lncRNA DIGIT and BRD3 protein form phase-separated condensates to regulate endoderm differentiation

Comprehensive identification of RNA–protein interactions in any organism using orthogonal organic phase separation (OOPS)

(2019) Rayner M. L. Queiroz et al.   NATURE BIOTECHNOLOGY

A Secreted RNA Binding Protein Forms RNA-Stabilizing Granules in the Honeybee Royal Jelly

(2019) Eyal Maori et al.   MOLECULAR CELL

H3K18ac Primes Mesendodermal Differentiation upon Nodal Signaling

(2019) Maoguo Luo et al.   Stem Cell Reports

Functional Classification and Experimental Dissection of Long Noncoding RNAs

(2018) Florian Kopp et al.   CELL

The BRD3 ET domain recognizes a short peptide motif through a mechanism that is conserved across chromatin remodelers and transcriptional regulators

(2018) Dorothy C. C. Wai et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Functional Domains of NEAT1 Architectural lncRNA Induce Paraspeckle Assembly through Phase Separation

(2018) Tomohiro Yamazaki et al.   MOLECULAR CELL

Targeted in situ genome-wide profiling with high efficiency for low cell numbers

(2018) Peter J Skene et al.   Nature Protocols

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

(2018) Benjamin R. Sabari et al.   SCIENCE

The lncRNA GATA6-AS epigenetically regulates endothelial gene expression via interaction with LOXL2

(2018) Philipp Neumann et al.   Nature Communications

Phase-separation mechanism for C-terminal hyperphosphorylation of RNA polymerase II

(2018) Huasong Lu et al.   NATURE

RNAs interact with BRD4 to promote enhanced chromatin engagement and transcription activation

(2018) Homa Rahnamoun et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Enhancer Activity Requires CBP/P300 Bromodomain-Dependent Histone H3K27 Acetylation

(2018) Ryan Raisner et al.   Cell Reports

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

(2018) Ann Boija et al.   CELL

Discovery of a selective catalytic p300/CBP inhibitor that targets lineage-specific tumours

(2017) Loren M. Lasko et al.   NATURE

Biomolecular condensates: organizers of cellular biochemistry

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

An efficient targeted nuclease strategy for high-resolution mapping of DNA binding sites

(2017) Peter J Skene et al.   eLife

Divergent lncRNAs Regulate Gene Expression and Lineage Differentiation in Pluripotent Cells

(2016) Sai Luo et al.   Cell Stem Cell

The functions of long noncoding RNAs in development and stem cells

(2016) Rotem Ben-Tov Perry et al.   DEVELOPMENT

Self-organization of human embryonic stem cells on micropatterns

(2016) Alessia Deglincerti et al.   Nature Protocols

deepTools2: a next generation web server for deep-sequencing data analysis

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

DIGIT Is a Conserved Long Noncoding RNA that Regulates GSC Expression to Control Definitive Endoderm Differentiation of Embryonic Stem Cells

(2016) Kaveh Daneshvar et al.   Cell Reports

BET Bromodomain Proteins Brd2, Brd3 and Brd4 Selectively Regulate Metabolic Pathways in the Pancreatic β-Cell

(2016) Jude T. Deeney et al.   PLoS One

Optimized Sleeping Beauty transposons rapidly generate stable transgenic cell lines

(2015) Eric Kowarz et al.   Biotechnology Journal

Phase Separation by Low Complexity Domains Promotes Stress Granule Assembly and Drives Pathological Fibrillization

(2015) Amandine Molliex et al.   CELL

Formation and Maturation of Phase-Separated Liquid Droplets by RNA-Binding Proteins

(2015) Yuan Lin et al.   MOLECULAR CELL

Chromatin architecture reorganization during stem cell differentiation

(2015) Jesse R. Dixon et al.   NATURE

Differential Association of Chromatin Proteins Identifies BAF60a/SMARCD1 as a Regulator of Embryonic Stem Cell Differentiation

(2015) Adi Alajem et al.   Cell Reports

The lncRNA DEANR1 Facilitates Human Endoderm Differentiation by Activating FOXA2 Expression

(2015) Wei Jiang et al.   Cell Reports

Optimized Sleeping Beauty transposons rapidly generate stable transgenic cell lines

(2015) Eric Kowarz et al.   Biotechnology Journal

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

Long Noncoding RNAs in Cell-Fate Programming and Reprogramming

(2014) Ryan A. Flynn et al.   Cell Stem Cell

Efficient Endoderm Induction from Human Pluripotent Stem Cells by Logically Directing Signals Controlling Lineage Bifurcations

(2014) Kyle M. Loh et al.   Cell Stem Cell

The Long Noncoding RNAs NEAT1 and MALAT1 Bind Active Chromatin Sites

(2014) Jason A. West et al.   MOLECULAR CELL

A method to recapitulate early embryonic spatial patterning in human embryonic stem cells

(2014) Aryeh Warmflash et al.   NATURE METHODS

Control of Embryonic Stem Cell Identity by BRD4-Dependent Transcriptional Elongation of Super-Enhancer-Associated Pluripotency Genes

(2014) Raffaella Di Micco et al.   Cell Reports

The CRAPome: a contaminant repository for affinity purification–mass spectrometry data

(2013) Dattatreya Mellacheruvu et al.   NATURE METHODS

An optimized streptavidin-binding RNA aptamer for purification of ribonucleoprotein complexes identifies novel ARE-binding proteins

(2013) Kathrin Leppek et al.   NUCLEIC ACIDS RESEARCH

An Efficient Low Cost Method for Gene Transfer to T Lymphocytes

(2013) Leonardo Chicaybam et al.   PLoS One

Cell-free Formation of RNA Granules: Low Complexity Sequence Domains Form Dynamic Fibers within Hydrogels

(2012) Masato Kato et al.   CELL

Histone Recognition and Large-Scale Structural Analysis of the Human Bromodomain Family

(2012) Panagis Filippakopoulos et al.   CELL

Bleach gel: A simple agarose gel for analyzing RNA quality

(2012) Patrick S. Aranda et al.   ELECTROPHORESIS

Phase transitions in the assembly of multivalent signalling proteins

(2012) Pilong Li et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

A Poised Chromatin Platform for TGF-β Access to Master Regulators

(2011) Qiaoran Xi et al.   CELL

Compaction of chromatin by diverse Polycomb group proteins requires localized regions of high charge

(2011) D. J. Grau et al.   GENES & DEVELOPMENT

BigWig and BigBed: enabling browsing of large distributed datasets

(2010) W. J. Kent et al.   BIOINFORMATICS

Distinct roles of GCN5/PCAF-mediated H3K9ac and CBP/p300-mediated H3K18/27ac in nuclear receptor transactivation

(2010) Qihuang Jin et al.   EMBO JOURNAL

A unique chromatin signature uncovers early developmental enhancers in humans

(2010) Alvaro Rada-Iglesias et al.   NATURE

Histone H3K27ac separates active from poised enhancers and predicts developmental state

(2010) M. P. Creyghton et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Double bromodomain-containing gene Brd2 is essential for embryonic development in mouse

(2009) Enyuan Shang et al.   DEVELOPMENTAL DYNAMICS

Early Cell Fate Decisions of Human Embryonic Stem Cells and Mouse Epiblast Stem Cells Are Controlled by the Same Signalling Pathways

(2009) Ludovic Vallier et al.   PLoS One

BAF60a Interacts with p53 to Recruit the SWI/SNF Complex

(2008) Jaehak Oh et al.   JOURNAL OF BIOLOGICAL CHEMISTRY