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。Early human embryonic development :Blastocyst formation to gastrulation
Janet Rossant et al.
DEVELOPMENTAL CELL (2022)
A balanced Oct4 interactome is crucial for maintaining pluripotency
Dong Han et al.
SCIENCE ADVANCES (2022)
Zygotic genome activation by the totipotency pioneer factor Nr5a2
Johanna Gassler et al.
SCIENCE (2022)
Chromatin sequesters pioneer transcription factor Sox2 from exerting force on DNA
Tuan Nguyen et al.
NATURE COMMUNICATIONS (2022)
The functional diversity of the POUV-class proteins across vertebrates
Evgeny I. Bakhmet et al.
OPEN BIOLOGY (2022)
OCT4 interprets and enhances nucleosome flexibility
Caitlin M. MacCarthy et al.
NUCLEIC ACIDS RESEARCH (2022)
Evolutionary origin of vertebrate OCT4/POU5 functions in supporting pluripotency
Woranop Sukparangsi et al.
NATURE COMMUNICATIONS (2022)
CpG-island-based annotation and analysis of human housekeeping genes
Le Zhang et al.
BRIEFINGS IN BIOINFORMATICS (2021)
B2 SINE Copies Serve as a Transposable Boundary of DNA Methylation and histone Modifications in the Mouse
Tomoko Ichiyanagi et al.
MOLECULAR BIOLOGY AND EVOLUTION (2021)
Mutation saturation for fitness effects at human CpG sites
Ipsita Agarwal et al.
ELIFE (2021)
Directed Evolution of an Enhanced POU Reprogramming Factor for Cell Fate Engineering
Daisylyn Senna Tan et al.
MOLECULAR BIOLOGY AND EVOLUTION (2021)
Modelling human blastocysts by reprogramming fibroblasts into iBlastoids
Xiaodong Liu et al.
NATURE (2021)
BANP opens chromatin and activates CpG-island-regulated genes
Ralph S. Grand et al.
NATURE (2021)
Dissecting OCT4 defines the role of nucleosome binding in pluripotency
Gareth A. Roberts et al.
NATURE CELL BIOLOGY (2021)
High throughput screening identifies SOX2 as a super pioneer factor that inhibits DNA methylation maintenance at its binding sites
Ludovica Vanzan et al.
NATURE COMMUNICATIONS (2021)
Liquid condensation of reprogramming factor KLF4 with DNA provides a mechanism for chromatin organization
Rajesh Sharma et al.
NATURE COMMUNICATIONS (2021)
Cancer-associated missense mutations enhance the pluripotency reprogramming activity of OCT4 and SOX17
Yogesh Srivastava et al.
FEBS JOURNAL (2020)
Toward a Mechanistic Understanding of DNA Methylation Readout by Transcription Factors
Judith F. Kribelbauer et al.
JOURNAL OF MOLECULAR BIOLOGY (2020)
Nucleosomal DNA Dynamics Mediate Oct4 Pioneer Factor Binding
Jan Huertas et al.
BIOPHYSICAL JOURNAL (2020)
Cytosine Methylation Affects the Mutability of Neighboring Nucleotides in Germline and Soma
Vassili Kusmartsev et al.
GENETICS (2020)
Mechanisms of OCT4-SOX2 motif readout on nucleosomes
Alicia K. Michael et al.
SCIENCE (2020)
A genome-scale map of DNA methylation turnover identifies site-specific dependencies of DNMT and TET activity
Paul Adrian Ginno et al.
NATURE COMMUNICATIONS (2020)
Supervised enhancer prediction with epigenetic pattern recognition and targeted validation
Anurag Sethi et al.
NATURE METHODS (2020)
An integrative ENCODE resource for cancer genomics
Jing Zhang et al.
NATURE COMMUNICATIONS (2020)
Reprogramming competence of OCT factors is determined by transactivation domains
Kee-Pyo Kim et al.
SCIENCE ADVANCES (2020)
MAnorm2 for quantitatively comparing groups of ChIP-seq samples
Shiqi Tu et al.
GENOME RESEARCH (2020)
CG dinucleotides enhance promoter activity independent of DNA methylation
Dominik Hartl et al.
GENOME RESEARCH (2019)
DNA Methylation Reprogramming during Mammalian Development
Yang Zeng et al.
GENES (2019)
Fusion of Reprogramming Factors Alters the Trajectory of Somatic Lineage Conversion
Sergiy Velychko et al.
CELL REPORTS (2019)
Zebrafish preserve global germline DNA methylation while sex-linked rDNA is amplified and demethylated during feminisation
Oscar Ortega-Recalde et al.
NATURE COMMUNICATIONS (2019)
Enhancer Features that Drive Formation of Transcriptional Condensates
Krishna Shrinivas et al.
MOLECULAR CELL (2019)
The diverse roles of DNA methylation in mammalian development and disease
Maxim V. C. Greenberg et al.
NATURE REVIEWS MOLECULAR CELL BIOLOGY (2019)
Pluripotency reprogramming by competent and incompetent POU factors uncovers temporal dependency for Oct4 and Sox2
Vikas Malik et al.
NATURE COMMUNICATIONS (2019)
Deterministic Somatic Cell Reprogramming Involves Continuous Transcriptional Changes Governed by Myc and Epigenetic-Driven Modules
Asaf Zviran et al.
CELL STEM CELL (2019)
Identification of Embryonic Neural Plate Border Stem Cells and Their Generation by Direct Reprogramming from Adult Human Blood Cells
Marc Christian Thier et al.
CELL STEM CELL (2019)
Interplay between Conformational Entropy and Solvation Entropy in Protein-Ligand Binding
Maria Luisa Verteramo et al.
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2019)
Transposable elements are regulated by context-specific patterns of chromatin marks in mouse embryonic stem cells
Jiangping He et al.
NATURE COMMUNICATIONS (2019)
Global DNA methylation remodeling during direct reprogramming of fibroblasts to neurons
Chongyuan Luo et al.
ELIFE (2019)
The Human Transcription Factors
Samuel A. Lambert et al.
CELL (2018)
Esrrb Unlocks Silenced Enhancers for Reprogramming to Naive Pluripotency
Kenjiro Adachi et al.
CELL STEM CELL (2018)
Diversity among POU transcription factors in chromatin recognition and cell fate reprogramming
Vikas Malik et al.
CELLULAR AND MOLECULAR LIFE SCIENCES (2018)
Reprogramming of H3K9me3-dependent heterochromatin during mammalian embryo development
Chenfei Wang et al.
NATURE CELL BIOLOGY (2018)
DNA-mediated dimerization on a compact sequence signature controls enhancer engagement and regulation by FOXA1
Xuecong Wang et al.
NUCLEIC ACIDS RESEARCH (2018)
Coactivator condensation at super-enhancers links phase separation and gene control
Benjamin R. Sabari et al.
SCIENCE (2018)
Brn2 Alone Is Sufficient to Convert Astrocytes into Neural Progenitors and Neurons
Xiaoqing Zhu et al.
STEM CELLS AND DEVELOPMENT (2018)
Systematic prediction of DNA shape changes due to CpG methylation explains epigenetic effects on protein-DNA binding
Satyanarayan Rao et al.
EPIGENETICS & CHROMATIN (2018)
DNA methylation reprogramming of functional elements during mammalian embryonic development
Congru Li et al.
CELL DISCOVERY (2018)
Epigenetic reprogramming enables the transition from primordial germ cell to gonocyte
Peter W. S. Hill et al.
NATURE (2018)
Transcription Factors Activate Genes through the Phase-Separation Capacity of Their Activation Domains
Ann Boija et al.
CELL (2018)
Changing POU dimerization preferences converts Oct6 into a pluripotency inducer
Stepan Jerabek et al.
EMBO REPORTS (2017)
Quantitative profiling of selective Sox/POU pairing on hundreds of sequences in parallel by Coop-seq
Yiming K. Chang et al.
NUCLEIC ACIDS RESEARCH (2017)
Genome editing reveals a role for OCT4 in human embryogenesis
Norah M. E. Fogarty et al.
NATURE (2017)
Impact of cytosine methylation on DNA binding specificities of human transcription factors
Yimeng Yin et al.
SCIENCE (2017)
DNA methylation and transcriptional trajectories during human development and reprogramming of isogenic pluripotent stem cells
Matthias S. Roost et al.
NATURE COMMUNICATIONS (2017)
Enforcement of developmental lineage specificity by transcription factor Oct1
Zuolian Shen et al.
