Concurrent binding to DNA and RNA facilitates the pluripotency reprogramming activity of Sox2

Interaction of Sox2 with RNA binding proteins in mouse embryonic stem cells

(2019) Samudyata et al.   EXPERIMENTAL CELL RESEARCH

Pluripotency reprogramming by competent and incompetent POU factors uncovers temporal dependency for Oct4 and Sox2

(2019) Vikas Malik et al.   Nature Communications

A role for SOX9 in post-transcriptional processes: insights from the amphibian oocyte

(2018) M. Penrad-Mobayed et al.   Scientific Reports

SFPQ associates to LSD1 and regulates the migration of newborn pyramidal neurons in the developing cerebral cortex

(2017) K. Saud et al.   INTERNATIONAL JOURNAL OF DEVELOPMENTAL NEUROSCIENCE

Catalytic-Independent Functions of PARP-1 Determine Sox2 Pioneer Activity at Intractable Genomic Loci

(2017) Ziying Liu et al.   MOLECULAR CELL

Molecular basis for the genome engagement by Sox proteins

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

Synergetic effects of DNA methylation and histone modification during mouse induced pluripotent stem cell generation

(2017) Guiying Wang et al.   Scientific Reports

Depletion ofTcf3andLef1maintains mouse embryonic stem cell self-renewal

(2017) Shoudong Ye et al.   Biology Open

Dicer, a new regulator of pluripotency exit and LINE-1 elements in mouse embryonic stem cells

(2017) Maxime Bodak et al.   FEBS Open Bio

Transcriptome-wide identification of the RNA-binding landscape of the chromatin-associated protein PARP1 reveals functions in RNA biogenesis

(2017) Manana Melikishvili et al.   Cell Discovery

Changing POU dimerization preferences converts Oct6 into a pluripotency inducer

(2016) Stepan Jerabek et al.   EMBO REPORTS

Protein Arginine Methyltransferase Product Specificity Is Mediated by Distinct Active-site Architectures

(2016) Kanishk Jain 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

Structure of the RBM7–ZCCHC8 core of the NEXT complex reveals connections to splicing factors

(2016) Sebastian Falk et al.   Nature Communications

Involvement of PARP1 in the regulation of alternative splicing

(2016) Elena Matveeva et al.   Cell Discovery

ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization

(2015) Guangchuang Yu et al.   BIOINFORMATICS

Meta- and Orthogonal Integration of Influenza “OMICs” Data Defines a Role for UBR4 in Virus Budding

(2015) Shashank Tripathi et al.   Cell Host & Microbe

Myc and SAGA rewire an alternative splicing network during early somatic cell reprogramming

(2015) Calley L. Hirsch et al.   GENES & DEVELOPMENT

Transcription factor trapping by RNA in gene regulatory elements

(2015) A. A. Sigova et al.   SCIENCE

Srebp-1 Interacts with c-Myc to Enhance Somatic Cell Reprogramming

(2015) Yi Wu et al.   STEM CELLS

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

Alternative Splicing of MBD2 Supports Self-Renewal in Human Pluripotent Stem Cells

(2014) Yu Lu et al.   Cell Stem Cell

The structure, function and evolution of proteins that bind DNA and RNA

(2014) William H. Hudson et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

rMATS: Robust and flexible detection of differential alternative splicing from replicate RNA-Seq data

(2014) Shihao Shen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Dynamic Integration of Splicing within Gene Regulatory Pathways

(2013) Ulrich Braunschweig et al.   CELL

The Sox Family of Transcription Factors: Versatile Regulators of Stem and Progenitor Cell Fate

(2013) Abby Sarkar et al.   Cell Stem Cell

Sox proteins: regulators of cell fate specification and differentiation

(2013) Y. Kamachi et al.   DEVELOPMENT

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

(2013) Alessia Gagliardi et al.   EMBO JOURNAL

Pick one, but be quick: 5' splice sites and the problems of too many choices

(2013) X. Roca et al.   GENES & DEVELOPMENT

The Long Noncoding RNA RMST Interacts with SOX2 to Regulate Neurogenesis

(2013) Shi-Yan Ng et al.   MOLECULAR CELL

Proteomic and genomic approaches reveal critical functions of H3K9 methylation and heterochromatin protein-1γ in reprogramming to pluripotency

