Conserved Alternative and Antisense Transcripts at the Programmed Cell Death 2 Locus

Overview

Journal BMC Genomics

Publisher Biomed Central

Specialty Genetics

Date 2007 Jan 20

PMID 17233890

Citations 6

Authors

Ondrej Mihola

Jiri Forejt

Zdenek Trachtulec

Affiliations

Soon will be listed here.

Abstract

Background: The programmed cell death 2 (Pdcd2) 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 (Hst1) gene.

Results: New mouse transcripts were identified at this locus: an alternative Pdcd2 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 Pdcd2 gene. The antisense RNAs are alternative transcripts of the neighboring TATA-binding protein gene (Tbp) 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 PDCD2 and TBP 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 Pdcd2 for Hst1. No correlated expression of Pdcd2 with the other two genes of the highly conserved synteny was observed. Pdcd2, Chd1, and four other genes from this region were not imprinted in the embryo.

Conclusion: The conservation of alternative transcription of the Pdcd2 gene in mouse, human and chicken suggests the biological importance of such truncated protein. The biological function of the alternative PDCD2 is likely to be opposite to that of the constitutive form. The ratio of the constitutive and alternative Pdcd2 mRNAs differs in the tissues, suggesting a developmental role. The identified Tbp-alternative Pdcd2-antisense transcripts may interfere with the transcription of the Pdcd2 gene, as they are transcribed at a comparable level. The conservation of the Pdcd2/Tbp 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.

Citing Articles

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Prdm9 incompatibility controls oligospermia and delayed fertility but no selfish transmission in mouse intersubspecific hybrids.

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Interallelic and intergenic incompatibilities of the Prdm9 (Hst1) gene in mouse hybrid sterility.

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References

KNEE R, Murphy P . Regulation of gene expression by natural antisense RNA transcripts. Neurochem Int. 1997; 31(3):379-92. DOI: 10.1016/s0197-0186(96)00108-8. View

Yamauchi J, Sugita A, Fujiwara M, Suzuki K, Matsumoto H, Yamazaki T . Two forms of avian(chicken) TATA-binding protein mRNA generated by alternative polyadenylation. Biochem Biophys Res Commun. 1997; 234(2):406-11. DOI: 10.1006/bbrc.1997.6653. View

Wang Q, Zhang Z, Blackwell K, Carmichael G . Vigilins bind to promiscuously A-to-I-edited RNAs and are involved in the formation of heterochromatin. Curr Biol. 2005; 15(4):384-91. DOI: 10.1016/j.cub.2005.01.046. View

Dahary D, Elroy-Stein O, Sorek R . Naturally occurring antisense: transcriptional leakage or real overlap?. Genome Res. 2005; 15(3):364-8. PMC: 551562. DOI: 10.1101/gr.3308405. View

Kiyosawa H, Mise N, Iwase S, Hayashizaki Y, Abe K . Disclosing hidden transcripts: mouse natural sense-antisense transcripts tend to be poly(A) negative and nuclear localized. Genome Res. 2005; 15(4):463-74. PMC: 1074361. DOI: 10.1101/gr.3155905. View

Chistiakov D, Seryogin Y, Turakulov R, Savostanov K, Titovich E, Zilberman L . Evaluation of IDDM8 susceptibility locus in a Russian simplex family data set. J Autoimmun. 2005; 24(3):243-50. DOI: 10.1016/j.jaut.2005.01.017. View

Bastos H, Lassalle B, Chicheportiche A, Riou L, Testart J, Allemand I . Flow cytometric characterization of viable meiotic and postmeiotic cells by Hoechst 33342 in mouse spermatogenesis. Cytometry A. 2005; 65(1):40-9. DOI: 10.1002/cyto.a.20129. View

Kaushik N, Fear D, Richards S, McDermott C, Nuwaysir E, Kellam P . Gene expression in peripheral blood mononuclear cells from patients with chronic fatigue syndrome. J Clin Pathol. 2005; 58(8):826-32. PMC: 1770875. DOI: 10.1136/jcp.2005.025718. View

Shakib K, Norman J, Fine L, Brown L, Godovac-Zimmermann J . Proteomics profiling of nuclear proteins for kidney fibroblasts suggests hypoxia, meiosis, and cancer may meet in the nucleus. Proteomics. 2005; 5(11):2819-38. DOI: 10.1002/pmic.200401108. View

10.

Carninci P, Kasukawa T, Katayama S, Gough J, Frith M, Maeda N . The transcriptional landscape of the mammalian genome. Science. 2005; 309(5740):1559-63. DOI: 10.1126/science.1112014. View

11.

Katayama S, Tomaru Y, Kasukawa T, Waki K, Nakanishi M, Nakamura M . Antisense transcription in the mammalian transcriptome. Science. 2005; 309(5740):1564-6. DOI: 10.1126/science.1112009. View

12.

Werner A, Berdal A . Natural antisense transcripts: sound or silence?. Physiol Genomics. 2005; 23(2):125-31. DOI: 10.1152/physiolgenomics.00124.2005. View

13.

Howell G, Munroe R, Schimenti J . Transgenic rescue of the mouse t complex haplolethal locus Thl1. Mamm Genome. 2005; 16(11):838-46. DOI: 10.1007/s00335-005-0045-8. View

14.

Chen Q, Qian K, Yan C . Cloning of cDNAs with PDCD2(C) domain and their expressions during apoptosis of HEK293T cells. Mol Cell Biochem. 2005; 280(1-2):185-91. DOI: 10.1007/s11010-005-8910-z. View

15.

Gregorova S, Forejt J . PWD/Ph and PWK/Ph inbred mouse strains of Mus m. musculus subspecies--a valuable resource of phenotypic variations and genomic polymorphisms. Folia Biol (Praha). 2000; 46(1):31-41. View

16.

Trachtulec Z, Forejt J . Synteny of orthologous genes conserved in mammals, snake, fly, nematode, and fission yeast. Mamm Genome. 2001; 12(3):227-31. DOI: 10.1007/s003350010259. View

17.

Pesole G, Mignone F, Gissi C, