Supplementary Figure 2 - Endometrial stromal cells - Genomic annotation of GATA2 and PGR ChIPseq

Cistromic analysis revealed similar genome-wide binding of GATA2 to promoter regions in both Veh and IVD-treated cells.<br>Supplementary dataset supporting manuscript currently under review.<br>Abstract: The transcription factor GATA2 is important for endometrial stromal cell decidualization in early pregnancy. Progesterone receptor (PGR) is also critical during decidualization but its interaction with GATA2 in regulating genes and pathways necessary for decidualization in human endometrium are unclear. RNA-sequencing (RNA-seq) was performed to compare gene expression profiles (n=3) and chromatin immunoprecipitation followed by sequencing (ChIP-seq) using an antibody against GATA2 (n=2) was performed to examine binding to target genes in human endometrial stromal cells undergoing in vitro decidualization (IVD including estrogen, progestin and cAMP analogue) or vehicle treatment. We identified 1232 differentially expressed genes (DEGs) in IVD vs. vehicle. GATA2 cistrome in IVD-treated cells was enriched with motifs for GATA, ATF, and JUN, and gene ontology analysis of GATA2 cistrome revealed pathways that regulate cholesterol storage, p38 MAPK and the c-Jun N-terminal kinase cascades. Integration of RNA-seq and ChIP-seq data revealed that the PGR motif is highly enriched at GATA2 binding regions surrounding upregulated genes in IVD-treated cells. The integration of a mined public PGR cistrome in IVD-treated human endometrial cells with our GATA2 cistrome showed that GATA2 binding was significantly enhanced at PGR-binding regions in IVD vs. vehicle. Interrogating two separate ChIP-seq datasets together with RNA-seq revealed integration of GATA2 and PGR action to co-regulate biologic processes during decidualization of human endometrial stromal cells, specifically via WNT activation and stem cell differentiation pathways. These findings reveal the key pathways that are co-activated by GATA2 and PGR that may be therapeutic targets for supporting implantation and early pregnancy.

顺反组分析（Cistromic analysis）显示，在溶剂处理（Veh）和体外蜕膜化处理（IVD）的细胞中，GATA2在全基因组范围内与启动子区域的结合模式相似。
支持当前处于评审阶段手稿的补充数据集。
摘要：转录因子GATA2对早孕期间子宫内膜基质细胞蜕膜化至关重要。孕酮受体（Progesterone receptor，PGR）在蜕膜化过程中也发挥关键作用，但其与GATA2在调控人类子宫内膜蜕膜化所需基因及通路中的相互作用尚不明确。本研究通过RNA测序（RNA-sequencing，RNA-seq）比较基因表达谱（n=3），并利用抗GATA2抗体进行染色质免疫沉淀测序（chromatin immunoprecipitation followed by sequencing，ChIP-seq）（n=2），以检测经历体外蜕膜化（in vitro decidualization，IVD，含雌激素、孕激素及环腺苷酸类似物）或溶剂处理的人类子宫内膜基质细胞中GATA2与靶基因的结合情况。我们在IVD处理组与溶剂处理组中鉴定出1232个差异表达基因（differentially expressed genes，DEGs）。IVD处理细胞中的GATA2顺反组富含GATA、ATF及JUN基序；对GATA2顺反组的基因本体论分析（gene ontology analysis）显示，其涉及调控胆固醇储存、p38丝裂原活化蛋白激酶（p38 MAPK）及c-Jun氨基末端激酶级联反应（c-Jun N-terminal kinase cascades）的通路。整合RNA-seq与ChIP-seq数据发现，在IVD处理细胞中，上调基因周围的GATA2结合区域高度富集PGR基序。将挖掘到的IVD处理人类子宫内膜细胞中公开的PGR顺反组与本研究的GATA2顺反组整合分析显示，与溶剂处理组相比，IVD处理组中PGR结合区域的GATA2结合显著增强。联合分析两个独立的ChIP-seq数据集与RNA-seq数据发现，GATA2与PGR协同作用，共同调控人类子宫内膜基质细胞蜕膜化过程中的生物学过程，具体通过WNT激活通路及干细胞分化通路实现。这些发现揭示了GATA2与PGR共同激活的关键通路，这些通路或可作为支持胚胎着床及早孕的治疗靶点。