Abstract 3858: Transcribed locus Hs.633957: A new tumor-associated primate-specific gene with possible microRNA function
Authors: Polev Dmitrii E. , Krukovskaia Larisa , Karnaukhova Iuliia , Kozlov Andrei 
Published: June 2012

Transcribed locus Hs.633957 had been previously shown to be over-expressed in various tumors, but its function remained unknown. We conducted a combined experimental and bioinformatical analysis of the locus to get an insight into its function. We used RACE (Rapid Amplification of cDNA Ends) to define the boundaries of the transcribed part of the locus and RT-PCR to identify its splice-forms. We analyzed the public data on chromatin modifications and association with transcription factors available at UCSC Genome Browser and modeled the RNA secondary structure using Vienna RNA Websuite.

We found out that locus Hs.633957 has a focused promoter with transcription start site varying within 35 bp. There are two introns in the locus: the first one is obligatory and the second is facultative. The first intron has three alternative 3’-acceptor splice sites. There are 2 possible polyadenylation sites. The maximum RNA length is 1003 nt, but the major transcription variant is about 630 nt length, and it resembles EST BX119057. Hs.633957 appeared to have its own promoter, with a GC-box-containing core promoter and 3 c-Myc/Max-dependent proximal promoter elements. One of these elements contains 7 E-boxes, which most probably makes this gene highly responsive to c-Myc and explains it's over expression in tumors. There are other transcription factor binding sites within the promoter region as well, but their significance is less obvious.

We BLASTed the gene RNA sequence against all available mRNAs, but did not find any orthologous or paralogous sequences. Thus this is a unique gene, which does not belong to any gene family. It is very unlikely to code for any proteins and we decided that it is more probable to be a RNA-gene. We used Vienna RNA Websuite to model the RNA secondary structure and identified a pre-miRNA-like hairpin within the structure. The aim strand of the predicted mature miRNA is highly complementary to a region in the DPYS mRNA. Of the 22 nucleotides 21 are complementary to the target sequence and only the ninth nucleotide is not complementary, which is considered obligatory for miRNAs. The gene DPYS codes for the dihydropyrimidinase protein, which catalyzes the second step of the reductive pyrimidine degradation. If proven to be true, this prediction means that Hs.633957 may play role in control of cell cycle through the regulation of pyrimidine katabolism.

Phylogenetic analysis of the gene revealed that it's functional and regulatory elements appeared together with the potential target site in DPYS before the divergence of the Old and New World monkeys.

We consider the transcribed locus Hs.633957 to be a novel primate-specific cancer gene with a possible miRNA function.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 3858. doi:10.1158/1538-7445.AM2011-3858