(6):686-91
pubmed: 18493667
J Bacteriol. 2008 Nov;190(22):7346-56
pubmed: 18790862
Mol Cell Biol. 2009 Jun;29(11):3124-33
pubmed: 19307304
PLoS Genet. 2009 Apr;5(4):e1000454
pubmed: 19360095
Mol Cell Biol. 2010 Jan;30(1):146-59
pubmed: 19841062
Proc Natl Acad Sci U S A. 1991 Feb 1;88(3):718-22
pubmed: 1992462
Genes Dev. 2010 Jul 15;24(14):1546-58
pubmed: 20634320
PLoS Comput Biol. 2011 Jan 20;7(1):e1001051
pubmed: 21283778
Biochim Biophys Acta. 2012 Jul;1819(7):632-8
pubmed: 22233557
Mol Cell. 2012 Mar 30;45(6):814-25
pubmed: 22387027
Proc Natl Acad Sci U S A. 1979 Aug;76(8):3870-4
pubmed: 226985
Nat Struct Mol Biol. 2013 Mar;20(3):396-403
pubmed: 23416947
J Mol Recognit. 2013 Aug;26(8):376-81
pubmed: 23784994
Genome Res. 2013 Oct;23(10):1590-600
pubmed: 23868195
Nucleic Acids Res. 2013 Nov;41(21):9610-21
pubmed: 23969416
Cell Biophys. 1987 Oct;10(3):193-204
pubmed: 2446766
Curr Opin Genet Dev. 2014 Apr;25:15-21
pubmed: 24584092
J Biol Chem. 1988 Oct 25;263(30):15282-7
pubmed: 2459121
PLoS Genet. 2014 Apr 17;10(4):e1004288
pubmed: 24743342
Bioinformatics. 2015 Feb 1;31(3):421-2
pubmed: 25282644
PLoS Genet. 2014 Oct 30;10(10):e1004716
pubmed: 25357144
Elife. 2015 Jul 16;4:null
pubmed: 26182405
Nucleic Acids Res. 2015 Nov 16;43(20):9729-41
pubmed: 26253743
Nat Rev Genet. 2015 Oct;16(10):583-97
pubmed: 26370899
Nat Struct Mol Biol. 2015 Dec;22(12):999-1007
pubmed: 26551076
Nat Commun. 2016 Jan 11;7:10208
pubmed: 26751768
Genes Dev. 2016 Jun 1;30(11):1327-38
pubmed: 27298336
Mol Cell. 2016 Jul 7;63(1):167-78
pubmed: 27373332
Elife. 2016 Aug 23;5:
pubmed: 27552054
Biophys Rev. 2016;8(3):245-258
pubmed: 27738453
Trends Genet. 2016 Dec;32(12):828-838
pubmed: 27793359
Proc Natl Acad Sci U S A. 1987 Oct;84(20):7024-7
pubmed: 2823250
ACS Chem Biol. 2017 Oct 20;12(10):2609-2618
pubmed: 28846373
Nat Plants. 2017 Sep;3(9):704-714
pubmed: 28848233
Mol Cell. 2017 Nov 16;68(4):745-757.e5
pubmed: 29104020
J Mol Biol. 2018 Feb 2;430(3):272-284
pubmed: 29289567
Genome Biol. 2018 Jul 30;19(1):100
pubmed: 30060749
DNA Repair (Amst). 2018 Nov;71:69-81
pubmed: 30190235
Nucleic Acids Res. 1979 Jan;6(1):331-57
pubmed: 424296
Nucleic Acids Res. 1980 Feb 11;8(3):555-66
pubmed: 6160477
Proc Natl Acad Sci U S A. 1983 Oct;80(20):6206-10
pubmed: 6578505
Biochemistry. 1994 May 3;33(17):5298-304
pubmed: 7513557
Biochemistry. 1995 Sep 5;34(35):11211-6
pubmed: 7545436
Proc Natl Acad Sci U S A. 1995 Jun 6;92(12):5625-9
pubmed: 7777560
J Biol Chem. 1994 Aug 26;269(34):21850-7
pubmed: 8063829
J Mol Biol. 1993 Dec 20;234(4):1184-96
pubmed: 8263920
J Biol Chem. 1994 Jan 21;269(3):2068-74
pubmed: 8294458
J Mol Biol. 1993 Feb 5;229(3):623-36
pubmed: 8433363
Nucleic Acids Res. 1995 Dec 25;23(24):5006-11
pubmed: 8559658
J Mol Biol. 1996 Jan 26;255(3):425-34
pubmed: 8568887
Nature. 1977 Sep 1;269(5623):29-36
pubmed: 895884
J Biol Chem. 1997 May 9;272(19):12816-23
pubmed: 9139742
Nature. 1997 Sep 18;389(6648):251-60
pubmed: 9305837

