Balanced SET levels favor the correct enhancer repertoire during cell fate acquisition

[1]  C. Ernst,et al.  Putative Roles of SETBP1 Dosage on the SET Oncogene to Affect Brain Development , 2022, Frontiers in Neuroscience.

[2]  Neville E. Sanjana,et al.  Autism genes converge on asynchronous development of shared neuron classes , 2022, Nature.

[3]  B. Bonev,et al.  Multimodal profiling of the transcriptional regulatory landscape of the developing mouse cortex identifies Neurog2 as a key epigenome remodeler , 2022, Nature Neuroscience.

[4]  A. Akhtar,et al.  Modulation of cellular processes by histone and non-histone protein acetylation , 2022, Nature Reviews Molecular Cell Biology.

[5]  T. Enver,et al.  The onset of circulation triggers a metabolic switch required for endothelial to hematopoietic transition , 2021, Cell reports.

[6]  Aleksandra A. Kolodziejczyk,et al.  Cell-type specialization is encoded by specific chromatin topologies , 2021, Nature.

[7]  V. Tarabykin,et al.  The Role of Neurod Genes in Brain Development, Function, and Disease , 2021, Frontiers in Molecular Neuroscience.

[8]  G. Ciriello,et al.  Histone acetylation dynamics modulates chromatin conformation and allele-specific interactions at oncogenic loci , 2021, Nature Genetics.

[9]  Howard Y. Chang,et al.  ArchR is a scalable software package for integrative single-cell chromatin accessibility analysis , 2021, Nature Genetics.

[10]  Zeba Wunderlich,et al.  Enhancer redundancy in development and disease , 2021, Nature Reviews Genetics.

[11]  Howard Y. Chang,et al.  Chromatin and gene-regulatory dynamics of the developing human cerebral cortex at single-cell resolution , 2020, Cell.

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

[13]  M. Levine,et al.  Enhancer-promoter communication: hubs or loops? , 2020, Current opinion in genetics & development.

[14]  H. van Bokhoven,et al.  The phenomenal epigenome in neurodevelopmental disorders , 2020, Human molecular genetics.

[15]  S. Canals,et al.  KAT3-dependent acetylation of cell type-specific genes maintains neuronal identity in the adult mouse brain , 2020, Nature Communications.

[16]  Qin Zhu,et al.  Developmental trajectory of pre-hematopoietic stem cell formation from endothelium. , 2020, Blood.

[17]  K. Adelman,et al.  Evaluating Enhancer Function and Transcription. , 2020, Annual review of biochemistry.

[18]  Angela L. Elwell,et al.  Cell-type specific effects of genetic variation on chromatin accessibility during human neuronal differentiation , 2020, Nature Neuroscience.

[19]  Fabian J Theis,et al.  Generalizing RNA velocity to transient cell states through dynamical modeling , 2019, Nature Biotechnology.

[20]  A. Sandelin,et al.  Determinants of enhancer and promoter activities of regulatory elements , 2019, Nature Reviews Genetics.

[21]  R. Tjian,et al.  Distinct Classes of Chromatin Loops Revealed by Deletion of an RNA-Binding Region in CTCF. , 2019, Molecular cell.

[22]  E. Heard,et al.  Advances in epigenetics link genetics to the environment and disease , 2019, Nature.

[23]  L. Nguyen,et al.  Temporal patterning of apical progenitors and their daughter neurons in the developing neocortex , 2019, Science.

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

[25]  W. Gu,et al.  Loss of SET reveals both the p53-dependent and the p53-independent functions in vivo , 2019, Cell Death & Disease.

[26]  Andrew J. Hill,et al.  The single cell transcriptional landscape of mammalian organogenesis , 2019, Nature.

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

[28]  Zhiping Weng,et al.  Neuron-specific signatures in the chromosomal connectome associated with schizophrenia risk , 2018, Science.

[29]  Lai Guan Ng,et al.  Dimensionality reduction for visualizing single-cell data using UMAP , 2018, Nature Biotechnology.

[30]  Mauro A. A. Castro,et al.  The chromatin accessibility landscape of primary human cancers , 2018, Science.

[31]  V. Corces,et al.  Organizational principles of 3D genome architecture , 2018, Nature Reviews Genetics.

[32]  Andrew C. Adey,et al.  Cicero Predicts cis-Regulatory DNA Interactions from Single-Cell Chromatin Accessibility Data. , 2018, Molecular cell.

