Proteins Recognizing DNA: Structural Uniqueness and Versatility of DNA-Binding Domains in Stem Cell Transcription Factors

Transitions of Double-Stranded DNA Between the A- and B-Forms

(2016) James T. Waters et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Structural and conformational insights into SOX2/OCT4-bound enhancer DNA: a computational perspective

(2016) Muhammad Ayaz Anwar et al.   RSC Advances

Pioneer Transcription Factors Target Partial DNA Motifs on Nucleosomes to Initiate Reprogramming

(2015) Abdenour Soufi et al.   CELL

Homeodomain proteins: an update

(2015) Thomas R. Bürglin et al.   CHROMOSOMA

The multifaceted roles of intrinsic disorder in protein complexes

(2015) Vladimir N. Uversky   FEBS LETTERS

A widespread role of the motif environment in transcription factor binding across diverse protein families

(2015) Iris Dror et al.   GENOME RESEARCH

Protein search for multiple targets on DNA

(2015) Martin Lange et al.   JOURNAL OF CHEMICAL PHYSICS

C2H2 zinc finger proteins greatly expand the human regulatory lexicon

(2015) Hamed S Najafabadi et al.   NATURE BIOTECHNOLOGY

MEF2D Drives Photoreceptor Development through a Genome-wide Competition for Tissue-Specific Enhancers

(2015) Milena M. Andzelm et al.   NEURON

Functional interplay between the RK motif and linker segment dictates Oct4–DNA recognition

(2015) Xiangqian Kong et al.   NUCLEIC ACIDS RESEARCH

ELM 2016—data update and new functionality of the eukaryotic linear motif resource

(2015) Holger Dinkel et al.   NUCLEIC ACIDS RESEARCH

Structure-based discovery of NANOG variant with enhanced properties to promote self-renewal and reprogramming of pluripotent stem cells

(2015) Yohei Hayashi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cooperative DNA Recognition Modulated by an Interplay between Protein-Protein Interactions and DNA-Mediated Allostery

(2015) Felipe Merino et al.   PLoS Computational Biology

Studying the organization of DNA repair by single-cell and single-molecule imaging

(2014) Stephan Uphoff et al.   DNA REPAIR

Pioneer transcription factors in cell reprogramming

(2014) Makiko Iwafuchi-Doi et al.   GENES & DEVELOPMENT

Myc and Max Genome-Wide Binding Sites Analysis Links the Myc Regulatory Network with the Polycomb and the Core Pluripotency Networks in Mouse Embryonic Stem Cells

(2014) Anna Krepelova et al.   PLoS One

Protein−DNA binding in the absence of specific base-pair recognition

(2014) Ariel Afek et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Absence of a simple code: how transcription factors read the genome

(2014) Matthew Slattery et al.   TRENDS IN BIOCHEMICAL SCIENCES

An Overview of MYC and Its Interactome

(2014) M. Conacci-Sorrell et al.   Cold Spring Harbor Perspectives in Medicine

OCT4: Dynamic DNA binding pioneers stem cell pluripotency

(2013) Stepan Jerabek et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

DNA-Binding Specificities of Human Transcription Factors

(2013) Arttu Jolma et al.   CELL

A direct physical interaction between Nanog and Sox2 regulates embryonic stem cell self-renewal

(2013) Alessia Gagliardi et al.   EMBO JOURNAL

Octamer-binding transcription factors: genomics and functions

(2013) Feng-Qi Zhao   Frontiers in Bioscience-Landmark

A unique Oct4 interface is crucial for reprogramming to pluripotency

(2013) Daniel Esch et al.   NATURE CELL BIOLOGY

Exploring bacterial cell biology with single-molecule tracking and super-resolution imaging

(2013) Andreas Gahlmann et al.   NATURE REVIEWS MICROBIOLOGY

DNA-recognition process described by MD simulations of the lactose repressor protein on a specific and a non-specific DNA sequence

(2013) Simone Furini et al.   NUCLEIC ACIDS RESEARCH

Structure of p53 binding to the BAX response element reveals DNA unwinding and compression to accommodate base-pair insertion

(2013) Yongheng Chen et al.   NUCLEIC ACIDS RESEARCH

Protein-DNA binding: complexities and multi-protein codes

(2013) T. Siggers et al.   NUCLEIC ACIDS RESEARCH

Probing Allostery Through DNA

(2013) S. Kim et al.   SCIENCE

Myc Function in Drosophila

(2013) P. Gallant   Cold Spring Harbor Perspectives in Medicine

Cys2His2 zinc finger protein family: Classification, functions, and major members

(2012) S. V. Razin et al.   BIOCHEMISTRY-MOSCOW

Facilitators and Impediments of the Pluripotency Reprogramming Factors' Initial Engagement with the Genome

(2012) Abdenour Soufi et al.   CELL

Towards a molecular view of transcriptional control

(2012) Krystyna Zakrzewska et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

