Genomic Organization of Two Novel Genes on Human Xq28: Compact Head to Head Arrangement of IDH and TRAP Is Conserved in Rat and Mouse

are associated with CpG islands. A large proportion of In this paper we present the entire genomic segenes with a tissue-restricted expression pattern also quence as well as the cDNA sequence of two new hucontain CpG islands. An interesting feature of CpG man genes encoding the g subunit of the NAD-depenislands is that at least some are capable of initiating dent isocitrate dehydrogenase (H-IDHg) and the transcription in both directions (Faranda et al., 1996; translocon-associated protein d subunit (TRAPd). Shinya and Shimada, 1994; Wright et al., 1995). These genes are located on region q28 of the human The two human genes described in this article encode X chromosome, approximately 70 kb telomeric to the the g subunit of the NAD-dependent isocitrate dehyadrenoleukodystrophy locus (ALD). The sequences of drogenase (H-IDHg) and the d subunit of the translothe transcripts of both genes were obtained by searchcon-associated protein (TRAPd). The gene products ing the EST database with genomic data. Identified show different cellular localizations and are involved in ESTs were completely sequenced and assembled to different biochemical pathways. H-IDHg is a subunit of cDNAs comprising the entire coding region. For IDHg, a heterotetrameric enzyme that is located in mitochonseveral EST clones indicate differential splicing. dria and presumed to play a major role in the oxidative IDHg and TRAPd are arranged in a compact head to decarboxylation of isocitrate in the tricarboxylic acid head manner. The nontranscribed intergenic region cycle (Nichols et al., 1993). TRAPd forms with three represents only 133 bp and is embedded in a CpG isother subunits a protein complex, which is located at land. The CpG island obviously functions as a bidireca specific site on the membrane of the endoplasmic tional promoter to initiate the transcription of both reticulum, the so-called translocon, where nascent sefunctionally unrelated genes with quite distinct excretory proteins enter the ER lumen (Hartmann et al., pression patterns. This exceptional gene arrangement 1993). prompted us to clone and sequence genomic DNA fragments containing the homologous intergenic regions We have obtained the complete genomic sequence of of rat and mouse. We show that in both species this human IDHg and TRAPd in the course of a large-scale area is similarly compact and represents less than 249 sequencing project covering about 400 kb of the region bp in rat and not more than 164 bp in mouse. In both q28 on the X chromosome (M. Platzer et al., in preparacases this intergenic region is embedded in a CpG istion). This region is one of the areas of the human land and is highly conserved with nucleotide identity genome with the highest gene density, approximately values ranging from 70.1% between human and rat to 1 gene every 20 kb, and is extremely G/C-rich (De 92.6% between mouse and rat. q 1997 Academic Press Sario et al., 1996). We present in this paper the genomic organization of the human IDHg and TRAPd genes as an example of an exceptional compact genomic arINTRODUCTION rangement. We have identified the corresponding cDNA clones by exploiting the EST database. The fullThe human genome contains approximately 45,000 length coding sequences of both human genes and of CpG islands (Antequera and Bird, 1993). In both humouse IDHg were obtained by the resequencing and man and mouse species all known housekeeping genes assembling of different EST clones. For comparative analysis of the intergenic region the syntenic loci in mouse and rat were amplified by genomic PCR and Sequence data from this article have been deposited with the EMBL Data Library under Accession Nos. U52111, U52112, Z68907, sequenced. Z69043, U68564, U63009, U73205, U69268, and U69269. 1 To whom correspondence should be addressed at Institut für MoMATERIALS AND METHODS lekulare Biotechnologie, Abteilung für Genomanalyse, Beutenbergstrasse 11, 07745 Jena, Germany. Telephone: 0049-3641-656242. Genomic sequencing. The human cosmid clones 10E8 and E153 were sequenced using a combination of the shotgun approach and Fax: 0049-3641-656255. E-mail: [email protected].