NANOG prion-like assembly mediates DNA bridging to facilitate chromatin reorganization and activation of pluripotency

Genome folding through loop extrusion by SMC complexes

(2021) Iain F. Davidson et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Enhancer RNA m6A methylation facilitates transcriptional condensate formation and gene activation

(2021) Joo-Hyung Lee et al.   MOLECULAR CELL

Liquid condensation of reprogramming factor KLF4 with DNA provides a mechanism for chromatin organization

(2021) Rajesh Sharma et al.   Nature Communications

CTCF is dispensable for immune cell transdifferentiation but facilitates an acute inflammatory response

(2020) Grégoire Stik et al.   NATURE GENETICS

A Prion-like Domain in Transcription Factor EBF1 Promotes Phase Separation and Enables B Cell Programming of Progenitor Chromatin

(2020) Yuanting Wang et al.   IMMUNITY

Pou5f3, SoxB1, and Nanog remodel chromatin on high nucleosome affinity regions at zygotic genome activation

(2019) Marina Veil et al.   GENOME RESEARCH

Considerations and Challenges in Studying Liquid-Liquid Phase Separation and Biomolecular Condensates

(2019) Simon Alberti et al.   CELL

Two major mechanisms of chromosome organization

(2019) Leonid A Mirny et al.   CURRENT OPINION IN CELL BIOLOGY

Organization of Chromatin by Intrinsic and Regulated Phase Separation

(2019) Bryan A. Gibson et al.   CELL

A chromosome folding intermediate at the condensin-to-cohesin transition during telophase

(2019) Kristin Abramo et al.   NATURE CELL BIOLOGY

Methods for mapping 3D chromosome architecture

(2019) Rieke Kempfer et al.   NATURE REVIEWS GENETICS

A Molecular Grammar Governing the Driving Forces for Phase Separation of Prion-like RNA Binding Proteins

(2018) Jie Wang et al.   CELL

Chicken NANOG self-associates via a novel folding-upon-binding mechanism

(2018) Hee Jung Choi et al.   FASEB JOURNAL

Coactivator condensation at super-enhancers links phase separation and gene control

(2018) Benjamin R. Sabari et al.   SCIENCE

Transcription Factors Activate Genes through the Phase-Separation Capacity of Their Activation Domains

(2018) Ann Boija et al.   CELL

HiCRep: assessing the reproducibility of Hi-C data using a stratum-adjusted correlation coefficient

(2017) Tao Yang et al.   GENOME RESEARCH

Phase separation drives heterochromatin domain formation

(2017) Amy R. Strom et al.   NATURE

Liquid droplet formation by HP1α suggests a role for phase separation in heterochromatin

(2017) Adam G. Larson et al.   NATURE

Biomolecular condensates: organizers of cellular biochemistry

(2017) Salman F. Banani et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

The Structure and Dynamics of Higher-Order Assemblies: Amyloids, Signalosomes, and Granules

(2016) Hao Wu et al.   CELL

The pluripotency factor Nanog regulates pericentromeric heterochromatin organization in mouse embryonic stem cells

(2016) Clara Lopes Novo et al.   GENES & DEVELOPMENT

NANOG alone induces germ cells in primed epiblast in vitro by activation of enhancers

(2016) Kazuhiro Murakami et al.   NATURE

Chromatin architecture reorganization during stem cell differentiation

(2015) Jesse R. Dixon et al.   NATURE

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

NMRFAM-SPARKY: enhanced software for biomolecular NMR spectroscopy

(2014) Woonghee Lee et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Resetting Transcription Factor Control Circuitry toward Ground-State Pluripotency in Human

(2014) Yasuhiro Takashima et al.   CELL

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping

(2014) Suhas S.P. Rao et al.   CELL

deepTools: a flexible platform for exploring deep-sequencing data

(2014) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Genome-wide Chromatin Interactions of the Nanog Locus in Pluripotency, Differentiation, and Reprogramming

(2013) Effie Apostolou et al.   Cell Stem Cell

Modulation of allostery by protein intrinsic disorder

(2013) Allan Chris M. Ferreon et al.   NATURE

The pluripotent genome in three dimensions is shaped around pluripotency factors

(2013) Elzo de Wit et al.   NATURE

Relaxation of backbone bond geometry improves protein energy landscape modeling

(2013) Patrick Conway et al.   PROTEIN SCIENCE

Blessings in disguise: biological benefits of prion-like mechanisms

(2013) Gregory A. Newby et al.   TRENDS IN CELL BIOLOGY

Control of ground-state pluripotency by allelic regulation of Nanog

(2012) Yusuke Miyanari et al.   NATURE

Iterative correction of Hi-C data reveals hallmarks of chromosome organization

(2012) Maxim Imakaev et al.   NATURE METHODS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Concise Review: Pluripotency and the Transcriptional Inactivation of the Female Mammalian X Chromosome

(2011) Alissa Minkovsky et al.   STEM CELLS

Features and development ofCoot

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

Axolotl Nanog activity in mouse embryonic stem cells demonstrates that ground state pluripotency is conserved from urodele amphibians to mammals

(2010) J. E. Dixon et al.   DEVELOPMENT

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Nanog Is the Gateway to the Pluripotent Ground State

(2009) Jose Silva et al.   CELL

Purification of human transcription factors Nanog and Sox2, each in complex with Skp, an Escherichia coli periplasmic chaperone

(2009) Sung Chul Ha et al.   PROTEIN EXPRESSION AND PURIFICATION

Molecular Characterization of the Human NANOG Protein

(2009) David F. Chang et al.   STEM CELLS

KLF4 and PBX1 Directly RegulateNANOGExpression in Human Embryonic Stem Cells

(2009) Ken Kwok-Keung Chan et al.   STEM CELLS

The pluripotency rheostat Nanog functions as a dimer

(2008) Nicholas P. Mullin et al.   BIOCHEMICAL JOURNAL

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

(2008) Xi Chen et al.   CELL

Requirement of Nanog dimerization for stem cell self-renewal and pluripotency

(2008) J. Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Burst analysis spectroscopy: A versatile single-particle approach for studying distributions of protein aggregates and fluorescent assemblies

(2008) J. Puchalla et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY

Precise Measurement of Diffusion Coefficients using Scanning Fluorescence Correlation Spectroscopy

(2007) Zdeněk Petrášek et al.   BIOPHYSICAL JOURNAL