ELIFE (2017)
Transient and Permanent Reconfiguration of Chromatin and Transcription Factor Occupancy Drive Reprogramming
Anja S. Knaupp et al.
CELL STEM CELL (2017)
Cooperative Binding of Transcription Factors Orchestrates Reprogramming
Constantinos Chronis et al.
CELL (2017)
Dissecting direct reprogramming from fibroblast to neuron using single-cell RNA-seq
Barbara Treutlein et al.
NATURE (2016)
deepTools2: a next generation web server for deep-sequencing data analysis
Fidel Ramirez et al.
NUCLEIC ACIDS RESEARCH (2016)
XDSAPP2.0
Karine M. Sparta et al.
JOURNAL OF APPLIED CRYSTALLOGRAPHY (2016)
Sambamba: fast processing of NGS alignment formats
Artem Tarasov et al.
BIOINFORMATICS (2015)
Pioneer Transcription Factors Target Partial DNA Motifs on Nucleosomes to Initiate Reprogramming
Abdenour Soufi et al.
CELL (2015)
Deconvolving the Recognition of DNA Shape from Sequence
Namiko Abe et al.
CELL (2015)
Selective influence of Sox2 on POU transcription factor binding in embryonic and neural stem cells
Tapan Kumar Mistri et al.
EMBO REPORTS (2015)
Transcription and imprinting dynamics in developing postnatal male germline stem cells
Saher Sue Hammoud et al.
GENES & DEVELOPMENT (2015)
DNA-dependent formation of transcription factor pairs alters their binding specificity
Arttu Jolma et al.
NATURE (2015)
DNA-mediated cooperativity facilitates the co-selection of cryptic enhancer sequences by SOX2 and PAX6 transcription factors
Kamesh Narasimhan et al.
NUCLEIC ACIDS RESEARCH (2015)
Functional interplay between the RK motif and linker segment dictates Oct4-DNA recognition
Xiangqian Kong et al.
NUCLEIC ACIDS RESEARCH (2015)
The macromolecular crystallography beamlines at BESSY II of the Helmholtz-Zentrum Berlin: Current status and perspectives
Uwe Mueller et al.
EUROPEAN PHYSICAL JOURNAL PLUS (2015)
featureCounts: an efficient general purpose program for assigning sequence reads to genomic features
Yang Liao et al.
BIOINFORMATICS (2014)
Effects of cytosine methylation on transcription factor binding sites
Yulia A. Medvedeva et al.
BMC GENOMICS (2014)
DNA methylation dynamics during epigenetic reprogramming in the germline and preimplantation embryos
Daniel M. Messerschmidt et al.
GENES & DEVELOPMENT (2014)
DNA demethylation, Tet proteins and 5-hydroxymethylcytosine in epigenetic reprogramming: An emerging complex story
PeterW. S. Hill et al.
GENOMICS (2014)
The Early Expansion and Evolutionary Dynamics of POU Class Genes
David A. Gold et al.
MOLECULAR BIOLOGY AND EVOLUTION (2014)
Structural Basis for the SOX-Dependent Genomic Redistribution of OCT4 in Stem Cell Differentiation
Felipe Merino et al.
STRUCTURE (2014)
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
Michael I. Love et al.
GENOME BIOLOGY (2014)
Hierarchical Mechanisms for Direct Reprogramming of Fibroblasts to Neurons
Orly L. Wapinski et al.
CELL (2013)
Oct4 switches partnering from Sox2 to Sox17 to reinterpret the enhancer code and specify endoderm
Irene Aksoy et al.
EMBO JOURNAL (2013)
Nanog, Pou5f1 and SoxB1 activate zygotic gene expression during the maternal-to-zygotic transition
Miler T. Lee et al.
NATURE (2013)
A unique Oct4 interface is crucial for reprogramming to pluripotency
Daniel Esch et al.
NATURE CELL BIOLOGY (2013)
DNA methylation: roles in mammalian development
Zachary D. Smith et al.
NATURE REVIEWS GENETICS (2013)
Pou5f1 Transcription Factor Controls Zygotic Gene Activation In Vertebrates
Manuel Leichsenring et al.
SCIENCE (2013)
SOX2 Co-Occupies Distal Enhancer Elements with Distinct POU Factors in ESCs and NPCs to Specify Cell State
Michael A. Lodato et al.
