Insights into GATA-1-Mediated Gene Activation versus Repression via Genome-wide Chromatin Occupancy Analysis

Abstract

Summary The transcription factor GATA-1 is required for terminal erythroid maturation and functions as an activator or repressor depending on gene context. Yet its in vivo site selectivity and ability to distinguish between activated versus repressed genes remain incompletely understood. In this study, we performed GATA-1 ChIP-seq in erythroid cells and compared it to GATA-1 induced gene expression changes. Bound and differentially expressed genes contain a greater number of GATA binding motifs, a higher frequency of palindromic GATA sites, and closer occupancy to the transcriptional start site versus non-differentially expressed genes. Moreover, we show that the transcription factor Zbtb7a occupies GATA-1 bound regions of some direct GATA-1 target genes, that the presence of SCL/TAL1 helps distinguish transcriptional activation versus repression, and that Polycomb Repressive Complex 2 (PRC2) is involved in epigenetic silencing of a subset of GATA-1 repressed genes. These data provide insights into GATA-1 mediated gene regulation in vivo.

CDC6 expression is regulated by lineage-specific transcription factor GATA1

“…10,12 Our results also validate the finding that CDC6 may be a real target of GATA1, as revealed by genome-wide chromatin occupancy data in mouse cells. 21 Ectopic expression of GATA1 results in increased levels of cdc6, not only in primary hematopoietic progenitors, but also in heterologous 293T cells. This may be somewhat surprising, as GATA1 transcriptional activity is functional in cells distant from the erythro-megakaryocytic lineages, not only on the exogenous reporter construct, but also on the endogenous locus.…”

“…In fact, only a small fraction of the in vitro characterized binding sites are actually occupied, according to various independent genome-wide occupancy analysis. [21][22][23] These reports have defined with further precision GATA1 preferred binding motif and unveiled a rich collection of targets that suggests a more global action of GATA 1 that would affect not only the lineage-specific program, but also cell processes such as signaling and cell cycle control.…”

“…19,20 GATA1 also cooperates with master hematopoietic regulator Scl/Tal1 at composite sites containing (CANNTG)-WGATAR sequences. 21,22 However, simple identification of putative single double, or composite GATA binding sequences, even when phylogenetically conserved, is a poor predictor of their use by GATA1. In fact, only a small fraction of the in vitro characterized binding sites are actually occupied, according to various independent genome-wide occupancy analysis.…”

Epigenetic silencing of Bim transcription by Spi-1/PU.1 promotes apoptosis resistance in leukaemia

“…The free pool of MCL-1 in a low BIM context might inhibit apoptosis by neutralizing other proapoptotic factors such as BAX/BAK, tBID and PUMA that are expressed in preleukaemic cells and are capable to interact with MCL-1. 37 BIM expression is regulated at the transcriptional and translational level in many cell types. The EPO signalling pathway through ERK-mediated phosphorylation of BIM induces its proteasomal degradation in erythroid cells.…”

“…29,33,46,47 Recruitment of PRC2 by GATA-1 has been reported during normal erythroid differentiation. 37 Abnormal recruitment of PRCs by the oncogenic transcription factors PML-RARa 48 and PLZF-RARa 49 participates in leukaemic transformation. PRC2 might also associate with CG-rich sequences in genes devoid of DNA motifs for transcriptional activators in ES cells.…”