Quantitative profiling of selective Sox/POU pairing on hundreds of sequences in parallel by Coop-seq

Molecular basis for the genome engagement by Sox proteins

(2017) Linlin Hou et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Changing POU dimerization preferences converts Oct6 into a pluripotency inducer

(2016) Stepan Jerabek et al.   EMBO REPORTS

Quantification of Cooperativity in Heterodimer-DNA Binding Improves the Accuracy of Binding Specificity Models

(2016) Alina Isakova et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

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

(2016) Miriam Klaus et al.   NUCLEIC ACIDS RESEARCH

Combinatorial Cis -regulation in Saccharomyces Species

(2016) Aaron T. Spivak et al.   G3-Genes Genomes Genetics

SOX17 Is a Critical Specifier of Human Primordial Germ Cell Fate

(2015) Naoko Irie et al.   CELL

Selective influence of Sox2 on POU transcription factor binding in embryonic and neural stem cells

(2015) T. K. Mistri et al.   EMBO REPORTS

DNA-dependent formation of transcription factor pairs alters their binding specificity

(2015) Arttu Jolma et al.   NATURE

DNA-mediated cooperativity facilitates the co-selection of cryptic enhancer sequences by SOX2 and PAX6 transcription factors

(2015) Kamesh Narasimhan et al.   NUCLEIC ACIDS RESEARCH

The transcription factors SOX9 and SOX5/SOX6 cooperate genome-wide through super-enhancers to drive chondrogenesis

(2015) Chia-Feng Liu et al.   NUCLEIC ACIDS RESEARCH

Dissecting the role of distinct OCT4-SOX2 heterodimer configurations in pluripotency

(2015) Natalia Tapia et al.   Scientific Reports

SOXE transcription factors form selective dimers on non-compact DNA motifs through multifaceted interactions between dimerization and high-mobility group domains

(2015) Yong-Heng Huang et al.   Scientific Reports

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

(2015) Felipe Merino et al.   PLoS Computational Biology

Spec-seq: determining protein-DNA-binding specificity by sequencing

(2014) G. D. Stormo et al.   Briefings in Functional Genomics

High-Resolution Specificity from DNA Sequencing Highlights Alternative Modes of Lac Repressor Binding

(2014) Z. Zuo et al.   GENETICS

Structural Basis for the SOX-Dependent Genomic Redistribution of OCT4 in Stem Cell Differentiation

(2014) Felipe Merino et al.   STRUCTURE

OCT4: Dynamic DNA binding pioneers stem cell pluripotency

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

Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes

(2013) Warren A. Whyte et al.   CELL

Oct4 switches partnering from Sox2 to Sox17 to reinterpret the enhancer code and specify endoderm

(2013) Irene Aksoy et al.   EMBO JOURNAL

Comprehensive prediction in 78 human cell lines reveals rigidity and compactness of transcription factor dimers

(2013) A. Jankowski et al.   GENOME RESEARCH

Identification of cis-regulatory modules in promoters of human genes exploiting mutual positioning of transcription factors

(2013) Soumyadeep Nandi et al.   NUCLEIC ACIDS RESEARCH

Probing Allostery Through DNA

(2013) S. Kim et al.   SCIENCE

SOX2 Co-Occupies Distal Enhancer Elements with Distinct POU Factors in ESCs and NPCs to Specify Cell State

(2013) Michael A. Lodato et al.   PLoS Genetics

Direct Reprogramming of Fibroblasts into Neural Stem Cells by Defined Factors

(2012) Dong Wook Han et al.   Cell Stem Cell

Deciphering the Sox-Oct partner code by quantitative cooperativity measurements

(2012) Calista K. L. Ng et al.   NUCLEIC ACIDS RESEARCH

Cofactor Binding Evokes Latent Differences in DNA Binding Specificity between Hox Proteins

(2011) Matthew Slattery et al.   CELL

Principles of dimer-specific gene regulation revealed by a comprehensive characterization of NF-κB family DNA binding

(2011) Trevor Siggers et al.   NATURE IMMUNOLOGY

Conversion of Sox17 into a Pluripotency Reprogramming Factor by Reengineering Its Association with Oct4 on DNA

(2011) Ralf Jauch et al.   STEM CELLS

Direct conversion of fibroblasts to functional neurons by defined factors

(2010) Thomas Vierbuchen et al.   NATURE

Transposable elements have rewired the core regulatory network of human embryonic stem cells

(2010) Galih Kunarso et al.   NATURE GENETICS

Generation of induced pluripotent stem cells from human cord blood cells with only two factors: Oct4 and Sox2

(2010) Alessandra Giorgetti et al.   Nature Protocols

Structure of Smad1 MH1/DNA complex reveals distinctive rearrangements of BMP and TGF-β effectors

(2010) Nithya BabuRajendran et al.   NUCLEIC ACIDS RESEARCH

Nucleosome-mediated cooperativity between transcription factors

(2010) L. A. Mirny   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Crystal structure of the dimeric Oct6 (POU3f1) POU domain bound to palindromic MORE DNA

(2010) Ralf Jauch et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Integration of External Signaling Pathways with the Core Transcriptional Network in Embryonic Stem Cells

(2008) Xi Chen et al.   CELL

An Extended Transcriptional Network for Pluripotency of Embryonic Stem Cells

(2008) Jonghwan Kim et al.   CELL

Induction of pluripotent stem cells from primary human fibroblasts with only Oct4 and Sox2

(2008) Danwei Huangfu et al.   NATURE BIOTECHNOLOGY