[33]  K. McGrath,et al.  Kit ligand has a critical role in mouse yolk sac and aorta–gonad–mesonephros hematopoiesis , 2018, EMBO reports.

[34]  Erik Sundström,et al.  RNA velocity of single cells , 2018, Nature.

[35]  T. Bourgeron,et al.  Both rare and common genetic variants contribute to autism in the Faroe Islands , 2018, bioRxiv.

[36]  R. Newbury-Ecob,et al.  SET de novo frameshift variants associated with developmental delay and intellectual disabilities , 2018, European Journal of Human Genetics.

[37]  M. Lalowski,et al.  SETBP1 induces transcription of a network of development genes by acting as an epigenetic hub , 2018, Nature Communications.

[38]  A. Tanay,et al.  Multiscale 3D Genome Rewiring during Mouse Neural Development , 2017, Cell.

[39]  William J. Greenleaf,et al.  chromVAR: Inferring transcription factor-associated accessibility from single-cell epigenomic data , 2017, Nature Methods.

[40]  C. Bonifer,et al.  Chromatin priming of genes in development: Concepts, mechanisms and consequences. , 2017, Experimental hematology.

[41]  Kin Chung Lam,et al.  High-resolution TADs reveal DNA sequences underlying genome organization in flies , 2017, Nature Communications.

[42]  Alessandro Sessa,et al.  Epigenetic Mistakes in Neurodevelopmental Disorders , 2017, Journal of Molecular Neuroscience.

[43]  C. Curti,et al.  SET oncoprotein accumulation regulates transcription through DNA demethylation and histone hypoacetylation , 2017, Oncotarget.

[44]  B. V. van Bon,et al.  Overlapping SETBP1 gain-of-function mutations in Schinzel-Giedion syndrome and hematologic malignancies , 2017, PLoS genetics.

[45]  I. Petersen,et al.  Pan-cancer analysis of somatic copy-number alterations implicates IRS4 and IGF2 in enhancer hijacking , 2016, Nature Genetics.

[46]  B. Honig,et al.  The p53-SET Interplays Reveal A New Mode of Acetylation-dependent Regulation , 2016, Nature.

[47]  Neva C. Durand,et al.  Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments. , 2016, Cell systems.

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

[49]  G. Daley,et al.  Hallmarks of pluripotency , 2015, Nature.

[50]  M. Manière,et al.  Long term follow up of two independent patients with Schinzel-Giedion carrying SETBP1 mutations. , 2015, European journal of medical genetics.

[51]  Qing-Yu He,et al.  ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization , 2015, Bioinform..

[52]  S. Amselem,et al.  RSPH3 Mutations Cause Primary Ciliary Dyskinesia with Central-Complex Defects and a Near Absence of Radial Spokes. , 2015, American journal of human genetics.

[53]  Andrew C. Adey,et al.  Multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing , 2015, Science.

[54]  Neva C. Durand,et al.  A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping , 2014, Cell.

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

[56]  Arne V. Blackman,et al.  Neuronal morphometry directly from bitmap images , 2014, Nature Methods.

[57]  O. Dovey,et al.  Histone deacetylase (HDAC) 1 and 2 are essential for accurate cell division and the pluripotency of embryonic stem cells , 2014, Proceedings of the National Academy of Sciences.

[58]  David P. Kreil,et al.  Assessing technical performance in differential gene expression experiments with external spike-in RNA control ratio mixtures , 2014, Nature Communications.

[59]  Björn Usadel,et al.  Trimmomatic: a flexible trimmer for Illumina sequence data , 2014, Bioinform..

[60]  Y. Gotoh,et al.  Transcriptional coupling of neuronal fate commitment and the onset of migration , 2013, Current Opinion in Neurobiology.

[61]  R. Young,et al.  Super-Enhancers in the Control of Cell Identity and Disease , 2013, Cell.

[62]  Howard Y. Chang,et al.  Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position , 2013, Nature Methods.

[63]  Shane J. Neph,et al.  Developmental Fate and Cellular Maturity Encoded in Human Regulatory DNA Landscapes , 2013, Cell.

[64]  T. Südhof,et al.  Rapid Single-Step Induction of Functional Neurons from Human Pluripotent Stem Cells , 2013, Neuron.

[65]  David A. Orlando,et al.  Master Transcription Factors and Mediator Establish Super-Enhancers at Key Cell Identity Genes , 2013, Cell.

