Transcription factor competition at the γ-globin promoters controls hemoglobin switching

[1]  Daniel Hidalgo,et al.  Dynamics of the 4D genome during in vivo lineage specification and differentiation , 2020, Nature Communications.

[2]  Mingyao Liu,et al.  Reactivation of γ-globin expression through Cas9 or base editor to treat β-hemoglobinopathies , 2020, Cell Research.

[3]  E. Wagner,et al.  The Integrator Complex Attenuates Promoter-Proximal Transcription at Protein-Coding Genes. , 2019, Molecular cell.

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

[5]  E. Lander,et al.  Control of human hemoglobin switching by LIN28B-mediated regulation of BCL11A translation , 2018, Nature Genetics.

[6]  A. Dean,et al.  Fetal γ-globin genes are regulated by the BGLT3 long noncoding RNA locus. , 2018, Blood.

[7]  Nozomu Yachie,et al.  Engineered CRISPR-Cas9 nuclease with expanded targeting space , 2018, Science.

[8]  Luca Pinello,et al.  CRISPR-SURF: discovering regulatory elements by deconvolution of CRISPR tiling screen data , 2018, bioRxiv.

[9]  H. Kono,et al.  MNase, as a probe to study the sequence-dependent site exposures in the +1 nucleosomes of yeast , 2018, Nucleic acids research.

[10]  Martha L. Bulyk,et al.  Direct Promoter Repression by BCL11A Controls the Fetal to Adult Hemoglobin Switch , 2018, Cell.

[11]  Laura J. Norton,et al.  Natural regulatory mutations elevate the fetal globin gene via disruption of BCL11A or ZBTB7A binding , 2018, Nature Genetics.

[12]  B. van Steensel,et al.  Easy quantification of template-directed CRISPR/Cas9 editing , 2017, bioRxiv.

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

[14]  R. Hardison,et al.  Comparative analysis of three-dimensional chromosomal architecture identifies a novel fetal hemoglobin regulatory element , 2017, Genes & development.

[15]  David Cowburn,et al.  A promiscuous split intein with expanded protein engineering applications , 2017, Proceedings of the National Academy of Sciences.

[16]  Gaelen T. Hess,et al.  Genome-scale measurement of off-target activity using Cas9 toxicity in high-throughput screens , 2017, Nature Communications.

[17]  K. Quinlan,et al.  The regulation of human globin promoters by CCAAT box elements and the recruitment of NF-Y. , 2017, Biochimica et biophysica acta. Gene regulatory mechanisms.

[18]  Steven Henikoff,et al.  An efficient targeted nuclease strategy for high-resolution mapping of DNA binding sites , 2016, bioRxiv.

[19]  Gaelen T. Hess,et al.  Directed evolution using dCas9-targeted somatic hypermutation in mammalian cells , 2016, Nature Methods.

[20]  R. Hardison,et al.  A genome-editing strategy to treat β-hemoglobinopathies that recapitulates a mutation associated with a benign genetic condition , 2016, Nature Medicine.

[21]  Leighton J. Core,et al.  Base-pair-resolution genome-wide mapping of active RNA polymerases using precision nuclear run-on (PRO-seq) , 2016, Nature Protocols.

[22]  L. Pennacchio,et al.  Genetic dissection of the α-globin super-enhancer in vivo , 2016, Nature Genetics.

[23]  David R. Liu,et al.  Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage , 2016, Nature.

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

[25]  G. Pavesi,et al.  A high definition look at the NF-Y regulome reveals genome-wide associations with selected transcription factors , 2016, Nucleic acids research.

[26]  Matthew C. Canver,et al.  Transcription factors LRF and BCL11A independently repress expression of fetal hemoglobin , 2016, Science.

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

[28]  H. Bussemaker,et al.  In search of the determinants of enhancer-promoter interaction specificity. , 2014, Trends in cell biology.

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

[30]  B. van Steensel,et al.  Easy quantitative assessment of genome editing by sequence trace decomposition , 2014, Nucleic acids research.

[31]  Sailu Yellaboina,et al.  Histone-fold domain protein NF-Y promotes chromatin accessibility for cell type-specific master transcription factors. , 2014, Molecular cell.

[32]  Neville E. Sanjana,et al.  Improved vectors and genome-wide libraries for CRISPR screening , 2014, Nature Methods.

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

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

[35]  Kevin Struhl,et al.  NF-Y coassociates with FOS at promoters, enhancers, repetitive elements, and inactive chromatin regions, and is stereo-positioned with growth-controlling transcription factors , 2013, Genome research.

[36]  S. Orkin,et al.  Corepressor-dependent silencing of fetal hemoglobin expression by BCL11A , 2013, Proceedings of the National Academy of Sciences.

[37]  M. Nardini,et al.  Sequence-Specific Transcription Factor NF-Y Displays Histone-like DNA Binding and H2B-like Ubiquitination , 2013, Cell.

[38]  D. Tuan,et al.  NF-Y Recruits Both Transcription Activator and Repressor to Modulate Tissue- and Developmental Stage-Specific Expression of Human γ-Globin Gene , 2012, PloS one.

[39]  Richard S. Sandstrom,et al.  BEDOPS: high-performance genomic feature operations , 2012, Bioinform..

[40]  Yukio Nakamura,et al.  Establishment of Immortalized Human Erythroid Progenitor Cell Lines Able to Produce Enucleated Red Blood Cells , 2012, PloS one.

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

[42]  Chris Fisher,et al.  A functional element necessary for fetal hemoglobin silencing. , 2011, The New England journal of medicine.

[43]  A. Nienhuis,et al.  Transcriptional regulation of fetal to adult hemoglobin switching: new therapeutic opportunities. , 2011, Blood.

[44]  Philip Machanick,et al.  MEME-ChIP: motif analysis of large DNA datasets , 2011, Bioinform..

[45]  Jacob F. Degner,et al.  Sequence and Chromatin Accessibility Data Accurate Inference of Transcription Factor Binding from Dna Material Supplemental Open Access , 2022 .

[46]  S. Orkin,et al.  Transcriptional silencing of {gamma}-globin by BCL11A involves long-range interactions and cooperation with SOX6. , 2010, Genes & development.

[47]  Stuart H. Orkin,et al.  Developmental and species-divergent globin switching are driven by BCL11A , 2009, Nature.

[48]  Gonçalo R. Abecasis,et al.  The Sequence Alignment/Map format and SAMtools , 2009, Bioinform..

[49]  J. Hirschhorn,et al.  Supporting Online Material Materials and Methods Figs. S1 to S10 Tables S1 to S7 References Human Fetal Hemoglobin Expression Is Regulated by the Developmental Stage-specific Repressor Bcl11a , 2022 .

[50]  S. Sen,et al.  Inhibition of CBF/NF-Y mediated transcription activation arrests cells at G2/M phase and suppresses expression of genes activated at G2/M phase of the cell cycle , 2006, Nucleic acids research.

[51]  Hiroshi Handa,et al.  NF-Y Is Essential for the Recruitment of RNA Polymerase II and Inducible Transcription of Several CCAAT Box-Containing Genes , 2005, Molecular and Cellular Biology.

[52]  G. Stamatoyannopoulos,et al.  Developmentally Specific Role of the CCAAT Box in Regulation of Human γ-Globin Gene Expression* , 2004, Journal of Biological Chemistry.

[53]  Suya Yang,et al.  Sequences in the Aγ–δ intergenic region are not required for stage-specific regulation of the human β-globin gene locus , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[54]  Erik Splinter,et al.  Looping and interaction between hypersensitive sites in the active beta-globin locus. , 2002, Molecular cell.

[55]  Cameron S. Osborne,et al.  Long-range chromatin regulatory interactions in vivo , 2002, Nature Genetics.

[56]  D. Moras,et al.  NF-Y Recruitment of TFIID, Multiple Interactions with Histone Fold TAFIIs* , 2002, The Journal of Biological Chemistry.

[57]  F. Coustry,et al.  CBF/NF-Y Functions Both in Nucleosomal Disruption and Transcription Activation of the Chromatin-assembled Topoisomerase IIα Promoter , 2001, Journal of Biological Chemistry.

[58]  G. Stamatoyannopoulos,et al.  Role of NF-Y in In Vivo Regulation of the γ-Globin Gene , 2001, Molecular and Cellular Biology.

[59]  M. Groudine,et al.  β-globin Gene Switching and DNase I Sensitivity of the Endogenous β-globin Locus in Mice Do Not Require the Locus Control Region , 2000 .

[60]  R. Mantovani,et al.  The molecular biology of the CCAAT-binding factor NF-Y. , 1999, Gene.

[61]  Y. Sasaguri,et al.  Transactivation of the Human cdc2 Promoter by Adenovirus E1A , 1999, The Journal of Biological Chemistry.

[62]  F. Rojo.  Repression of Transcription Initiation in Bacteria , 1999, Journal of bacteriology.

[63]  R. Mantovani,et al.  NF-Y binding to twin CCAAT boxes: role of Q-rich domains and histone fold helices. , 1999, Journal of molecular biology.

[64]  R. Mantovani,et al.  NF-Y Organizes the γ-Globin CCAAT Boxes Region* , 1998, The Journal of Biological Chemistry.

[65]  R. Roeder,et al.  CCAAT binding NF-Y-TBP interactions: NF-YB and NF-YC require short domains adjacent to their histone fold motifs for association with TBP basic residues. , 1997, Nucleic acids research.

[66]  P. Milos,et al.  A ubiquitous factor is required for C/EBP-related proteins to form stable transcription complexes on an albumin promoter segment in vitro. , 1992, Genes & development.

[67]  F. Costantini,et al.  An embryonic pattern of expression of a human fetal globin gene in transgenic mice , 1986, Nature.

[68]  F. Costantini,et al.  Developmental regulation of a cloned adult β-globin gene in transgenic mice , 1985, Nature.

[69]  S. Orkin,et al.  METHOD Open Access , 2014 .

[70]  Wouter de Laat,et al.  The β-globin nuclear compartment in development and erythroid differentiation , 2003, Nature Genetics.

[71]  J. Starck,et al.  Developmental regulation of human gamma- and beta-globin genes in the absence of the locus control region. , 1994, Blood.