Cargando…

Real sequence effects on the search dynamics of transcription factors on DNA

Recent experiments show that transcription factors (TFs) indeed use the facilitated diffusion mechanism to locate their target sequences on DNA in living bacteria cells: TFs alternate between sliding motion along DNA and relocation events through the cytoplasm. From simulations and theoretical analy...

Descripción completa

Detalles Bibliográficos
Autores principales:	Bauer, Maximilian, Rasmussen, Emil S., Lomholt, Michael A., Metzler, Ralf
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Nature Publishing Group 2015
Materias:	Article
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5507490/ https://www.ncbi.nlm.nih.gov/pubmed/26154484 http://dx.doi.org/10.1038/srep10072

Ejemplares similares

Corrigendum: Real sequence effects on the search dynamics of transcription factors on DNA
por: Bauer, Maximilian, et al.
Publicado: (2015)

In Vivo Facilitated Diffusion Model
por: Bauer, Maximilian, et al.
Publicado: (2013)

Dynamic approach to DNA breathing
por: Metzler, R, et al.
Publicado: (2004)

DNA dynamics play a role as a basal transcription factor in the positioning and regulation of gene transcription initiation
por: Alexandrov, Boian S., et al.
Publicado: (2010)

Using Sequence-Specific Chemical and Structural Properties of DNA to Predict Transcription Factor Binding Sites
por: Bauer, Amy L., et al.
Publicado: (2010)

Target search of N sliding proteins on a DNA
por: Sokolov, I, et al.
Publicado: (2004)

Binding dynamics of single-stranded DNA binding proteins to fluctuating bubbles in breathing DNA
por: Ambjornsson, T, et al.
Publicado: (2004)

Coupled dynamics of DNA-breathing and binding of proteins that selectively bind to single-stranded DNA
por: Amjornsson, T, et al.
Publicado: (2004)

Sequence dependence of transcription factor-mediated DNA looping
por: Johnson, Stephanie, et al.
Publicado: (2012)

DNA breathing dynamics distinguish binding from nonbinding consensus sites for transcription factor YY1 in cells
por: Alexandrov, Boian S., et al.
Publicado: (2012)

Sequence-specific dynamics of DNA response elements and their flanking sites regulate the recognition by AP-1 transcription factors
por: Hörberg, Johanna, et al.
Publicado: (2021)

ProteDNA: a sequence-based predictor of sequence-specific DNA-binding residues in transcription factors
por: Chu, Wen-Yi, et al.
Publicado: (2009)

Mapping DNA sequence to transcription factor binding energy in vivo
por: Barnes, Stephanie L., et al.
Publicado: (2019)

Towards Interactive Search: Investigating Visual Search in a Novel Real-World Paradigm
por: Sauter, Marian, et al.
Publicado: (2020)

Dynamic DNA binding licenses a repair factor to bypass roadblocks in search of DNA lesions
por: Brown, Maxwell W., et al.
Publicado: (2016)

Mitochondrial Transcription Factors TFA, TFB1 and TFB2: A Search for DNA Variants/Haplotypes and the Risk of Cardiac Hypertrophy
por: Alonso-Montes, Cristina, et al.
Publicado: (2008)

Uncovering the interplay between DNA sequence preferences of transcription factors and nucleosomes
por: Teichmann, Sarah A., et al.
Publicado: (2012)

Predicting Preference of Transcription Factors for Methylated DNA Using Sequence Information
por: Liu, Meng-Lu, et al.
Publicado: (2020)

From sequence to dynamics: the effects of transcription factor and polymerase concentration changes on activated and repressed promoters
por: González Pérez, Abel, et al.
Publicado: (2009)

FOXO transcription factors differ in their dynamics and intra/intermolecular interactions
por: Spreitzer, Emil, et al.
Publicado: (2022)

How proteins bind to DNA: target discrimination and dynamic sequence search by the telomeric protein TRF1
por: Wieczór, Miłosz, et al.
Publicado: (2017)

A nonlinear dynamic model of DNA with a sequence-dependent stacking term
por: Alexandrov, Boian S., et al.
Publicado: (2009)

Search by proteins for their DNA target site: 2. The effect of DNA conformation on the dynamics of multidomain proteins
por: Bhattacherjee, Arnab, et al.
Publicado: (2014)

Real-time imaging of Huntingtin aggregates diverting target search and gene transcription
por: Li, Li, et al.
Publicado: (2016)

DNA-mediated cooperativity facilitates the co-selection of cryptic enhancer sequences by SOX2 and PAX6 transcription factors
por: Narasimhan, Kamesh, et al.
Publicado: (2015)

Transcription factor localization dynamics and DNA binding drive distinct promoter interpretations
por: Sweeney, Kieran, et al.
Publicado: (2023)

Factor-independent transcription pausing caused by recognition of the RNA–DNA hybrid sequence
por: Bochkareva, Aleksandra, et al.
Publicado: (2012)

Uncoupling evolutionary changes in DNA sequence, transcription factor occupancy and enhancer activity
por: Khoueiry, Pierre, et al.
Publicado: (2017)

TRACE: transcription factor footprinting using chromatin accessibility data and DNA sequence
por: Ouyang, Ningxin, et al.
Publicado: (2020)

Systematic Evaluation of DNA Sequence Variations on in vivo Transcription Factor Binding Affinity
por: Jin, Yutong, et al.
Publicado: (2021)

A human transcription factor in search mode
por: Hauser, Kevin, et al.
Publicado: (2016)

Inhibitory Effects of Bangladeshi Medicinal Plant Extracts on Interactions between Transcription Factors and Target DNA Sequences
por: Lampronti, Ilaria, et al.
Publicado: (2008)

Complete Genome Sequence of a Staphylococcus epidermidis Strain with Exceptional Antimicrobial Activity
por: Lassen, Simon B., et al.
Publicado: (2017)

How motif environment influences transcription factor search dynamics: Finding a needle in a haystack
por: Dror, Iris, et al.
Publicado: (2016)

Targeted bisulfite sequencing of the dynamic DNA methylome
por: Ziller, Michael J., et al.
Publicado: (2016)

Searching target sites on DNA by proteins: Role of DNA dynamics under confinement
por: Mondal, Anupam, et al.
Publicado: (2015)

Kethoxal-assisted single-stranded DNA sequencing captures global transcription dynamics and enhancer activity in situ
por: Wu, Tong, et al.
Publicado: (2020)

Transcript counting in single cells reveals dynamics of rDNA transcription
por: Tan, Rui Zhen, et al.
Publicado: (2010)

Understanding the Effect of Structural Diversity in WRKY Transcription Factors on DNA Binding Efficiency through Molecular Dynamics Simulation
por: Singh, Akshay, et al.
Publicado: (2019)

Genomewide protein-DNA binding dynamics suggest a clutch for transcription factor function
por: Lickwar, Colin R., et al.
Publicado: (2012)

Cannot write session to /tmp/vufind_sessions/sess_p0fgbv53vp942i2jlv0mo0miml