In vivo screening characterizes chromatin factor functions during normal and malignant hematopoiesis

[1]  S. Jarmalaitė,et al.  The Emerging Role of Chromatin Remodeling Complexes in Ovarian Cancer , 2022, International journal of molecular sciences.

[2]  G. Greene,et al.  Targeting MYC with modular synthetic transcriptional repressors derived from bHLH DNA-binding domains , 2022, Nature Biotechnology.

[3]  Liliang Jin,et al.  Regulation of emergency granulopoiesis during infection , 2022, Frontiers in Immunology.

[4]  Mihai I Truica,et al.  A MYC inhibitor selectively alters the MYC and MAX cistromes and modulates the epigenomic landscape to regulate target gene expression , 2022, Science advances.

[5]  Ana Bošković,et al.  Transcriptional and epigenetic control of early life cell fate decisions , 2022, Current opinion in oncology.

[6]  R. Jaenisch,et al.  OCT4 cooperates with distinct ATP-dependent chromatin remodelers in naïve and primed pluripotent states in human , 2021, Nature Communications.

[7]  Michele K. Anderson,et al.  DL4-μbeads induce T cell lineage differentiation from stem cells in a stromal cell-free system , 2021, Nature Communications.

[8]  Cameron S. Osborne,et al.  Mutational synergy during leukemia induction remodels chromatin accessibility, modification and 3-Dimensional DNA topology to alter gene expression , 2021, Nature Genetics.

[9]  J. D. Engel,et al.  An erythroid to myeloid cell fate conversion is elicited by LSD1 inactivation. , 2021, Blood.

[10]  D. Hafler,et al.  NEBULA is a fast negative binomial mixed model for differential or co-expression analysis of large-scale multi-subject single-cell data , 2021, Communications Biology.

[11]  Santiago J. Carmona,et al.  Interpretation of T cell states from single-cell transcriptomics data using reference atlases , 2021, Nature Communications.

[12]  Feng Liu,et al.  Transcriptional and epigenetic control of hematopoietic stem cell fate decisions in vertebrates. , 2021, Developmental biology.

[13]  André F. Rendeiro,et al.  Acute BAF perturbation causes immediate changes in chromatin accessibility , 2021, Nature Genetics.

[14]  J. Doench,et al.  In vivo screens using a selective CRISPR antigen removal lentiviral vector system reveal immune dependencies in renal cell carcinoma. , 2021, Immunity.

[15]  Jieping Chen,et al.  Targeting BRD9 by I-BRD9 efficiently inhibits growth of acute myeloid leukemia cells , 2021, Translational cancer research.

[16]  Thomas M. Keane,et al.  Twelve years of SAMtools and BCFtools , 2020, GigaScience.

[17]  P. Becker,et al.  Variation on a theme: Evolutionary strategies for H2A.Z exchange by SWR1-type remodelers. , 2020, Current opinion in cell biology.

[18]  P. Fenaux,et al.  Preliminary Data on a Phase 1/2A First in Human Study of the Menin-KMT2A (MLL) Inhibitor KO-539 in Patients with Relapsed or Refractory Acute Myeloid Leukemia , 2020 .

[19]  Raphael Gottardo,et al.  Integrated analysis of multimodal single-cell data , 2020, Cell.

[20]  S. Barry,et al.  Development of an ObLiGaRe Doxycycline Inducible Cas9 system for pre-clinical cancer drug discovery , 2020, Nature Communications.

[21]  L. M. Soares,et al.  Mammalian SWI/SNF Chromatin Remodeling Complexes: Emerging Mechanisms and Therapeutic Strategies. , 2020, Trends in genetics : TIG.

[22]  Weidong Wang,et al.  Interplay of BAF and MLL4 promotes cell type-specific enhancer activation , 2020, Nature Communications.

[23]  Tingting Fu,et al.  Histone methyltransferase MLL4 controls myofiber identity and muscle performance through MEF2 interaction. , 2020, The Journal of clinical investigation.

[24]  S. Orkin,et al.  An Engineered CRISPR-Cas9 Mouse Line for Simultaneous Readout of Lineage Histories and Gene Expression Profiles in Single Cells , 2020, Cell.

[25]  A. Shilatifard,et al.  Uncoupling histone H3K4 trimethylation from developmental gene expression via an equilibrium of COMPASS, Polycomb and DNA methylation , 2020, Nature Genetics.

[26]  Thomas M. Norman,et al.  Combinatorial single-cell CRISPR screens by direct guide RNA capture and targeted sequencing , 2020, Nature Biotechnology.

[27]  Rafael C. Schulman,et al.  DNA methylation disruption reshapes the hematopoietic differentiation landscape , 2020, Nature Genetics.

