4.6 Article

Modelling chromosome-wide target search

相关参考文献

注意:仅列出部分参考文献,下载原文获取全部文献信息。
Article Multidisciplinary Sciences

Sequence specificity in DNA binding is mainly governed by association

Emil Marklund et al.

Summary: This study investigates the sequence-specific binding of proteins and DNA, revealing an anticorrelation between the association and dissociation rates of DNA binding proteins. Experimental results show that the efficiency with which the proteins recognize different targets primarily determines sequence specificity.

SCIENCE (2022)

Article Chemistry, Physical

DNA Looping and DNA Conformational Fluctuations Can Accelerate Protein Target Search

Cayke Felipe et al.

Summary: This theoretical study investigates the role of DNA looping and conformational fluctuations in protein target search, finding that stronger nonspecific interactions between DNA and proteins lead to faster search on looped DNA conformation. The study also shows that DNA fluctuations between looped and unlooped conformations influence search dynamics, depending on transition rates and energetically stable conformations. Arguments based on physical-chemical principles are presented to explain these observations.

JOURNAL OF PHYSICAL CHEMISTRY B (2021)

Article Physics, Multidisciplinary

Search and Localization Dynamics of the CRISPR-Cas9 System

Qiao Lu et al.

Summary: The CRISPR-Cas9 system is an important gene editing tool where the key component Cas9 can search for and cleave specific target sequences on the DNA through sliding. Studies have shown that the sliding length of Cas9 is short, and the distribution of Cas9 molecules along the DNA can be rationalized through the theory of Anderson localization.

PHYSICAL REVIEW LETTERS (2021)

Article Physics, Multidisciplinary

Modeling protein target search in human chromosomes

Markus Nyberg et al.

Summary: The study finds that the 3D conformation of DNA is crucial for protein search times in vivo, with segments enriched with active gene starts showing higher rates. The research also offers a method for interpreting protein-binding profiles in eukaryotes.

PHYSICAL REVIEW RESEARCH (2021)

Article Biochemistry & Molecular Biology

JASPAR 2020: update of the open-access database of transcription factor binding profiles

Oriol Fornes et al.

NUCLEIC ACIDS RESEARCH (2020)

Article Multidisciplinary Sciences

Mapping the spectrum of 3D communities in human chromosome conformation capture data

Sang Hoon Lee et al.

SCIENTIFIC REPORTS (2019)

Article Biochemistry & Molecular Biology

CRISPR/Cas9 searches for a protospacer adjacent motif by lateral diffusion

Viktorija Globyte et al.

EMBO JOURNAL (2019)

Article Biochemistry & Molecular Biology

Energetic funnel facilitates facilitated diffusion

Massimo Cencini et al.

NUCLEIC ACIDS RESEARCH (2018)

Article Multidisciplinary Sciences

Theoretical principles of transcription factor traffic on folded chromatin

Ruggero Cortini et al.

NATURE COMMUNICATIONS (2018)

Review Chemistry, Multidisciplinary

Facilitated Diffusion Mechanisms in DNA Base Excision Repair and Transcriptional Activation

Alexandre Esadze et al.

CHEMICAL REVIEWS (2018)

Article Biochemistry & Molecular Biology

Genome contact map explorer: a platform for the comparison, interactive visualization and analysis of genome contact maps

Rajendra Kumar et al.

NUCLEIC ACIDS RESEARCH (2017)

Article Physics, Fluids & Plasmas

Facilitated diffusion of proteins through crumpled fractal DNA globules

Jan Smrek et al.

PHYSICAL REVIEW E (2015)

Article Multidisciplinary Sciences

Chromatin extrusion explains key features of loop and domain formation in wild-type and engineered genomes

Adrian L. Sanborn et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2015)

Article Multidisciplinary Sciences

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

Maximilian Bauer et al.

SCIENTIFIC REPORTS (2015)

Article Multidisciplinary Sciences

Inter-Chromosomal Contact Networks Provide Insights into Mammalian Chromatin Organization

Stefanie Kaufmann et al.

PLOS ONE (2015)

Article Biochemistry & Molecular Biology

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

Suhas S. P. Rao et al.

Article Mathematics, Applied

A fast algorithm for matrix balancing

Philip A. Knight et al.

IMA JOURNAL OF NUMERICAL ANALYSIS (2013)

Article Multidisciplinary Sciences

The lac Repressor Displays Facilitated Diffusion in Living Cells

Petter Hammar et al.

SCIENCE (2012)

Article Physics, Multidisciplinary

Intermittent search strategies

O. Benichou et al.

REVIEWS OF MODERN PHYSICS (2011)

Article Biochemistry & Molecular Biology

Translational control analysis by translationally active RNA capture/microarray analysis (TrIP-Chip)

Kenji Kudo et al.

NUCLEIC ACIDS RESEARCH (2010)

Article Biochemical Research Methods

MOODS: fast search for position weight matrix matches in DNA sequences

Janne Korhonen et al.

BIOINFORMATICS (2009)

Article Physics, Multidisciplinary

How a protein searches for its site on DNA: the mechanism of facilitated diffusion

Leonid Mirny et al.

JOURNAL OF PHYSICS A-MATHEMATICAL AND THEORETICAL (2009)

Review Genetics & Heredity

Insights from genomic profiling of transcription factors

Peggy J. Farnham

NATURE REVIEWS GENETICS (2009)

Article Multidisciplinary Sciences

Facilitated diffusion with DNA coiling

Michael A. Lomholt et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2009)

Article Multidisciplinary Sciences

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

Erez Lieberman-Aiden et al.

SCIENCE (2009)

Article Chemistry, Physical

Diffusion constant of a nonspecifically bound protein undergoing curvilinear motion along DNA

Biman Bagchi et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2008)

Article Multidisciplinary Sciences

How DNA coiling enhances target localization by proteins

B. van den Broek et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2008)

Article Physics, Multidisciplinary

Optimal target search on a fast-folding polymer chain with volume exchange -: art. no. 260603

MA Lomholt et al.

PHYSICAL REVIEW LETTERS (2005)

Article Biochemistry & Molecular Biology

The human genome browser at UCSC

WJ Kent et al.

GENOME RESEARCH (2002)

Article Biochemistry & Molecular Biology

Gene Expression Omnibus: NCBI gene expression and hybridization array data repository

R Edgar et al.

NUCLEIC ACIDS RESEARCH (2002)