Interrogation of enhancer function by enhancer-targeting CRISPR epigenetic editing

[1]  C. Gersbach,et al.  The next generation of CRISPR–Cas technologies and applications , 2019, Nature Reviews Molecular Cell Biology.

[2]  Antonia A. Dominguez,et al.  Reversible Disruption of Specific Transcription Factor-DNA Interactions Using CRISPR/Cas9. , 2019, Molecular cell.

[3]  Xiaoshu Xu,et al.  A CRISPR-dCas Toolbox for Genetic Engineering and Synthetic Biology. , 2019, Journal of molecular biology.

[4]  Samira Kiani,et al.  An enhanced CRISPR repressor for targeted mammalian gene regulation , 2018, Nature Methods.

[5]  David R. Liu,et al.  Evolved Cas9 variants with broad PAM compatibility and high DNA specificity , 2018, Nature.

[6]  T. Sauka-Spengler,et al.  Genome and epigenome engineering CRISPR toolkit for in vivo modulation of cis-regulatory interactions and gene expression in the chicken embryo , 2018, Development.

[7]  Kristofer C. Berrett,et al.  Multiplex Enhancer Interference Reveals Collaborative Control of Gene Regulation by Estrogen Receptor α-Bound Enhancers. , 2017, Cell systems.

[8]  Michael Q. Zhang,et al.  In Situ Capture of Chromatin Interactions by Biotinylated dCas9 , 2017, Cell.

[9]  Timothy E. Reddy,et al.  CRISPR–Cas9 epigenome editing enables high-throughput screening for functional regulatory elements in the human genome , 2017, Nature Biotechnology.

[10]  Davide Cittaro,et al.  Inheritable Silencing of Endogenous Genes by Hit-and-Run Targeted Epigenetic Editing , 2016, Cell.

[11]  Neville E. Sanjana,et al.  High-resolution interrogation of functional elements in the noncoding genome , 2016, Science.

[12]  Isaac B. Hilton,et al.  Editing the epigenome: technologies for programmable transcription and epigenetic modulation , 2016, Nature Methods.

[13]  L. Zon,et al.  Dynamic Control of Enhancer Repertoires Drives Lineage and Stage-Specific Transcription during Hematopoiesis. , 2016, Developmental cell.

[14]  Antonia A. Dominguez,et al.  Transcriptional regulation of hepatic lipogenesis , 2015, Nature Reviews Molecular Cell Biology.

[15]  Timothy E. Reddy,et al.  Highly Specific Epigenome Editing by CRISPR/Cas9 Repressors for Silencing of Distal Regulatory Elements , 2015, Nature Methods.

[16]  Matthew C. Canver,et al.  BCL11A enhancer dissection by Cas9-mediated in situ saturating mutagenesis , 2015, Nature.

[17]  William H. Majoros,et al.  Massively parallel quantification of the regulatory effects of noncoding genetic variation in a human cohort , 2015, Genome research.

[18]  S. Spicuglia Faculty Opinions recommendation of Oncogene regulation. An oncogenic super-enhancer formed through somatic mutation of a noncoding intergenic element. , 2015 .

[19]  Christopher M. Vockley,et al.  Epigenome editing by a CRISPR/Cas9-based acetyltransferase activates genes from promoters and enhancers , 2015, Nature Biotechnology.

[20]  R. Maehr,et al.  Functional annotation of native enhancers with a Cas9 -histone demethylase fusion , 2015, Nature Methods.

[21]  Luke A. Gilbert,et al.  Engineering Complex Synthetic Transcriptional Programs with CRISPR RNA Scaffolds , 2015, Cell.

[22]  Ron Weiss,et al.  Highly-efficient Cas9-mediated transcriptional programming , 2014, Nature Methods.

[23]  Alexandro E. Trevino,et al.  Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex , 2014, Nature.

[24]  Jun S. Liu,et al.  MAGeCK enables robust identification of essential genes from genome-scale CRISPR/Cas9 knockout screens , 2014, Genome Biology.

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

[26]  R. Young,et al.  An oncogenic super-enhancer formed through somatic mutation of a noncoding intergenic element , 2014, Science.

[27]  Ronald D. Vale,et al.  A Protein-Tagging System for Signal Amplification in Gene Expression and Fluorescence Imaging , 2014, Cell.

[28]  Max A. Horlbeck,et al.  Genome-Scale CRISPR-Mediated Control of Gene Repression and Activation , 2014, Cell.

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

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

[31]  Philip D. Gregory,et al.  Reactivation of Developmentally Silenced Globin Genes by Forced Chromatin Looping , 2014, Cell.

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

[33]  A. Visel,et al.  Rapid and Pervasive Changes in Genome-wide Enhancer Usage during Mammalian Development , 2013, Cell.

[34]  Matthew C. Canver,et al.  An Erythroid Enhancer of BCL11A Subject to Genetic Variation Determines Fetal Hemoglobin Level , 2013, Science.

[35]  Luke A. Gilbert,et al.  CRISPR-Mediated Modular RNA-Guided Regulation of Transcription in Eukaryotes , 2013, Cell.

[36]  Łukasz M. Boryń,et al.  Genome-Wide Quantitative Enhancer Activity Maps Identified by STARR-seq , 2013, Science.

