A CpG island promoter drives the CXXC5 gene expression

Abstract

CXXC5 is a member of the zinc-finger CXXC family that binds to unmethylated CpG dinucleotides. CXXC5 modulates gene expressions resulting in diverse cellular events mediated by distinct signaling pathways. However, the mechanism responsible for CXXC5 expression remains largely unknown. We found here that of the 14 annotated CXXC5 transcripts with distinct 5′ untranslated regions encoding the same protein, transcript variant 2 with the highest expression level among variants represents the main transcript in cell models. The DNA segment in and at the immediate 5′-sequences of the first exon of variant 2 contains a core promoter within which multiple transcription start sites are present. Residing in a region with high G–C nucleotide content and CpG repeats, the core promoter is unmethylated, deficient in nucleosomes, and associated with active RNA polymerase-II. These findings suggest that a CpG island promoter drives CXXC5 expression. Promoter pull-down revealed the association of various transcription factors (TFs) and transcription co-regulatory proteins, as well as proteins involved in histone/chromatin, DNA, and RNA processing with the core promoter. Of the TFs, we verified that ELF1 and MAZ contribute to CXXC5 expression. Moreover, the first exon of variant 2 may contain a G-quadruplex forming region that could modulate CXXC5 expression.

A prelude to the proximity interaction mapping of CXXC5

“…Based on these analyses, we assessed the possible association of CXXC5 or MeCP2 with the promoter region of HDAC11 , NFKBIZ , or IL12A in MCF7 cells. We also used as a negative control Exon10 of CXXC5 , which is highly methylated 64 and to which MeCP2 does not show binding as assessed with the Cistrome Data Browser (data not shown). Cells transiently transfected with the expression vector bearing the 3F-CXXC5 or HA-MeCP2 cDNA for 48 h were subjected to ChIP using the Flag or HA antibody followed by qPCR using primers specific to the promoter region of HDAC11 , NFKBIZ, IL12A , or Exon10 of CXXC5 .…”