Aspartyl beta -hydroxylase (Asph) and an evolutionarily conserved isoform of Asph missing the catalytic domain share exons with junctin

The mouse aspartyl beta-hydroxylase gene (Asph, BAH) has been cloned and characterized. The mouse BAH gene spans 200 kilobase pairs of genomic DNA and contains 24 exons. Of three major BAH-related transcripts, the two largest (6,629 and 4,419 base pairs) encode full-length protein and differ only in the use of alternative polyadenylation signals. The smallest BAH-related transcript (2,789 base pairs) uses an alternative 3' terminal exon, resulting in a protein lacking a catalytic domain. Evolutionary conservation of this noncatalytic isoform of BAH (humbug) is demonstrated in mouse, man, and Drosophila. Monoclonal antibody reagents were generated, epitope-mapped, and used to definitively correlate RNA bands on Northern blots with protein species on Western blots. The gene for mouse junctin, a calsequestrin-binding protein, was cloned and characterized and shown to be encoded from the same locus. When expressed in heart tissue, BAH/humbug preferably use the first exon and often the fourth exon of junctin while preserving the reading frame. Thus, three individual genes share common exons and open reading frames and use separate promoters to achieve differential expression, splicing, and function in a variety of tissues. This unusual form of exon sharing suggests that the functions of junctin, BAH, and humbug may be linked.

RNA mapping: selection of potent oligonucleotide sequences for antisense experiments

The importance of finding good antisense sequences cannot be underestimated. Poor inhibition of the targeted protein can compromise the final outcome of an antisense experiment, making it difficult to arrive at a definitive understanding of the function of the protein of interest. In antisense therapeutics, identification of potent sequences becomes even more important. RNA mapping greatly increases the odds of finding active sequences. When antisense sequences are selected randomly or by gene walking, a substantial number of the oligonucleotides have little to no activity. In contrast, oligonucleotides selected by RNA mapping typically produce an antisense inhibition of greater than 50%. Oligonucleotides targeted to 60% of the accessible sites in the 5' portion of the multidrug resistance transcript inhibited P-glycoprotein function with high potency. In the angiotensin type 1 receptor system, oligonucleotides to the eight accessible sites examined inhibited AT1 receptor binding by at least 50%, with oligonucleotides to four of the sites producing at least 70% inhibition. The RNA mapping assay, which is based on standard molecular techniques, therefore provides an easy and reliable method for potent antisense sequence selection.

Biased VH gene usage in early lineage human B cells: evidence for preferential Ig gene rearrangement in the absence of selection

Certain VH genes are predominantly expressed in mature B cells. We hypothesized that several, mutually nonexclusive VH-dependent mechanisms operating at distinct stages during B cell development may be responsible for overrepresentation of these VH genes. In the present study, we have assessed whether one of the mechanisms involves preferential rearrangement at the pro-B cell stage. The frequency of individual VH4 and VH3 genes in rearrangement libraries from FACS-purified human CD34+/CD19+ pro-B and CD34-/CD19+ pre-B cells was assessed. The in-frame and out-of-frame rearrangements from both cell populations were analyzed using a high resolution PAGE system. The frequencies of individual VH gene segments among out-of-frame rearrangements from pro-B cells were determined, because these frequencies should reflect only processes before the translation of the mu-heavy chain and should not be biased by selection mechanisms. Our results demonstrate that, at the pro-B cell stage, the V4-34, V4-39, and V4-59 gene segments are the most frequently rearranged VH4 family genes, and the V3-23 and V3-30 gene segments are the most frequently rearranged VH3 family genes. This finding suggests that the predominant expression of these VH genes in peripheral mature B cells is determined to a significant degree by their preferential rearrangement during V-DJ recombination.