| Summary: | <p>Abstract</p> <p>Background</p> <p>The programmed cell death 2 (<it>Pdcd2</it>) gene on mouse chromosome 17 was evaluated as a member of a highly conserved synteny, a candidate for an imprinted locus, and a candidate for the Hybrid sterility 1 (<it>Hst1</it>) gene.</p> <p>Results</p> <p>New mouse transcripts were identified at this locus: an alternative <it>Pdcd2 </it>mRNA skipping the last two coding exons and two classes of antisense RNAs. One class of the antisense RNA overlaps the alternative exon and the other the entire <it>Pdcd2 </it>gene. The antisense RNAs are alternative transcripts of the neighboring TATA-binding protein gene (<it>Tbp</it>) that are located mainly in the cell nucleus. Analogous alternative PDCD2 forms truncating the C-terminal domain were also detected in human and chicken. Alternative transcripts of the chicken <it>PDCD2 </it>and <it>TBP </it>genes also overlap. No correlation in the transcription of the alternative and overlapping mRNAs was detected. Allelic sequencing and transcription studies did not reveal any support for the candidacy of <it>Pdcd2 </it>for <it>Hst1</it>. No correlated expression of <it>Pdcd2 </it>with the other two genes of the highly conserved synteny was observed. <it>Pdcd2</it>, <it>Chd1</it>, and four other genes from this region were not imprinted in the embryo.</p> <p>Conclusion</p> <p>The conservation of alternative transcription of the <it>Pdcd2 </it>gene in mouse, human and chicken suggests the biological importance of such truncated protein. The biological function of the alternative <it>PDCD2 </it>is likely to be opposite to that of the constitutive form. The ratio of the constitutive and alternative <it>Pdcd2 </it>mRNAs differs in the tissues, suggesting a developmental role.</p> <p>The identified <it>Tbp-</it>alternative <it>Pdcd2</it>-antisense transcripts may interfere with the transcription of the <it>Pdcd2 </it>gene, as they are transcribed at a comparable level. The conservation of the <it>Pdcd2</it>/<it>Tbp </it>sense-antisense overlap in the mouse and chicken points out its biological relevance. Our results also suggest that some cDNAs in databases labeled as noncoding are incomplete alternative cDNAs of neighboring protein-coding genes.</p>
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