Bioinformatic analysis of the human DHRS4 gene cluster and a proposed mechanism for its transcriptional regulation

Abstract

BackgroundThe human DHRS4 gene cluster consists of three genes, DHRS4, DHRS4L2 and DHRS4L1. Among them, DHRS4 encodes NADP(H)-dependent retinol dehydrogenase/reductase. In a previous study, we investigated the alternative splicing of DHRS4 and DHRS4L2. DHRS4L1 was added to the gene cluster recently, but little is known about its structure and expression. To reveal the regulatory mechanism of the DHRS4 gene cluster expression, we studied the structure and transcription of DHRS4L1 in the context of the transcriptional behaviors of the human DHRS4 gene cluster. Based on the results of bioinformatics analysis, we propose a possible mechanism for the transcriptional regulation of the human DHRS4 gene cluster.ResultsThe homologous comparison analysis suggests that DHRS4, DHRS4L2 and DHRS4L1 are three homologous genes in human. DHRS4L1 and DHRS4L2 are paralogues of DHRS4, and DHRS4L2 is the most recent member of the DHRS4 gene cluster. In the minus strand of the human DHRS4 gene cluster, a gene transcribed in an antisense direction was found containing a 5' sequence overlapping the region of exon 1 and promoter of DHRS4. By cloning the full length of RNA variants through 5'RACE and 3'RACE, we identified two transcription start sites, within exon a2 and exon 1, of this newly named gene DHRS4L1 using neuroblastoma cell line BE(2)-M17. Analysis of exon composition in the transcripts of DHRS4 gene cluster revealed that exon 1 was absent in all the transcripts initiated from exon a1 of DHRS4L2 and exon a2 of DHRS4L1.ConclusionsAlternatively spliced RNA variants are prevalent in the human DHRS4 gene cluster. Based on the analysis of gene transcripts and bioinformatic prediction, we propose here that antisense transcription may be involved in the transcriptional initiation regulation of DHRS4 and in the posttranscriptional splicing of DHRS4L2 and DRHS4L1 for the homologous identity of DHRS4 gene cluster. Beside the alternative transcriptional start sites, the antisense RNA is novel possible factor serving to remove exon 1 from the transcripts initiated from exon a1 and exon a2.

Comprehensive identification and characterization of somatic copy number alterations in triple‑negative breast cancer

“…Another candidate gene dehydrogenase/reductase 4 like 2 (DHRS4L2) is located in the deletion region of 14q11.2 and is a member of the short-chain dehydrogenases/reductases family. DHRS4L2 produces multiple transcript variants through alternative splicing (55,56). The encoded protein may be an NADPH dependent retinol oxidoreductase.…”

“…The encoded protein may be an NADPH dependent retinol oxidoreductase. Genomic loss of DHRS4L2 may lead to low expression and has been demonstrated to be associated with risk of diseases (56,57). The DHRS4L2 gene has not yet been reported to be involved in cancer and could be considered a novel candidate gene for TNBC.…”

Identification of a novel isoform of DHRS4 protein with a nuclear localization signal

“…The majority of genes are alternatively spliced to express multiple proteins to increase the proteomic complexity, correlating with physiological function (Maniatis and Tasic, 2002;Modrek et al, 2001;Neverov et al, 2005), cell differentiation (Terenzi et al, 2009;Valenzuela et al, 2004), and certain diseases of human body (Tazi et al, 2009). We have previously reported that alternatively spliced RNAs are common in the posttranscriptional processing of DHRS4, DHRS4L2, and DHRS4L1, which comprise the human DHRS4 gene cluster (Du et al, 2004;Song et al, 2007;Su et al, 2010;Zhang et al, 2009a), while only one spliced variant protein, NRDRB1, of the DHRS4 gene was identified in human cervical squamous carcinoma tissues and HeLa cells. NRDRB1 has a complete deletion of exon 3, and is considered associated with cervical tumorigenesis (Song et al, 2007).…”

CpG island evolution in the mammalian DHRS4 gene cluster and its role in the regulation of gene transcription

“…Total RNA was extracted from the mouse, chimpanzee, and human cell lines and prepared as described in a previous study (Su et al, 2010). In short, the RNA was extracted using TRIzol ® reagent (Invitrogen) and reverse-transcribed with a QuantiTect Reverse Transcription kit (Qiagen, Venlo, Netherlands).…”

“…Mammals such as mice, pigs, and members of the Canis family possess only one copy of the DHRS4 gene, while the chimpanzee genome harbors both the DHRS4 gene and its copy DHRS4L1. On the other hand, humans express a DHRS4 gene cluster comprising three homologous genes: DHRS4, DHRS4L2, and DHRS4L1 (Su et al, 2010). The copied DHRS4 gene cluster is arranged in tandem in chromosome 14 of the chimpanzee and human genome.…”