The selector gene Pax7 dictates alternate pituitary cell fates through its pioneer action on chromatin remodeling

(2012) L. Budry et al.   GENES & DEVELOPMENT

Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors

(2012) J. Wang et al.   GENOME RESEARCH

A- to B-Form Transition in DNA Between Gold Surfaces

(2012) One-Sun Lee et al.   JOURNAL OF PHYSICAL CHEMISTRY B

DNA Binding by GATA Transcription Factor Suggests Mechanisms of DNA Looping and Long-Range Gene Regulation

(2012) Yongheng Chen et al.   Cell Reports

The Binding Process of a Nonspecific Enzyme with DNA

(2011) Chuanying Chen et al.   BIOPHYSICAL JOURNAL

Frustration in protein-DNA binding influences conformational switching and target search kinetics

(2011) A. Marcovitz et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Dynamic protein–DNA recognition: beyond what can be seen

(2011) Monika Fuxreiter et al.   TRENDS IN BIOCHEMICAL SCIENCES

The Discovery of Zinc Fingers and Their Applications in Gene Regulation and Genome Manipulation

(2010) Aaron Klug   Annual Review of Biochemistry

Origins of Specificity in Protein-DNA Recognition

(2010) Remo Rohs et al.   Annual Review of Biochemistry

HMGB proteins: Interactions with DNA and chromatin

(2010) Michal Štros   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

CTCF shapes chromatin by multiple mechanisms: the impact of 20 years of CTCF research on understanding the workings of chromatin

(2010) Rolf Ohlsson et al.   CHROMOSOMA

The shape of the DNA minor groove directs binding by the DNA-bending protein Fis

(2010) S. Stella et al.   GENES & DEVELOPMENT

Visualizing one-dimensional diffusion of eukaryotic DNA repair factors along a chromatin lattice

(2010) Jason Gorman et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Physics of protein–DNA interactions: mechanisms of facilitated target search

(2010) Anatoly B. Kolomeisky   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Mechanisms of transcription factor selectivity

(2010) Yongping Pan et al.   TRENDS IN GENETICS

The dynamics of HMG protein–chromatin interactions in living cellsThis paper is one of a selection of papers published in this Special Issue, entitled CSBMCB’s 51st Annual Meeting – Epigenetics and Chromatin Dynamics, and has undergone the Journal’s usual peer review process.

(2009) Gabi Gerlitz et al.   Biochemistry and Cell Biology

Predicting intrinsic disorder in proteins: an overview

(2009) Bo He et al.   CELL RESEARCH

Nuance in the double-helix and its role in protein–DNA recognition

(2009) Remo Rohs et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Searching DNA via a “Monkey Bar” Mechanism: The Significance of Disordered Tails

(2009) Dana Vuzman et al.   JOURNAL OF MOLECULAR BIOLOGY

The role of DNA shape in protein–DNA recognition

(2009) Remo Rohs et al.   NATURE

Searching Fast for a Target on DNA without Falling to Traps

(2009) O. Bénichou et al.   PHYSICAL REVIEW LETTERS

Amplification of signaling via cellular allosteric relay and protein disorder

(2009) B. Ma et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Facilitated diffusion with DNA coiling

(2009) M. A. Lomholt et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The unique structure of A-tracts and intrinsic DNA bending

(2009) Tali E. Haran et al.   QUARTERLY REVIEWS OF BIOPHYSICS

Prediction of Protein Binding Regions in Disordered Proteins

(2009) Bálint Mészáros et al.   PLoS Computational Biology

Adaptive Evolution in Zinc Finger Transcription Factors

(2009) Ryan O. Emerson et al.   PLoS Genetics

Keep Your Fingers Off My DNA: Protein–Protein Interactions Mediated by C2H2 Zinc Finger Domains

(2008) Kathryn J. Brayer et al.   CELL BIOCHEMISTRY AND BIOPHYSICS

Understanding eukaryotic linear motifs and their role in cell signaling and regulation

(2008) Francesca Diella   Frontiers in Bioscience-Landmark

Max-independent functions of Myc in Drosophila melanogaster

(2008) Dominik Steiger et al.   NATURE GENETICS

High-density mapping of single-molecule trajectories with photoactivated localization microscopy

(2008) Suliana Manley et al.   NATURE METHODS

Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data

(2008) Anton Valouev et al.   NATURE METHODS

Hopping of a processivity factor on DNA revealed by single-molecule assays of diffusion

(2008) G. Komazin-Meredith et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Global jumping and domain-specific intersegment transfer between DNA cognate sites of the multidomain transcription factor Oct-1

(2008) M. Doucleff et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

How DNA coiling enhances target localization by proteins

(2008) B. van den Broek et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Crystal Structure and DNA Binding of the Homeodomain of the Stem Cell Transcription Factor Nanog

(2007) Ralf Jauch et al.   JOURNAL OF MOLECULAR BIOLOGY