ThreaDNA: predicting DNA mechanics’ contribution to sequence selectivity of proteins along whole genomes

Autor: Sam Meyer, Cédric Vaillant, Burkhard Rost, Jasmin Cevost
Přispěvatelé: Microbiologie, adaptation et pathogénie (MAP), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Laboratoire Joliot Curie, École normale supérieure de Lyon (ENS de Lyon)-Centre National de la Recherche Scientifique (CNRS), Chromatine et Régulation de la Pathogénie bactérienne (CRP), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), École normale supérieure - Lyon (ENS Lyon)-Centre National de la Recherche Scientifique (CNRS), Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL)
Jazyk: angličtina
Rok vydání: 2018
Předmět:
0301 basic medicine
Statistics and Probability
Models
Molecular
Web server
Protein Conformation
Saccharomyces cerevisiae
Biology
computer.software_genre
Biochemistry
Genome
Histones
03 medical and health sciences
chemistry.chemical_compound
0302 clinical medicine
Software
Factor For Inversion Stimulation Protein
Escherichia coli
Nucleosome
[PHYS.COND]Physics [physics]/Condensed Matter [cond-mat]
Molecular Biology
ComputingMilieux_MISCELLANEOUS
Graphical user interface
Genetics
[PHYS]Physics [physics]
business.industry
Escherichia coli Proteins
Computational Biology
computer.file_format
DNA
[SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM]
Computer Science Applications
Nucleosomes
DNA-Binding Proteins
Computational Mathematics
030104 developmental biology
Computational Theory and Mathematics
chemistry
Nucleic Acid Conformation
Executable
Sequence motif
business
Biological system
computer
030217 neurology & neurosurgery
Zdroj: Bioinformatics
Bioinformatics, 2018, 34 (4), pp.609-616. ⟨10.1093/bioinformatics/btx634⟩
Bioinformatics, Oxford University Press (OUP), 2018, 34 (4), pp.609-616. ⟨10.1093/bioinformatics/btx634⟩
ISSN: 1367-4803
1367-4811
Popis: Motivation Many DNA-binding proteins recognize their target sequences indirectly, by sensing DNA’s response to mechanical distortion. ThreaDNA estimates this response based on high-resolution structures of the protein–DNA complex of interest. Implementing an efficient nanoscale modeling of DNA deformations involving essentially no adjustable parameters, it returns the profile of deformation energy along whole genomes, at base-pair resolution, within minutes on usual laptop/desktop computers. Our predictions can also be easily combined with estimations of direct selectivity through a generalized form of position-weight-matrices. The formalism of ThreaDNA is accessible to a wide audience. Results We demonstrate the importance of indirect readout for the nucleosome as well as the bacterial regulators Fis and CRP. Combined with the direct contribution provided by usual sequence motifs, it significantly improves the prediction of sequence selectivity, and allows quantifying the two distinct physical mechanisms underlying it. Availability and implementation Python software available at bioinfo.insa-lyon.fr, natively executable on Linux/MacOS systems with a user-friendly graphical interface. Galaxy webserver version available. Supplementary information Supplementary data are available at Bioinformatics online.
Databáze: OpenAIRE
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