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

Mechanisms governing the pioneering and redistribution capabilities of the non-classical pioneer PU.1

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Phase separation of ligand-activated enhancers licenses cooperative chromosomal enhancer assembly

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

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FET family fusion oncoproteins target the SWI/SNF chromatin remodeling complex

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Pioneer Factor-Nucleosome Binding Events during Differentiation Are Motif Encoded

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Pre-marked chromatin and transcription factor co-binding shape the pioneering activity of Foxa2

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Organization of Chromatin by Intrinsic and Regulated Phase Separation

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HP1 reshapes nucleosome core to promote phase separation of heterochromatin

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

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FUS Phase Separation Is Modulated by a Molecular Chaperone and Methylation of Arginine Cation-π Interactions

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Dynamic EBF1 occupancy directs sequential epigenetic and transcriptional events in B-cell programming

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Transcription Factor PU.1 Represses and Activates Gene Expression in Early T Cells by Redirecting Partner Transcription Factor Binding

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Genetic determinants and epigenetic effects of pioneer-factor occupancy

(2018) Julie Donaghey et al.   NATURE GENETICS

Imaging dynamic and selective low-complexity domain interactions that control gene transcription

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

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Mediator and RNA polymerase II clusters associate in transcription-dependent condensates

(2018) Won-Ki Cho et al.   SCIENCE

BRG1 governs glucocorticoid receptor interactions with chromatin and pioneer factors across the genome

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Pioneering, chromatin remodeling, and epigenetic constraint in early T-cell gene regulation by SPI1 (PU.1)

(2018) Jonas Ungerbäck et al.   GENOME RESEARCH

The interaction landscape between transcription factors and the nucleosome

(2018) Fangjie Zhu et al.   NATURE

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

(2018) Ann Boija et al.   CELL

PU.1 Regulates Ig Light Chain Transcription and Rearrangement in Pre-B Cells during B Cell Development

(2017) Carolina R. Batista et al.   JOURNAL OF IMMUNOLOGY

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

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The pioneer factor OCT4 requires the chromatin remodeller BRG1 to support gene regulatory element function in mouse embryonic stem cells

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Pioneer factors and ATP-dependent chromatin remodeling factors interact dynamically: A new perspective

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Steroid Receptors Reprogram FoxA1 Occupancy through Dynamic Chromatin Transitions

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Cell fate control by pioneer transcription factors

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Pioneering Activity of the C-Terminal Domain of EBF1 Shapes the Chromatin Landscape for B Cell Programming

(2016) Sören Boller et al.   IMMUNITY

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Biochemical Properties and Biological Functions of FET Proteins

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

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

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The chromatin remodeler Brg1 activates enhancer repertoires to establish B cell identity and modulate cell growth

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Liquid-Liquid Phase Separation in Biology

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EBF1 Is Essential for B-Lineage Priming and Establishment of a Transcription Factor Network in Common Lymphoid Progenitors

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Single-molecule analysis of transcription factor binding at transcription sites in live cells

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Protein disorder, prion propensities, and self-organizing macromolecular collectives

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Transcription factor EBF1 is essential for the maintenance of B cell identity and prevention of alternative fates in committed cells

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

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The B-cell identity factor Pax5 regulates distinct transcriptional programmes in early and late B lymphopoiesis

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The SWI/SNF-like BAF Complex Is Essential for Early B Cell Development

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Global changes in the nuclear positioning of genes and intra- and interdomain genomic interactions that orchestrate B cell fate

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Fast gapped-read alignment with Bowtie 2

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Inferring direct DNA binding from ChIP-seq

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Pioneer transcription factors: establishing competence for gene expression

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Multilineage Priming of Enhancer Repertoires Precedes Commitment to the B and Myeloid Cell Lineages in Hematopoietic Progenitors

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Structure of an Ebf1:DNA complex reveals unusual DNA recognition and structural homology with Rel proteins

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Early B Cell Factor 1 Regulates B Cell Gene Networks by Activation, Repression, and Transcription- Independent Poising of Chromatin

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

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A global network of transcription factors, involving E2A, EBF1 and Foxo1, that orchestrates B cell fate

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The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Opposing effects of SWI/SNF and Mi-2/NuRD chromatin remodeling complexes on epigenetic reprogramming by EBF and Pax5

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Regulation of B cell fate commitment and immunoglobulin heavy-chain gene rearrangements by Ikaros

(2008) Damien Reynaud et al.   NATURE IMMUNOLOGY

Transcription factor EBF restricts alternative lineage options and promotes B cell fate commitment independently of Pax5

(2008) Jagan M R Pongubala et al.   NATURE IMMUNOLOGY

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY