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Genome-wide analysis of the role of FOG-1 in GATA-1 chromatin occupancy

ABSTRACT: We report ChIP-Seq data for GATA-1 and the FOG-binding mutant of GATA-1 (GATA-1^V205G) in G1ME cells, a Gata1-null cell line with both erythroid and megakaryocytic differentiation potential. We introduced HA-tagged GATA-1 or V205G into G1ME cells via retroviral transduction. The cells were crosslinked at 48h post-transduction, and an HA antibody was used for chromatin immunoprecipitation (ChIP). ChIP and input samples were sequenced on Illumina GAII high-throughput sequencer. The data reveal GATA-1-specific and V205G-specific bidning sites, indicating that FOG-1 both faacilitates and prohibits GATA-1 chromatin occupancy in a context-dependent manner. Examinaton of chromatin occupancy of GATA-1 anda FOG-binding mutant of GATA-1 in G1ME cells cultured in TPO.

ORGANISM(S): Mus musculus

SUBMITTER: Timothy Chlon

PROVIDER: E-GEOD-35644 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Cofactor-mediated restriction of GATA-1 chromatin occupancy coordinates lineage-specific gene expression.

Chlon Timothy M TM Doré Louis C LC Crispino John D JD

Molecular cell 20120705 4

GATA-1 and its cofactor FOG-1 are required for the differentiation of erythrocytes and megakaryocytes. In contrast, mast cell development requires GATA-1 and the absence of FOG-1. Through genome-wide comparison of the chromatin occupancy of GATA-1 and a naturally occurring mutant that cannot bind FOG-1 (GATA-1(V205G)), we reveal that FOG-1 intricately regulates the chromatin occupancy of GATA-1. We identified GATA1-selective and GATA-1(V205G)-selective binding sites and show that GATA-1, in the ...[more]

PMID: 22771118

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Cofactor-mediated Restriction of GATA-1 Chromatin Occupancy Coordinates Lineage-specific Gene Expression

Project description:This SuperSeries is composed of the following subset Series: GSE35644: Genome-wide analysis of the role of FOG-1 in GATA-1 chromatin occupancy GSE35695: Differential gene regulation by disease-associated mutants of GATA-1 during megakaryocyte differentiation Refer to individual Series

2012-07-29 | E-GEOD-35708 | biostudies-arrayexpress

Genome-wide transcription factor binding and chromatin methylation marks in the G1ME megakaryocytic progenitor model cell line

Project description:There are many examples of transcription factor families whose members control gene expression profiles of diverse cell types. However, the mechanism by which closely related factors occupy distinct regulatory elements and impart lineage specificity is largely undefined. Here we demonstrate on a genome wide scale that the hematopoietic GATA factors GATA-1 and GATA-2 bind overlapping sets of genes, often at distinct sites, as a means to differentially regulate target gene expression and to regulate the balance between proliferation and differentiation. We also reveal that the GATA switch, which entails a chromatin occupancy exchange between GATA2 and GATA1 in the course of differentiation, operates on more than a third of GATA1 bound genes. The switch is equally likely to lead to transcriptional activation or repression and, in general, GATA1 and GATA2 act oppositely on switch target genes. In addition, we reveal that genomic regions co-occupied by GATA2 and the ETS factor ETS1 are strongly enriched for regions marked by H3K4me3 and occupied by Pol II. Finally, by comparing GATA1 occupancy in erythroid cells and megakaryocytes, we find that the presence of ETS factor motifs is a major discriminator of megakaryocyte versus red cell specification. We used Illumina ChIP-Seq to examine binding of GATA1, GATA2, and ETS1 transcription factors as well as the genomic locations of two histone methylation marks, H3K4me3 and H3K27me3. Except H3K4me3 (1 sample), all data were generated from at least 2 biological replicates of immunoprecipitations from megakaryocyte progenitor cells, G1ME. Input DNA was prepared and sequenced along with each immunoprecipitation and used as a control dataset for binding site identification.

2012-03-05 | E-GEOD-31331 | biostudies-arrayexpress

Scl specifies hemogenic endothelium and inhibits cardiogenesis via primed enhancers [ChIP-seq]

Project description:Scl/Tal1 confers hemogenic competence and prevents cardiomyogenesis in embryonic endothelium. Here we show that Scl both directly activates a broad gene regulatory network required for hematopoietic stem/progenitor cell (HS/PC) development, and represses transcriptional regulators required for cardiogenesis. Cardiac repression occurs during a short developmental window through Scl binding to distant cardiac enhancers that harbor H3K4me1 at this stage. Scl binding to hematopoietic regulators extends throughout HS/PC and erythroid development and spreads from distant enhancers to promoters. Surprisingly, Scl complex partners Gata 1 and 2 are dispensable for hematopoietic versus cardiac specification and Scl binding to the majority of its target genes. Nevertheless, Gata factors co-operate with Scl to activate selected transcription factors to facilitate HS/PC emergence from hemogenic endothelium. These results uncover a dual function for Scl in dictating hematopoietic versus cardiac fate choice and suggest a mechanism by which lineage-specific bHLH factors direct the divergence of competing fates. ChIP-seq with Scl, Hand1, Lsd1, Ezh2, H3K4me1 and H3K27ac in different cell types with mesodermal origin. Scl ChIP-seq in WT, SclKO, SclKO-iScl and Gata12KO mES cell derived day4 EB (embryoid body) Flk1+ mesodermal cells, SclKO-iScl ES cells and MEL cells; Hand1 ChIP-seq in WT mES cell derived day4 EB Flk1+ mesodermal cells; Lsd1 and Ezh2 ChIP-seq in WT and SclKO mES cell derived day4 EB Flk1+ mesodermal cells. ChIP-seq of histone modifications H3K4me1 and H3K27ac in WT, SclKO and Gata12KO mES cell derived day4 EB Flk1+ mesodermal cells, HPC7 hematopoietic progenitor cells and HL1 cardiomyogenic cells

2015-01-01 | E-GEOD-47082 | biostudies-arrayexpress

GATA-2 controls megakaryocyte proliferation

Project description:Downregulation of GATA-2 in megakaryocytic cells G1ME caused cell cycle arrest. To identify GATA-2 target genes, we transduced G1ME cells with control vector or a vector expressing shRNA specific for mouse GATA-2. The transduced cells were purified by sorting and the RNA were used for microarry.

2009-06-10 | GSE16521 | GEO

Dynamic analysis of gene expression and genome wide transcription factor binding during lineage-specification of multipotent progenitors [ChIP-seq].

Project description:We used the paradigmatic 'GATA-PU.1 axis’ to explore, at systems-level, dynamic relationships between transcription factor (TF) binding and global gene expression programs as multipotent cells differentiate. We combined global ChIPSeq of GATA1, GATA2 and PU.1 with expression profiling during differentiation to erythroid and neutrophil lineages. Our analysis reveals (i) differential complexity of sequence motifs bound by GATA1, GATA2 and PU.1; (ii) the scope and interplay of the GATA1 and GATA2 programs within, and during transitions between, different cell compartments, and the extent of their hard-wiring by DNA motifs; (iii) the potential to predict gene expression trajectories based on global associations between TF-binding data and target gene expression and (iv) how dynamic modeling of DNA-binding and gene expression data can be used to infer regulatory logic of TF circuitry. This 'rubric' exemplifies the utility of this cross-platform resource for deconvoluting the complexity of transcriptional programs controlling stem/progenitor cell fate in hematopoiesis. We examine binding of three factors Gata1, Gata2 and Pu1 at 3 stages of differentiation (multipotential, 5 days of erytroid and neutrophil) , while looking at 2 intermeditate stages of erythroid differentiation for factors Gata2 and Gata1. We also look at Gata2 and Gata1 binding after Gata1 induction using an ER fusion protein.

2013-10-17 | E-GEOD-50406 | biostudies-arrayexpress

RNAi-independent role for Argonaute2 in CTCF/CP190 chromatin insulator function

Project description:Chromatin insulators and Polycomb group (PcG) complexes control nuclear organization to effect changes in gene expression. In Drosophila, RNA silencing pathways influence long range interactions mediated by PcG proteins and nuclear localization of the gypsy insulator; however, the underlying mechanisms are unknown. Here, we identify a singular requirement for Argonaute2 (AGO2) for the activity of the CCCTC-binding factor (CTCF)/Centrosomal protein 190 (CP190) dependent Fab-8 insulator. AGO2 and CP190 interact physically, and genome wide localization of AGO2 by chromatin immunoprecipitation and sequencing (ChIP-seq) reveals extensive colocalization of AGO2 with insulators and Polycomb Response Elements (PREs) but minimal overlap with regions of endogenous small interfering RNA (endo-siRNA) production. Finally, depletion of either CTCF or CP190 results in loss of AGO2 association with insulators, PREs, and other cis-regulatory regions. Our findings suggest that Dicer-independent recruitment of AGO2 to chromatin by insulator proteins promotes the definition of transcriptional domains throughout the genome. ChIP-seq of AGO2 in two Drosophila cell types (S2 and S3)

2011-08-15 | E-GEOD-22623 | biostudies-arrayexpress

The role of FOG-1 in GATA-1 transcriptional regulation of megakaryocyte differentiation

2012-03-05 | GSE35695 | GEO

The role of FOG-1 in GATA-1 transcriptional regulation of megakaryocyte differentiation

Project description:We explored the role of FOG-1 in GATA-1 transcriptional regulation of megakaryocyte differentiation through expression of wild-type GATA-1 and the FOG-binding mutant of GATA-1 (GATA-1^V205G) in G1ME cells. G1ME cells were derived from Gata1-null mouse ES cells and have both megakaryocyte and erythrocyte differentiation potential upon reconstitution of GATA-1 expression (Stachura 2006). HA-tagged wild-type or mutant GATA-1 were expressed in G1ME cells grown in TPO via retroviral transductions. The cells were sorted for GFP positivity 68 hours post-transduction and then were allowed to recover in normal growth medium for 4h. Total RNA was then isolated using RNeasy kit from Qiagen 72 hours post-transduction.

2012-03-05 | E-GEOD-35695 | biostudies-arrayexpress

Genome-wide analysis of the role of FOG-1 in GATA-1 chromatin occupancy

Project description:We report ChIP-Seq data for GATA-1 and the FOG-binding mutant of GATA-1 (GATA-1^V205G) in G1ME cells, a Gata1-null cell line with both erythroid and megakaryocytic differentiation potential. We introduced HA-tagged GATA-1 or V205G into G1ME cells via retroviral transduction. The cells were crosslinked at 48h post-transduction, and an HA antibody was used for chromatin immunoprecipitation (ChIP). ChIP and input samples were sequenced on Illumina GAII high-throughput sequencer. The data reveal GATA-1-specific and V205G-specific bidning sites, indicating that FOG-1 both faacilitates and prohibits GATA-1 chromatin occupancy in a context-dependent manner.

2012-07-30 | GSE35644 | GEO

Genome-wide analysis of the role of FOG-1 in GATA-1 chromatin occupancy

2012-07-30 | GSE35644 | GEO

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