Nucleosome-bound SOX2 and SOX11 structures elucidate pioneer factor function

Negative reciprocity, not ordered assembly, underlies the interaction of Sox2 and Oct4 on DNA

(2019) John W Biddle et al.   eLife

Dissociation rate compensation mechanism for budding yeast pioneer transcription factors

(2019) Benjamin T Donovan et al.   eLife

Pioneer Factor-Nucleosome Binding Events during Differentiation Are Motif Encoded

(2019) Michael P. Meers et al.   MOLECULAR CELL

Nonreciprocal and Conditional Cooperativity Directs the Pioneer Activity of Pluripotency Transcription Factors

(2019) Sai Li et al.   Cell Reports

Real-time cryo-electron microscopy data preprocessing with Warp

(2019) Dimitry Tegunov et al.   NATURE METHODS

Excluding Oct4 from Yamanaka Cocktail Unleashes the Developmental Potential of iPSCs

(2019) Sergiy Velychko et al.   Cell Stem Cell

The Human Transcription Factors

(2018) Samuel A. Lambert et al.   CELL

Defining B Cell Chromatin: Lessons from EBF1

(2018) Sören Boller et al.   TRENDS IN GENETICS

Structural rearrangements of the histone octamer translocate DNA

(2018) Silvija Bilokapic et al.   Nature Communications

The interaction landscape between transcription factors and the nucleosome

(2018) Fangjie Zhu et al.   NATURE

cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination

(2017) Ali Punjani et al.   NATURE METHODS

Addressing preferred specimen orientation in single-particle cryo-EM through tilting

(2017) Yong Zi Tan et al.   NATURE METHODS

Histone octamer rearranges to adapt to DNA unwrapping

(2017) Silvija Bilokapic et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Histone octamer rearranges to adapt to DNA unwrapping

(2017) Silvija Bilokapic et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Insights into Nucleosome Organization in Mouse Embryonic Stem Cells through Chemical Mapping

(2016) Lilien N. Voong et al.   CELL

Cell fate control by pioneer transcription factors

(2016) Makiko Iwafuchi-Doi et al.   DEVELOPMENT

Gctf: Real-time CTF determination and correction

(2016) Kai Zhang   JOURNAL OF STRUCTURAL BIOLOGY

Structure and decoy-mediated inhibition of the SOX18/Prox1-DNA interaction

(2016) Miriam Klaus et al.   NUCLEIC ACIDS RESEARCH

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

(2015) Abdenour Soufi et al.   CELL

Single-Molecule Dynamics of Enhanceosome Assembly in Embryonic Stem Cells

(2014) Jiji Chen et al.   CELL

Cryo-EM Study of the Chromatin Fiber Reveals a Double Helix Twisted by Tetranucleosomal Units

(2014) F. Song et al.   SCIENCE

Intra- and inter-nucleosome interactions of the core histone tail domains in higher-order chromatin structure

(2013) Sharon Pepenella et al.   CHROMOSOMA

Sox proteins: regulators of cell fate specification and differentiation

(2013) Y. Kamachi et al.   DEVELOPMENT

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

(2012) J. Wang et al.   GENOME RESEARCH

RELION: Implementation of a Bayesian approach to cryo-EM structure determination

(2012) Sjors H.W. Scheres   JOURNAL OF STRUCTURAL BIOLOGY

The crystal structure of the Sox4 HMG domain–DNA complex suggests a mechanism for positional interdependence in DNA recognition

(2011) Ralf Jauch et al.   BIOCHEMICAL JOURNAL

Sequentially acting Sox transcription factors in neural lineage development

(2011) M. Bergsland et al.   GENES & DEVELOPMENT

Preparation of Fully Synthetic Histone H3 Reveals That Acetyl-Lysine 56 Facilitates Protein Binding Within Nucleosomes

(2011) John C. Shimko et al.   JOURNAL OF MOLECULAR BIOLOGY

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega

(2011) F. Sievers et al.   Molecular Systems Biology

Sox2 cooperates with Chd7 to regulate genes that are mutated in human syndromes

(2011) Erik Engelen et al.   NATURE GENETICS

XDS

(2010) Wolfgang Kabsch   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

Features and development ofCoot

(2010) P. Emsley et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

PHENIX: a comprehensive Python-based system for macromolecular structure solution

(2010) Paul D. Adams et al.   ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY

The Structure of Sox17 Bound to DNA Reveals a Conserved Bending Topology but Selective Protein Interaction Platforms

(2009) Paaventhan Palasingam et al.   JOURNAL OF MOLECULAR BIOLOGY

Defining mechanisms that regulate RNA polymerase II transcription in vivo

(2009) Nicholas J. Fuda et al.   NATURE

High-resolution dynamic mapping of histone-DNA interactions in a nucleosome

(2009) Michael A Hall et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Diversity and Complexity in DNA Recognition by Transcription Factors

(2009) G. Badis et al.   SCIENCE