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

[1]  Martin Eisenacher,et al.  The PRIDE database and related tools and resources in 2019: improving support for quantification data , 2018, Nucleic Acids Res..

[2]  Mark Gerstein,et al.  GENCODE reference annotation for the human and mouse genomes , 2018, Nucleic Acids Res..

[3]  K. Nakayama,et al.  Transcription Factor PU.1 Represses and Activates Gene Expression in Early T Cells by Redirecting Partner Transcription Factor Binding , 2018, Immunity.

[4]  P. Cramer,et al.  The interaction landscape between transcription factors and the nucleosome , 2017, Nature.

[5]  E. Morgunova,et al.  Structural perspective of cooperative transcription factor binding. , 2017, Current opinion in structural biology.

[6]  W. Shi,et al.  Environmental sensing by mature B cells is controlled by the transcription factors PU.1 and SpiB , 2017, Nature Communications.

[7]  K. Rippe,et al.  CHD3 and CHD4 form distinct NuRD complexes with different yet overlapping functionality , 2017, Nucleic acids research.

[8]  Nicholas A. Sinnott-Armstrong,et al.  An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues , 2017, Nature Methods.

[9]  A. Schäffer,et al.  Chromatin-remodeling factor SMARCD2 regulates transcriptional networks controlling differentiation of neutrophil granulocytes , 2017, Nature Genetics.

[10]  P. Park,et al.  The SWI/SNF chromatin remodelling complex is required for maintenance of lineage specific enhancers , 2017, Nature Communications.

[11]  P. Park,et al.  ARID1A loss impairs enhancer-mediated gene regulation and drives colon cancer in mice , 2016, Nature Genetics.

[12]  Shawn M. Gillespie,et al.  SMARCB1-mediated SWI/SNF complex function is essential for enhancer regulation , 2016, Nature Genetics.

[13]  Gwendolyn M. Jang,et al.  Meta- and Orthogonal Integration of Influenza "OMICs" Data Defines a Role for UBR4 in Virus Budding. , 2015, Cell host & microbe.

[14]  M. Pellegrini,et al.  Pioneer Transcription Factors Target Partial DNA Motifs on Nucleosomes to Initiate Reprogramming , 2015, Cell.

[15]  Aaron N. Chang,et al.  Brg1 activates enhancer repertoires to establish B cell identity and modulate cell growth , 2015, Nature Immunology.

[16]  C. Glass,et al.  The selection and function of cell type-specific enhancers , 2015, Nature Reviews Molecular Cell Biology.

[17]  Makiko Iwafuchi‐Doi,et al.  Pioneer transcription factors in cell reprogramming , 2014, Genes & development.

[18]  W. Huber,et al.  Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 , 2014, Genome Biology.

[19]  Piero Carninci,et al.  Redefinition of the human mast cell transcriptome by deep-CAGE sequencing. , 2014, Blood.

[20]  P. Matthias,et al.  The Interplay between Chromatin and Transcription Factor Networks during B Cell Development: Who Pulls the Trigger First? , 2014, Front. Immunol..

[21]  T. Meehan,et al.  An atlas of active enhancers across human cell types and tissues , 2014, Nature.

[22]  Cesare Furlanello,et al.  A promoter-level mammalian expression atlas , 2015 .

[23]  B. Burke,et al.  BioID: A Screen for Protein‐Protein Interactions , 2013, Current protocols in protein science.

[24]  C. Benner,et al.  Mechanisms of in vivo binding site selection of the hematopoietic master transcription factor PU.1 , 2013, Nucleic acids research.

[25]  M. Rehli,et al.  5-Hydroxymethylcytosine is an essential intermediate of active DNA demethylation processes in primary human monocytes , 2013, Genome Biology.

[26]  Thomas R. Gingeras,et al.  STAR: ultrafast universal RNA-seq aligner , 2013, Bioinform..

[27]  M. Rehli,et al.  5-Hydroxymethylcytosine is an essential intermediate of active DNA demethylation processes in primary human monocytes , 2013, Genome Biology.

[28]  Greg Donahue,et al.  Facilitators and Impediments of the Pluripotency Reprogramming Factors' Initial Engagement with the Genome , 2012, Cell.

[29]  Data production leads,et al.  An integrated encyclopedia of DNA elements in the human genome , 2012 .

[30]  ENCODEConsortium,et al.  An Integrated Encyclopedia of DNA Elements in the Human Genome , 2012, Nature.

[31]  Michael Rehli,et al.  Dynamic epigenetic enhancer signatures reveal key transcription factors associated with monocytic differentiation states. , 2012, Blood.

