ZFX acts as a transcriptional activator in multiple types of human tumors by binding downstream from transcription start sites at the majority of CpG island promoters

Abstract

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.

CRISPR-mediated deletion of prostate cancer risk-associated CTCF loop anchors identifies repressive chromatin loops

“…All ChIP-seq samples were performed in duplicate according to a previously published protocol [ 57 – 59 ]. Five micrograms of CTCF antibody (Active Motif #61311) was used to precipitate 20 μg chromatin for 22Rv1, PrEC, RWPE-2, VCaP (rep1) cells, and 10 ul CTCF antibody (Cell Signaling #3418S) were used to precipitate 20 μg chromatin for LNCaP, C4-2B, RWPE-1, VCaP (rep2) cells.…”

HOXA-AS2 promotes type I endometrial carcinoma via miRNA-302c-3p-mediated regulation of ZFX

“…ZFX can be used as a prognostic biomarker for malignant tumors [ 47 , 50 , 52 ]. ZFX acts as a transcriptional activator in various human malignancies mainly by binding downstream of the transcription initiation site in the CpG island promoter of target genes [ 53 ]. Recent studies have shown that miRNAs affect the biological behavior of tumors by regulating ZFX.…”

<p>Clinical Significance of ZNF711 in Human Breast Cancer</p>

“…21 ZNF711 and zinc-finger protein X-linked (ZFX) are known to bind to gene promoter regions in the breast cancer cell line MCF7 and participate in transcriptional regulation. 9 However, the specific function and mechanism of ZNF711 in breast cancer cells remain unclear. In this study, the association between ZNF711 expression and clinical characteristics was analyzed in breast cancer patients.…”

“…Zinc-finger proteins are correlated with tumorigenesis and the development of multiple types of human cancers and may be useful as prognostic factors. [4][5][6][7][8][9] ZNF711 is a newly discovered zinc-finger protein involved in the development of neurons. Recent studies have shown that ZNF711 is expressed in BCa cell lines, but its function and regulatory mechanisms are unclear.…”