[66]  David A. Orlando,et al.  Selective Inhibition of Tumor Oncogenes by Disruption of Super-Enhancers , 2013, Cell.

[67]  J. Wysocka,et al.  Modification of enhancer chromatin: what, how, and why? , 2013, Molecular cell.

[68]  D. Brautigan,et al.  Protein Ser/ Thr phosphatases – the ugly ducklings of cell signalling , 2013, The FEBS journal.

[69]  Roberta Spinelli,et al.  Recurrent SETBP1 mutations in atypical chronic myeloid leukemia , 2012, Nature Genetics.

[70]  E. Furlong,et al.  Transcription factors: from enhancer binding to developmental control , 2012, Nature Reviews Genetics.

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

[72]  Ryan A. Flynn,et al.  A unique chromatin signature uncovers early developmental enhancers in humans , 2011, Nature.

[73]  Fred H. Gage,et al.  A Model for Neural Development and Treatment of Rett Syndrome Using Human Induced Pluripotent Stem Cells , 2010, Cell.

[74]  Nobuhiko Okamoto,et al.  Reduced expression by SETBP1 haploinsufficiency causes developmental and expressive language delay indicating a phenotype distinct from Schinzel–Giedion syndrome , 2010, Journal of Medical Genetics.

[75]  Christian Gilissen,et al.  De novo mutations of SETBP1 cause Schinzel-Giedion syndrome , 2010, Nature Genetics.

[76]  David S. Lapointe,et al.  ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data , 2010, BMC Bioinformatics.

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

[78]  T. Südhof Neuroligins and neurexins link synaptic function to cognitive disease , 2008, Nature.

[79]  A. Hadjantonakis,et al.  Tbr2 Directs Conversion of Radial Glia into Basal Precursors and Guides Neuronal Amplification by Indirect Neurogenesis in the Developing Neocortex , 2008, Neuron.

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

[81]  M. Horikoshi,et al.  Relationship between the structure of SET/TAF-Iβ/INHAT and its histone chaperone activity , 2007, Proceedings of the National Academy of Sciences.

[82]  T. Kouzarides Chromatin Modifications and Their Function , 2007, Cell.

[83]  Tetsuichiro Saito In vivo electroporation in the embryonic mouse central nervous system , 2006, Nature Protocols.

[84]  James A. Cuff,et al.  A Bivalent Chromatin Structure Marks Key Developmental Genes in Embryonic Stem Cells , 2006, Cell.

[85]  P. Lichter,et al.  Histone acetylation increases chromatin accessibility , 2005, Journal of Cell Science.

[86]  M. Abdelrahim,et al.  Sp transcription factor family and its role in cancer. , 2005, European journal of cancer.

[87]  Anirvan Ghosh,et al.  Semaphorin 3A is a chemoattractant for cortical apical dendrites , 2000, Nature.

[88]  O. Kretz,et al.  Disruption of the glucocorticoid receptor gene in the nervous system results in reduced anxiety , 1999, Nature Genetics.

[89]  P. Marks,et al.  A class of hybrid polar inducers of transformed cell differentiation inhibits histone deacetylases. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[90]  Z. Damuni,et al.  The Myeloid Leukemia-associated Protein SET Is a Potent Inhibitor of Protein Phosphatase 2A (*) , 1996, The Journal of Biological Chemistry.

[91]  G. Grosveld,et al.  Characterization of the translocation breakpoint sequences of two DEK‐CAN fusion genes present in t(6;9) acute myeloid leukemia and a SET‐CAN fusion gene found in a case of acute undifferentiated leukemia , 1992, Genes, chromosomes & cancer.

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

[93]  I. Amit,et al.  Comprehensive mapping of long-range interactions reveals folding principles of the human genome. , 2009, Science.

[94]  J. Frisén,et al.  Deconstructing stemness , 2005, The EMBO journal.

[95]  H. Drexler,et al.  Tartrate-resistant acid phosphatase: gene structure and function , 1997, Leukemia.

[96]  K. Rajewsky,et al.  A cre-transgenic mouse strain for the ubiquitous deletion of loxP-flanked gene segments including deletion in germ cells. , 1995, Nucleic acids research.

[97]  A. Schinzel,et al.  A syndrome of severe midface retraction, multiple skull anomalies, clubfeet, and cardiac and renal malformations in sibs. , 1978, American journal of medical genetics.