Complex RNA processing of TDRKH, a novel gene encoding the putative RNA-binding tudor and KH domains

Abstract

The sequence from a human EST (IMAGE:259322) with homology to the nucleotide-sensitive chloride conductance regulator (ICln) was used to screen a human aortic cDNA library. The probe sequence was from a region of the EST lacking homology to ICln, and the goal was to isolate an ICln-like gene. A 2843bp cDNA clone with an open reading frame coding for a 561 amino acid protein was isolated. This clone had no homology to ICln. PROSITE analysis of the putative protein sequence reveals one tudor and two K homology (KH) domains. The gene has therefore been named TDRKH. Both KH and tudor motifs are involved in binding to RNA or single-strand DNA. PCR analysis demonstrated that TDRKH is alternatively spliced in several ways and alternatively polyadenylated at multiple sites. Northern analysis confirmed the presence of messages of multiple lengths with predominant bands at 2.8 and 4.0 kb and also demonstrated that TDRKH is widely expressed in human tissues. Within an intron of TDRKH, there is a region with 90% homology to ICln. This sequence, which is incorporated into the alternatively spliced message represented by IMAGE:259322, contains a 2 bp deletion that disrupts the ICln reading frame and therefore represents an ICln pseudogene. The TDRKH gene was mapped to the Epidermal Differentiation Complex (EDC) at chromosome 1q21 by radiation hybrid mapping and STS content of genomic clones from that region. The EDC contains a large cluster of related genes involved in terminal differentiation of the epidermis. It remains to be determined whether TDRKH has a specific role in epithelial function.