[28]  Cameron S. Osborne,et al.  Cohesin-dependent regulation of gene expression during differentiation is lost in Cohesin-mutated myeloid malignancies. , 2019, Blood.

[29]  M. Looso,et al.  Beyond accessibility: ATAC-seq footprinting unravels kinetics of transcription factor binding during zygotic genome activation , 2019, bioRxiv.

[30]  Gennady Korotkevich,et al.  Fast gene set enrichment analysis , 2019, bioRxiv.

[31]  William J. R. Longabaugh,et al.  Absolute quantification of transcription factors reveals principles of gene regulation in erythropoiesis , 2019, bioRxiv.

[32]  Alexander V Penson,et al.  Spliceosomal disruption of the non-canonical BAF complex in cancer , 2019, Nature.

[33]  Cigall Kadoch.  Diverse compositions and functions of chromatin remodeling machines in cancer , 2019, Science Translational Medicine.

[34]  Andrew J. Bannister,et al.  The roles of DNA, RNA and histone methylation in ageing and cancer , 2019, Nature Reviews Molecular Cell Biology.

[35]  Anshul Kundaje,et al.  The ENCODE Blacklist: Identification of Problematic Regions of the Genome , 2019, Scientific Reports.

[36]  Aaron M. Newman,et al.  Single-cell transcriptional diversity is a hallmark of developmental potential , 2019, Science.

[37]  Adam C. Wilkinson,et al.  Long-term ex vivo hematopoietic stem cell expansion affords nonconditioned transplantation , 2019, Nature.

[38]  T. Milne,et al.  Why are so many MLL lysine methyltransferases required for normal mammalian development? , 2019, Cellular and Molecular Life Sciences.

[39]  Guillaume J. Filion,et al.  Transcription factors and 3D genome conformation in cell-fate decisions , 2019, Nature.

[40]  Michael B. Stadler,et al.  Mammalian ISWI and SWI/SNF selectively mediate binding of distinct transcription factors , 2019, Nature.

[41]  Olga Tanaseichuk,et al.  Metascape provides a biologist-oriented resource for the analysis of systems-level datasets , 2019, Nature Communications.

[42]  Cigall Kadoch,et al.  Chromatin regulatory mechanisms and therapeutic opportunities in cancer , 2019, Nature Cell Biology.

[43]  A. Butte,et al.  Reference-based analysis of lung single-cell sequencing reveals a transitional profibrotic macrophage , 2018, Nature Immunology.

[44]  E. Petretto,et al.  Control of inducible gene expression links cohesin to hematopoietic progenitor self-renewal and differentiation , 2018, Nature Immunology.

[45]  W. Hahn,et al.  Binding of TMPRSS2-ERG to BAF Chromatin Remodeling Complexes Mediates Prostate Oncogenesis. , 2018, Molecular cell.

[46]  R. Evans,et al.  Vitamin D Switches BAF Complexes to Protect β Cells , 2018, Cell.

[47]  Fabian J Theis,et al.  SCANPY: large-scale single-cell gene expression data analysis , 2018, Genome Biology.

[48]  B. Göttgens,et al.  From haematopoietic stem cells to complex differentiation landscapes , 2018, Nature.

[49]  M. Greenberg,et al.  AP-1 Transcription Factors and the BAF Complex Mediate Signal-Dependent Enhancer Selection. , 2017, Molecular cell.

[50]  Berthold Göttgens,et al.  Critical Modulation of Hematopoietic Lineage Fate by Hepatic Leukemia Factor , 2017, Cell reports.

[51]  A. F. Stewart,et al.  KMT2A and KMT2B Mediate Memory Function by Affecting Distinct Genomic Regions. , 2017, Cell reports.

[52]  Sandipan Brahma,et al.  INO80 exchanges H2A.Z for H2A by translocating on DNA proximal to histone dimers , 2017, Nature Communications.

[53]  B. Garcia,et al.  Mll3 and Mll4 Facilitate Enhancer RNA Synthesis and Transcription from Promoters Independently of H3K4 Monomethylation. , 2017, Molecular cell.

[54]  G. Sauvageau,et al.  SMARCD2 subunit of SWI/SNF chromatin-remodeling complexes mediates granulopoiesis through a CEBPɛ dependent mechanism , 2017, Nature Genetics.

[55]  A. Shilatifard,et al.  Multiple Roles for the MLL/COMPASS Family in the Epigenetic Regulation of Gene Expression and in Cancer , 2017 .

[56]  Hiroshi Kimura,et al.  Setdb1 maintains hematopoietic stem and progenitor cells by restricting the ectopic activation of nonhematopoietic genes. , 2016, Blood.