Auteurs

Robert Stolz (R)

Department of Molecular and Cellular Biology, University of California, Davis, CA 95616.
Integrative Genetics and Genomics Graduate Group, University of California, Davis, CA 95616.

Shaheen Sulthana (S)

Department of Molecular and Cellular Biology, University of California, Davis, CA 95616.

Stella R Hartono (SR)

Department of Molecular and Cellular Biology, University of California, Davis, CA 95616.

Maika Malig (M)

Department of Molecular and Cellular Biology, University of California, Davis, CA 95616.
Integrative Genetics and Genomics Graduate Group, University of California, Davis, CA 95616.

Craig J Benham (CJ)

Department of Mathematics, University of California, Davis, CA 95616; cjbenham@ucdavis.edu flchedin@ucdavis.edu.
Department of Biomedical Engineering, University of California, Davis, CA 95616.
Genome Center, University of California, Davis, CA 95616.

Frederic Chedin (F)

Department of Molecular and Cellular Biology, University of California, Davis, CA 95616; cjbenham@ucdavis.edu flchedin@ucdavis.edu.
Genome Center, University of California, Davis, CA 95616.
ORCID: 0000-0002-1306-5335

Articles similaires

Biological functions and molecular mechanisms of exosome-derived circular RNAs and their clinical implications in digestive malignancies: the vintage in the bottle.

Yuanyan Lou, Jianing Yan, Qingqing Liu et al.
1.00
Humans RNA, Circular Exosomes Cell Proliferation Epithelial-Mesenchymal Transition

From cactus to crop: genomic insights of a beneficial and non-pathogenic Curtobacterium flaccumfaciens strain and the evolution of its pathosystem.

Dilson Fagundes Ribeiro, Jéssica Pereira de Matos, Lorrana Cachuite Mendes Rocha et al.
1.00
Genome, Bacterial Virulence Phylogeny Genomics Plant Diseases

A computational model for bacteriophage ϕX174 gene expression.

Alexis M Hill, Tanvi A Ingle, Claus O Wilke
1.00
Gene Expression Regulation, Viral Promoter Regions, Genetic Bacteriophage phi X 174 Computer Simulation Models, Genetic

iDNA-ITLM: An interpretable and transferable learning model for identifying DNA methylation.

Xia Yu, Cui Yani, Zhichao Wang et al.
1.00
DNA Methylation Humans DNA Animals Machine Learning

Classifications MeSH

questionsmedicales.fr › Sciences de l'information › Sources d'information › Services d'information › Documentation › Données de séquences moléculaires › Séquence nucléotidique › Interplay between DNA sequence and negative...
questionsmedicales.fr › Acides nucléiques, nucléotides et nucléosides › Acides nucléiques › ADN › Interplay between DNA sequence and negative...
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Conformation d'acide nucléique › ADN simple brin › Interplay between DNA sequence and negative...
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Conformation d'acide nucléique › ADN circulaire › ADN superhélicoïdal › Interplay between DNA sequence and negative...
questionsmedicales.fr › Techniques d'investigation › Modèles théoriques › Modèles biologiques › Modèles génétiques › Interplay between DNA sequence and negative...
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Conformation d'acide nucléique › Interplay between DNA sequence and negative...
questionsmedicales.fr › Phénomènes chimiques › Phénomènes biochimiques › Hybridation d'acides nucléiques › Interplay between DNA sequence and negative...
questionsmedicales.fr › Phénomènes génétiques › Structures génétiques › Plasmides › Interplay between DNA sequence and negative...
questionsmedicales.fr › Acides nucléiques, nucléotides et nucléosides › Acides nucléiques › ARN › Interplay between DNA sequence and negative...
questionsmedicales.fr › Phénomènes génétiques › Expression des gènes › Transcription génétique › Interplay between DNA sequence and negative...