The sequence diversity and transcriptional activity of members of the mouse 4.5 S RNA gene family

Abstract

The 4.5 S RNA is an RNA polymerase III transcript found in rodent cells that has sequence similarity to, but is distinct from, highly abundant B1 interspersed repeats. 4.5 S RNAs are found in the nucleus and cytoplasm hydrogen bonded with poly(A)-terminated RNAs, but their cellular function remains unknown. There are approximately 850 copies of the 4.5 S RNA gene in the mouse haploid genome and it has been reported that the majority exist as single genes on 4.2 kb repeating units in a long tandem array. To characterize this potentially large multigene family, I initiated an investigation of the genomic organization, sequence heterogeneity, and transcriptional properties of individual members. Seven genomic clones containing 4.5 S RNA related sequences were isolated. Three of the seven clones resemble a previously described member of the tandem array but differ most notably by having an additional 13 bases immediately adjacent to the start of the 4.5 S RNA transcript. These three clones define two distinct repeat subclasses based on the flanking sequences and one clone is likely to represent a gene situated at the end of the tandem array. Each of these clones is expressed upon transfection into human tissue culture cells, demonstrating that they are transcriptionally competent. The remaining four genomic clones do not conform to the 4.2 kb tandem repeats. In addition to having completely divergent flanking sequences, each gene contains nucleotide substitutions relative to the 4.5 S RNA sequence. Transcription from these four clones is not detected upon transfection into human cells. Sequence evidence indicates that these clones represent 4.5 S RNA pseudogenes that have arisen by retroposition and in each clone the pseudogene is located in the vicinity of other interspersed repeated elements. Nearly half of the 4.5 S RNA sequences in the mouse genome probably correspond to processed pseudogenes. That the cloned pseudogenes are transcriptionally silent provides an initial indication of what bases may be important in the regulation of 4.5 S RNA gene expression.