PLOS GENETICS (2013)
Facilitators and Impediments of the Pluripotency Reprogramming Factors' Initial Engagement with the Genome
Abdenour Soufi et al.
CELL (2012)
Fast gapped-read alignment with Bowtie 2
Ben Langmead et al.
NATURE METHODS (2012)
Deciphering the Sox-Oct partner code by quantitative cooperativity measurements
Calista K. L. Ng et al.
NUCLEIC ACIDS RESEARCH (2012)
De novo DNA methylation: a germ cell perspective
Sebastien A. Smallwood et al.
TRENDS IN GENETICS (2012)
Contribution of Intragenic DNA Methylation in Mouse Gametic DNA Methylomes to Establish Oocyte-Specific Heritable Marks
Hisato Kobayashi et al.
PLOS GENETICS (2012)
Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications
Felix Krueger et al.
BIOINFORMATICS (2011)
GC-Content Normalization for RNA-Seq Data
Davide Risso et al.
BMC BIOINFORMATICS (2011)
CpG islands and the regulation of transcription
Aimee M. Deaton et al.
GENES & DEVELOPMENT (2011)
DNA-binding factors shape the mouse methylome at distal regulatory regions
Michael B. Stadler et al.
NATURE (2011)
Crystal structure of the dimeric Oct6 (Pou3f1) POU domain bound to palindromic MORE DNA
Ralf Jauch et al.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2011)
Conversion of Sox17 into a Pluripotency Reprogramming Factor by Reengineering Its Association with Oct4 on DNA
Ralf Jauch et al.
STEM CELLS (2011)
Features and development of Coot
P. Emsley et al.
ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY (2010)
PHENIX: a comprehensive Python-based system for macromolecular structure solution
Paul D. Adams et al.
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY (2010)
BEDTools: a flexible suite of utilities for comparing genomic features
Aaron R. Quinlan et al.
BIOINFORMATICS (2010)
An Expanded Oct4 Interaction Network: Implications for Stem Cell Biology, Development, and Disease
Mercedes Pardo et al.
CELL STEM CELL (2010)
Detection of nonneutral substitution rates on mammalian phylogenies
Katherine S. Pollard et al.
GENOME RESEARCH (2010)
Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities
Sven Heinz et al.
MOLECULAR CELL (2010)
Direct conversion of fibroblasts to functional neurons by defined factors
Thomas Vierbuchen et al.
NATURE (2010)
Structure of Smad1 MH1/DNA complex reveals distinctive rearrangements of BMP and TGF-β effectors
Nithya BabuRajendran et al.
NUCLEIC ACIDS RESEARCH (2010)
The Sequence Alignment/Map format and SAMtools
Heng Li et al.
BIOINFORMATICS (2009)
The role of DNA shape in protein-DNA recognition
Remo Rohs et al.
NATURE (2009)
Post-Translational Regulation of Oct4 Transcriptional Activity
Jonathan P. Saxe et al.
PLOS ONE (2009)
Global jumping and domain-specific intersegment transfer between DNA cognate sites of the multidomain transcription factor Oct-1
Michaeleen Doucleff et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2008)
Model-based Analysis of ChIP-Seq (MACS)
Yong Zhang et al.
GENOME BIOLOGY (2008)
Generation of induced pluripotent stem cells without Myc from mouse and human fibroblasts
Masato Nakagawa et al.
NATURE BIOTECHNOLOGY (2008)
Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome
Michael Weber et al.
NATURE GENETICS (2007)
Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors
Kazutoshi Takahashi et al.
CELL (2006)
Oct4 is required for primordial germ cell survival
J Kehler et al.
EMBO REPORTS (2004)
UCSF chimera - A visualization system for exploratory research and analysis
EF Pettersen et al.
JOURNAL OF COMPUTATIONAL CHEMISTRY (2004)
Crystal structure of a POU/HMG/DNA ternary complex suggests differential assembly of Oct4 and Sox2 on two enhancers
A Reményi et al.
GENES & DEVELOPMENT (2003)
Differential dimer activities of the transcription factor Oct-1 by DNA-Induced interface swapping
A Reményi et al.
MOLECULAR CELL (2001)
Synergism with the coactivator OBF-1 (OCA-B, BOB-1) is mediated by a specific POU dimer configuration
A Tomilin et al.
CELL (2000)