[37]  Luke A. Gilbert,et al.  Repurposing CRISPR as an RNA-Guided Platform for Sequence-Specific Control of Gene Expression , 2013, Cell.

[38]  Luca Pinello,et al.  Combinatorial assembly of developmental stage-specific enhancers controls gene expression programs during human erythropoiesis. , 2012, Developmental cell.

[39]  Nathan C. Sheffield,et al.  The accessible chromatin landscape of the human genome , 2012, Nature.

[40]  Raymond K. Auerbach,et al.  An Integrated Encyclopedia of DNA Elements in the Human Genome , 2012, Nature.

[41]  Cong Peng,et al.  Correction of Sickle Cell Disease in Adult Mice by Interference with Fetal Hemoglobin Silencing , 2011, Science.

[42]  Colin N. Dewey,et al.  RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome , 2011, BMC Bioinformatics.

[43]  V. Corces,et al.  Enhancer function: new insights into the regulation of tissue-specific gene expression , 2011, Nature Reviews Genetics.

[44]  Guy Sauvageau,et al.  Polycomb group proteins: multi-faceted regulators of somatic stem cells and cancer. , 2010, Cell stem cell.

[45]  A. Visel,et al.  Genomic Views of Distant-Acting Enhancers , 2009, Nature.

[46]  Cole Trapnell,et al.  Ultrafast and memory-efficient alignment of short DNA sequences to the human genome , 2009, Genome Biology.

[47]  Nathaniel D. Heintzman,et al.  Histone modifications at human enhancers reflect global cell-type-specific gene expression , 2009, Nature.

[48]  A. Visel,et al.  ChIP-seq accurately predicts tissue-specific activity of enhancers , 2009, Nature.

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

[50]  Nathaniel D. Heintzman,et al.  Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome , 2007, Nature Genetics.

[51]  Rudolf Jaenisch,et al.  Efficient method to generate single‐copy transgenic mice by site‐specific integration in embryonic stem cells , 2006, Genesis.

[52]  K. Akashi,et al.  Distinctive and indispensable roles of PU.1 in maintenance of hematopoietic stem cells and their differentiation. , 2005, Blood.

[53]  Rudolf Jaenisch,et al.  Ectopic Expression of Oct-4 Blocks Progenitor-Cell Differentiation and Causes Dysplasia in Epithelial Tissues , 2005, Cell.

[54]  Yang Shi,et al.  Histone Demethylation Mediated by the Nuclear Amine Oxidase Homolog LSD1 , 2004, Cell.

[55]  J. Kutok,et al.  Loss of Runx1 perturbs adult hematopoiesis and is associated with a myeloproliferative phenotype. , 2004, Blood.

[56]  J. Kutok,et al.  Acute myeloid leukemia induced by graded reduction of a lineage-specific transcription factor, PU.1 , 2004, Nature Genetics.

[57]  R. Urrutia KRAB-containing zinc-finger repressor proteins , 2003, Genome Biology.

[58]  Xiangdong Fang,et al.  Locus control regions. , 2002, Blood.

[59]  S. Orkin,et al.  Targeted Deletion of a High-Affinity GATA-binding Site in the GATA-1 Promoter Leads to Selective Loss of the Eosinophil Lineage In Vivo , 2002, The Journal of experimental medicine.

[60]  D. Tenen,et al.  Absence of granulocyte colony-stimulating factor signaling and neutrophil development in CCAAT enhancer binding protein alpha-deficient mice. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[61]  L. Zon,et al.  Expression of GATA-binding proteins during embryonic development in Xenopus laevis. , 1991, Proceedings of the National Academy of Sciences of the United States of America.

[62]  M. Klemsz,et al.  The macrophage and B cell-specific transcription factor PU.1 is related to the ets oncogene , 1990, Cell.

[63]  Shih-Feng Tsai,et al.  Cloning of cDNA for the major DNA-binding protein of the erythroid lineage through expression in mammalian cells , 1989, Nature.

[64]  J. Banerji,et al.  Expression of a β-globin gene is enhanced by remote SV40 DNA sequences , 1981, Cell.

[65]  Carmen Domingo Biology , 1929, Nature.

[66]  R. Deberardinis,et al.  Loss of EZH2 Reprograms BCAA Metabolism to Drive Leukemic Transformation. , 2019, Cancer discovery.

[67]  M. Rehli,et al.  An autonomous CEBPA enhancer specific for myeloid-lineage priming and neutrophilic differentiation. , 2016, Blood.

[68]  N. Perrimon,et al.  Comparative Analysis of Cas9 Activators Across Multiple Species , 2016, Nature Methods.

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

[70]  S. Orkin,et al.  MAnorm: a robust model for quantitative comparison of ChIP-Seq data sets , 2012 .

[71]  Rudolf Jaenisch,et al.  Single-gene transgenic mouse strains for reprogramming adult somatic cells , 2010, Nature Methods.

[72]  N. Speck,et al.  Purification of core-binding factor, a protein that binds the conserved core site in murine leukemia virus enhancers. , 1992, Molecular and cellular biology.

[73]  J. Banerji,et al.  Expression of a beta-globin gene is enhanced by remote SV40 DNA sequences. , 1981, Cell.

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