[57]  Howard Y. Chang,et al.  Lineage-specific and single cell chromatin accessibility charts human hematopoiesis and leukemia evolution , 2016, Nature Genetics.

[58]  Nicola D. Roberts,et al.  Genomic Classification and Prognosis in Acute Myeloid Leukemia. , 2016, The New England journal of medicine.

[59]  M. Koegl,et al.  Sensitivity and engineered resistance of myeloid leukemia cells to BRD9 inhibition , 2016, Nature chemical biology.

[60]  K. Zhao,et al.  Setd1a and NURF mediate chromatin dynamics and gene regulation during erythroid lineage commitment and differentiation , 2016, Nucleic acids research.

[61]  Fidel Ramírez,et al.  deepTools2: a next generation web server for deep-sequencing data analysis , 2016, Nucleic Acids Res..

[62]  Fabian J Theis,et al.  Diffusion pseudotime robustly reconstructs lineage branching , 2016, Nature Methods.

[63]  Matthew E. Ritchie,et al.  limma powers differential expression analyses for RNA-sequencing and microarray studies , 2015, Nucleic acids research.

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

[65]  J. O’Shea,et al.  Faculty Opinions recommendation of Immunogenetics. Chromatin state dynamics during blood formation. , 2014 .

[66]  N. Friedman,et al.  Chromatin state dynamics during blood formation , 2014, Science.

[67]  Kristian Helin,et al.  Chromatin repressive complexes in stem cells, development, and cancer. , 2014, Cell stem cell.

[68]  Cole Trapnell,et al.  Pseudo-temporal ordering of individual cells reveals dynamics and regulators of cell fate decisions , 2014, Nature Biotechnology.

[69]  M. Roussel,et al.  Miz1 is required to maintain autophagic flux , 2013, Nature Communications.

[70]  G. Crabtree,et al.  The BAF complex interacts with Pax6 in adult neural progenitors to establish a neurogenic cross-regulatory transcriptional network. , 2013, Cell stem cell.

[71]  Christina E. Wells,et al.  HDAC3 is essential for DNA replication in hematopoietic progenitor cells. , 2013, The Journal of clinical investigation.

[72]  Wei Shi,et al.  featureCounts: an efficient general purpose program for assigning sequence reads to genomic features , 2013, Bioinform..

[73]  O. Dovey,et al.  A powerful molecular synergy between mutant Nucleophosmin and Flt3-ITD drives acute myeloid leukemia in mice , 2013, Leukemia.

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

[75]  P. Wade,et al.  Cancer biology and NuRD: a multifaceted chromatin remodelling complex , 2011, Nature Reviews Cancer.

[76]  Howard Cedar,et al.  Epigenetics of haematopoietic cell development , 2011, Nature Reviews Immunology.

[77]  Marcel Martin.  Cutadapt removes adapter sequences from high-throughput sequencing reads , 2011 .

[78]  R. Andrews,et al.  Mutant nucleophosmin and cooperating pathways drive leukemia initiation and progression in mice , 2011, Nature Genetics.

[79]  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.

[80]  Davis J. McCarthy,et al.  edgeR: a Bioconductor package for differential expression analysis of digital gene expression data , 2009, Bioinform..

[81]  Clifford A. Meyer,et al.  Model-based Analysis of ChIP-Seq (MACS) , 2008, Genome Biology.

[82]  W. Rottbauer,et al.  Regulation of muscle development by DPF3, a novel histone acetylation and methylation reader of the BAF chromatin remodeling complex. , 2008, Genes & development.

[83]  H. Koeffler,et al.  ATF4 differentially regulates transcriptional activation of myeloid‐specific genes by C/EBPε and C/EBPα , 2007 .

[84]  Daniel G. Tenen,et al.  Transcription factors in myeloid development: balancing differentiation with transformation , 2007, Nature Reviews Immunology.

[85]  J. Downing.  The core-binding factor leukemias: lessons learned from murine models. , 2003, Current opinion in genetics & development.

[86]  C. Begley,et al.  The scl gene product is required for the generation of all hematopoietic lineages in the adult mouse. , 1996, The EMBO journal.

[87]  Ira M. Hall,et al.  BEDTools: a flexible suite of utilities for comparing genomic features , 2010, Bioinform..

[88]  H. Koeffler,et al.  ATF4 differentially regulates transcriptional activation of myeloid-specific genes by C/EBPepsilon and C/EBPalpha. , 2007, Journal of Leukocyte Biology.

[89]  L. Zon,et al.  Hematopoiesis: An Evolving Paradigm for Stem Cell Biology , 2008, Cell.