Comparative integromics on JMJD1C gene encoding histone demethylase: Conserved POU5F1 binding site elucidating mechanism of JMJD1C expression in undifferentiated ES cells and diffuse-type gastric cancer

Epigenetic modifications of genomic DNA and histones alter the chromatin structure to regulate the accessibility of transcription factors to the promoter or enhancer regions. In 2003, we identified and characterized JMJD1C (TRIP8) consisting of TRI8H1 domain with C2HC4-type zinc finger-like motif, TRI8H2 domain with thyroid hormone receptor β-binding region, and JmjC domain. JMJD1A (TSGA), JMJD1B (5qNCA) and JMJD1C with the common domain architecture are histone H3K9 demethylases implicated in the nuclear hormone receptor-based transcriptional regulation. Here, comparative integromics on JMJD1C gene is reported. JMJD1C variant 1, previously reported, consists of exons 1, 2 and 3-26, while JMJD1C variant 2 characterized in this study was transcribed from novel exon 1B located 5' to exon 3. Four human JMJD1C ESTs were transcribed from exon 1, while 14 human JMJD1C ESTs from exon 1B. All of 26 mouse Jmjd1c ESTs were transcribed from exon 1b. These facts indicate that JMJD1C variant 2 transcribed from exon 1B was the major transcript. Human JMJD1C variant 2 with TRI8H1, TRI8H2, and JmjC domains showed 85.7% total-amino-acid identity with mouse Jmjd1c. Human JMJD1C mRNA was expressed in undifferentiated embryonic stem (ES) cells, pancreatic islet, diffuse-type gastric cancer, and other tissues or tumors. Mouse Jmjd1c mRNA was expressed in fertilized egg, blastocyst, undifferentiated ES cells, embryonic germ cells, c-Kit+/Sca-1+/Lin− hematopoietic stem cells, pancreatic islet, and other tissues. Comparative genomics analyses revealed that binding sites for POU5F1 (OCT3/OCT4), AP-1, and bHLH transcription factors within the promoter region located 5' to exon 1B of human JMJD1C gene were conserved in chimpanzee, cow, mouse and rat JMJD1C orthologs. POU5F1-mediated expression of JMJD1C histone demethylase is implicated in the reactivation of silenced genes in undifferentiated ES cells, pancreatic islet, and diffuse-type gastric cancer.