Genome-Wide Analysis Reveals Unique Regulation of Transcription of Th2-Specific Genes by GATA3

Abstract

Differentiation of naive CD4 T cells into Th2 cells is accompanied by chromatin remodeling and increased expression of a set of Th2-specific genes, including those encoding Th2 cytokines. IL-4–mediated STAT6 activation induces high levels of transcription of GATA3, a master regulator of Th2 cell differentiation, and enforced expression of GATA3 induces Th2 cytokine expression. However, it remains unclear whether the expression of other Th2-specific genes is induced directly by GATA3. A genome-wide unbiased chromatin immunoprecipitation assay coupled with massive parallel sequencing analysis revealed that GATA3 bound to 1279 genes selectively in Th2 cells, and 101 genes in both Th1 and Th2 cells. Simultaneously, we identified 26 highly Th2-specific STAT6-dependent inducible genes by DNA microarray analysis-based three-step selection processes, and among them 17 genes showed GATA3 binding. We assessed dependency on GATA3 for the transcription of these 26 Th2-specific genes, and 10 genes showed increased transcription in a GATA3-dependent manner, whereas 16 genes showed no significant responses. The transcription of the 16 GATA3-nonresponding genes was clearly increased by the introduction of an active form of STAT6, STAT6VT. Therefore, although GATA3 has been recognized as a master regulator of Th2 cell differentiation, many Th2-specific genes are not regulated by GATA3 itself, but in collaboration with STAT6.

Functionally distinct Gata3/Chd4 complexes coordinately establish T helper 2 (Th2) cell identity

“…Recent genome-wide analyses suggest that Gata3 mediates both activating and repressive gene regulation (4,5). We therefore reasoned that Gata3 might interact with different cofactors to perform appropriate regulatory functions.…”

“…Several lines of evidence identify Gata3 as a regulator of histone modifications, including histone H3-K9 acetylation (H3-K9Ac); H3-K4me1, 2, and 3; and H3-K27me3 (4,5,15). Such modifications influence transcription by modulating interactions of transcription factors with chromatin (16).…”

“…Among the six vertebrate homologs, Gata1-3 play key roles in the development and maintenance of hematopoietic and immune cells (2). Gata3 plays a critical role in T-cell development in the thymus; it has roles in the CD4 vs. CD8 lineage choice and at the β-selection checkpoint (3), as well as in T helper 2 (Th2) cell differentiation through the activation and repression of transcription (4,5). After antigenic stimulation in a particular cytokine milieu, naïve CD4 T cells differentiate into one of several Th cell subsets including Th1 and Th2 cells (6).…”

“…Conversely, the overexpression of Gata3 in Th1 cells switches their polarity to a Th2 phenotype (11). Recent genome-wide analyses using chromatin immunoprecipitation and microarray analysis (ChIP-chip), ChIP sequence, and RNA sequence (4,5,12) have indicated that Gata3 can directly or indirectly control a large number of Th2 cell-specific genes, as well as other genes including transcription factors such as T-bet (encoded by Tbx21), a key regulator of Th1 cell fate determination (13). Despite its fundamental importance, little is known regarding how the Gata3 transcriptional complex positively and negatively regulates T-cell lineage gene profiles in a cell type-specific manner.…”

The Interplay between Transcription Factors and Epigenetic Modifications in Th2 Cells

“…Th2-speciic genes, which have been identiied by gene expression proiling [8,9], participate in this regulatory network and are controlled by neither, either or both GATA3 and Menin [10]. In fact, GATA3 or Menin deletion results in the loss of Th2 identity [10,11].…”