ChIP-seq analysis of genome-wide DNA-binding by STAT3 alternative spliceforms following Oncostatin M stimulation

Alternative splicing in the Signal Transducer and Activator of Transcription 3 (STAT3) transcription factor gene generates the STAT3α and STAT3β spliceforms that have identical DNA-binding domains but C-terminal transactivation domains that differ in both length and sequence. To delineate the impact that the different STAT3α and STAT3β transactivation domains have on cytokine-activated genome-wide DNA-binding, we measured STAT3α and STAT3β DNA-binding at identified STAT3 transcription factor binding sites within the mouse genome using cells engineered to express either the STAT3α or STAT3β spliceform only. The analyses show that ~40% of STAT3-bound genomic regions (2280 of 5343 regions) are commonly targeted by both STAT3 spliceforms. The remaining STAT3-bound genomic regions are preferentially targeted by either STAT3α or STAT3β (1450 and 1613 regions, respectively) and associated with genes enriched in unique biological functions. Motif enrichment analyses not only confirm the targeting of the canonical STAT3 target DNA motif by both spliceforms but reveal several co-occurring DNA motifs known to be targeted by transcription factors that can act cooperatively with STAT3 during target gene transcription regulation. Multiple additional co-occurring DNA motifs selectively enriched in STAT3α- or STAT3β-associated regions were also identified. NGS analysis of ChIP DNA prepared from STAT3-/- Mouse Embryonic Fibroblasts re-expressing only STAT3α and STAT3β following treatment with Oncostatin M