(2013) Rupa Sridharan et al.   NATURE CELL BIOLOGY

The RNA-binding protein repertoire of embryonic stem cells

(2013) S Chul Kwon et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Sox Transcription Factors Require Selective Interactions with Oct4 and Specific Transactivation Functions to Mediate Reprogramming

(2013) Irene Aksoy et al.   STEM CELLS

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

Insights into RNA Biology from an Atlas of Mammalian mRNA-Binding Proteins

(2012) Alfredo Castello et al.   CELL

Chromatin-modifying enzymes as modulators of reprogramming

(2012) Tamer T. Onder et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Identifying ChIP-seq enrichment using MACS

(2012) Jianxing Feng et al.   Nature Protocols

Deciphering the Sox-Oct partner code by quantitative cooperativity measurements

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

Reprogramming to pluripotency is an ancient trait of vertebrate Oct4 and Pou2 proteins

(2012) Natalia Tapia et al.   Nature Communications

Differential GC Content between Exons and Introns Establishes Distinct Strategies of Splice-Site Recognition

(2012) Maayan Amit et al.   Cell Reports

DREME: motif discovery in transcription factor ChIP-seq data

(2011) Timothy L. Bailey   BIOINFORMATICS

An Alternative Splicing Switch Regulates Embryonic Stem Cell Pluripotency and Reprogramming

(2011) Mathieu Gabut et al.   CELL

Human long non-coding RNAs promote pluripotency and neuronal differentiation by association with chromatin modifiers and transcription factors

(2011) Shi-Yan Ng et al.   EMBO JOURNAL

De novo DNA methylation by Dnmt3a and Dnmt3b is dispensable for nuclear reprogramming of somatic cells to a pluripotent state

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

Sequentially acting Sox transcription factors in neural lineage development

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

Predicting protein associations with long noncoding RNAs

(2011) Matteo Bellucci et al.   NATURE METHODS

A DNMT3B Alternatively Spliced Exon and Encoded Peptide Are Novel Biomarkers of Human Pluripotent Stem Cells

(2011) Sailesh Gopalakrishna-Pillai et al.   PLoS One

Landscape of the SOX2 protein-protein interactome

(2011) Xuefeng Fang et al.   PROTEOMICS

PARalyzer: definition of RNA binding sites from PAR-CLIP short-read sequence data

(2011) David L Corcoran et al.   GENOME BIOLOGY

Transcriptome-wide Identification of RNA-Binding Protein and MicroRNA Target Sites by PAR-CLIP

(2010) Markus Hafner et al.   CELL

Vitamin C Enhances the Generation of Mouse and Human Induced Pluripotent Stem Cells

(2010) Miguel Angel Esteban et al.   Cell Stem Cell

Double-stranded DNA Binding Domain of Poly(ADP-ribose) Polymerase-1 and Molecular Insight into the Regulation of Its Activity

(2010) Orlando Huambachano et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Phosphorylation-Dependent Regulation of PSF by GSK3 Controls CD45 Alternative Splicing

(2010) Florian Heyd et al.   MOLECULAR CELL

Sox2 Uses Multiple Domains to Associate with Proteins Present in Sox2-Protein Complexes

(2010) Jesse L. Cox et al.   PLoS One

Dynamic transcriptomes during neural differentiation of human embryonic stem cells revealed by short, long, and paired-end sequencing

(2010) J. Q. Wu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Noncoding RNA Gas5 Is a Growth Arrest- and Starvation-Associated Repressor of the Glucocorticoid Receptor

(2010) T. Kino et al.   Science Signaling

Proteomic Analysis of Sox2-Associated Proteins During Early Stages of Mouse Embryonic Stem Cell Differentiation Identifies Sox21 as a Novel Regulator of Stem Cell Fate

(2010) Sunil K. Mallanna et al.   STEM CELLS

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

C-terminal binding proteins (CtBPs) attenuate KLF4-mediated transcriptional activation

(2009) Gang Liu et al.   FEBS LETTERS

The zinc fingers of the SR-like protein ZRANB2 are single-stranded RNA-binding domains that recognize 5' splice site-like sequences

(2009) F. E. Loughlin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Lymphoid Enhancer Factor 1-Mediated Wnt Signaling Promotes the Initiation of Trophoblast Lineage Differentiation in Mouse Embryonic Stem Cells

(2008) Shuyang He et al.   STEM CELLS