High expression of the transcription factor ZFX is correlated with proliferation, tumorigenesis, and patient survival in multiple types of human cancers. However, the mechanism by which ZFX influences transcriptional regulation has not been determined. We performed ChIP-seq in four cancer cell lines (representing kidney, colon, prostate, and breast cancers) to identify ZFX binding sites throughout the human genome. We identified roughly 9000 ZFX binding sites and found that most of the sites are in CpG island promoters. Moreover, genes with promoters bound by ZFX are expressed at higher levels than genes with promoters not bound by ZFX. To determine if ZFX contributes to regulation of the promoters to which it is bound, we performed RNA-seq analysis after knockdown of ZFX by siRNA in prostate and breast cancer cells. Many genes with promoters bound by ZFX were down-regulated upon ZFX knockdown, supporting the hypothesis that ZFX acts as a transcriptional activator. Surprisingly, ZFX binds at +240 bp downstream from the TSS of the responsive promoters. Using Nucleosome Occupancy and Methylome Sequencing (NOMe-seq), we show that ZFX binds between the open chromatin region at the TSS and the first downstream nucleosome, suggesting that ZFX may play a critical role in promoter architecture. We have also shown that a closely related zinc finger protein ZNF711 has a similar binding pattern at CpG island promoters, but ZNF711 may play a subordinate role to ZFX. This functional characterization of ZFX provides important new insights into transcription, chromatin structure, and the regulation of the cancer transcriptome.

转录因子 ZFX 的高表达与多种人类癌症的增殖、肿瘤发生和患者生存相关。然而，ZFX影响转录调控的机制尚未确定。我们在四种癌细胞系（代表肾癌、结肠癌、前列腺癌和乳腺癌）中进行了 ChIP-seq，以确定整个人类基因组中的 ZFX 结合位点。我们鉴定了大约 9000 个 ZFX 结合位点，发现大多数位点位于 CpG 岛启动子中。此外，具有与ZFX结合的启动子的基因比具有未与ZFX结合的启动子的基因表达水平更高。为了确定 ZFX 是否有助于对其所结合的启动子的调节，我们在前列腺癌细胞和乳腺癌细胞中通过 siRNA 敲低 ZFX 后进行了 RNA-seq 分析。许多具有与 ZFX 结合的启动子的基因在 ZFX 敲低后被下调，支持了 ZFX 作为转录激活剂的假设。令人惊讶的是，ZFX 结合在响应启动子 TSS 下游 +240 bp 处。使用核小体占据和甲基化测序 (NOMe-seq)，我们发现 ZFX 结合在 TSS 的开放染色质区域和第一个下游核小体之间，表明 ZFX 可能在启动子结构中发挥关键作用。我们还表明，密切相关的锌指蛋白 ZNF711 在 CpG 岛启动子处具有相似的结合模式，但 ZNF711 可能发挥 ZFX 的从属作用。 ZFX 的这种功能表征为转录、染色质结构和癌症转录组的调控提供了重要的新见解。