[32]  Steven L Salzberg,et al.  Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.

[33]  David G. Knowles,et al.  Fast Computation and Applications of Genome Mappability , 2012, PloS one.

[34]  Tatiana Popova,et al.  Supplementary Methods , 2012, Acta Neuropsychiatrica.

[35]  Ty C. Voss,et al.  Dynamic Exchange at Regulatory Elements during Chromatin Remodeling Underlies Assisted Loading Mechanism , 2011, Cell.

[36]  Helga Thorvaldsdóttir,et al.  Integrative Genomics Viewer , 2011, Nature Biotechnology.

[37]  G. Stein,et al.  The human SWI/SNF complex associates with RUNX1 to control transcription of hematopoietic target genes , 2010, Journal of cellular physiology.

[38]  Galt P. Barber,et al.  BigWig and BigBed: enabling browsing of large distributed datasets , 2010, Bioinform..

[39]  C. Glass,et al.  Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. , 2010, Molecular cell.

[40]  J. Ragoussis,et al.  Identification and characterization of enhancers controlling the inflammatory gene expression program in macrophages. , 2010, Immunity.

[41]  Aaron R. Quinlan,et al.  Bioinformatics Applications Note Genome Analysis Bedtools: a Flexible Suite of Utilities for Comparing Genomic Features , 2022 .

[42]  Mark D. Robinson,et al.  edgeR: a Bioconductor package for differential expression analysis of digital gene expression data , 2009, Bioinform..

[43]  T. Graf,et al.  PU.1 and C/EBPα/β convert fibroblasts into macrophage-like cells , 2008, Proceedings of the National Academy of Sciences.

[44]  A. Friedman.  Transcriptional control of granulocyte and monocyte development , 2007, Oncogene.

[45]  L. Schwarzfischer,et al.  CCAAT Enhancer-binding Protein Regulates Constitutive Gene Expression during Late Stages of Monocyte to Macrophage Differentiation* , 2007 .

[46]  Merlin Crossley,et al.  Molecular Analysis of the Interaction between the Hematopoietic Master Transcription Factors GATA-1 and PU.1* , 2006, Journal of Biological Chemistry.

[47]  P. Shannon,et al.  Cytoscape: a software environment for integrated models of biomolecular interaction networks. , 2003, Genome research.

[48]  M. Mann,et al.  Stop and go extraction tips for matrix-assisted laser desorption/ionization, nanoelectrospray, and LC/MS sample pretreatment in proteomics. , 2003, Analytical chemistry.

[49]  E. Querfurth,et al.  GATA-1 interacts with the myeloid PU.1 transcription factor and represses PU.1-dependent transcription. , 2000, Blood.

[50]  Achim Leutz,et al.  A C/EBPβ Isoform Recruits the SWI/SNF Complex to Activate Myeloid Genes , 1999 .

[51]  B. Cairns,et al.  Activation domain-mediated targeting of the SWI/SNF complex to promoters stimulates transcription from nucleosome arrays. , 1999, Molecular cell.

[52]  D. Tenen,et al.  Negative cross-talk between hematopoietic regulators: GATA proteins repress PU.1. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[53]  A. Leutz,et al.  A C/EBP beta isoform recruits the SWI/SNF complex to activate myeloid genes. , 1999, Molecular cell.

[54]  B. Emerson,et al.  A SWI/SNF–Related Chromatin Remodeling Complex, E-RC1, Is Required for Tissue-Specific Transcriptional Regulation by EKLF In Vitro , 1998, Cell.

[55]  D. Tenen,et al.  Multiple Functional Domains of AML1: PU.1 and C/EBPα Synergize with Different Regions of AML1 , 1998, Molecular and Cellular Biology.

[56]  Michael C. Ostrowski,et al.  Interaction between PU.1 and Another Ets Family Transcription Factor Promotes Macrophage-specific Basal Transcription Initiation* , 1998, The Journal of Biological Chemistry.

[57]  M. Klemsz,et al.  Activation of transcription by PU.1 requires both acidic and glutamine domains , 1996, Molecular and cellular biology.

[58]  U. Storb,et al.  Pip, a novel IRF family member, is a lymphoid-specific, PU.1-dependent transcriptional activator. , 1995, Genes & development.

[59]  Andrew J. Bannister,et al.  The activation domain of transcription factor PU.1 binds the retinoblastoma (RB) protein and the transcription factor TFIID in vitro: RB shows sequence similarity to TFIID and TFIIB. , 1993, Proceedings of the National Academy of Sciences of the United States of America.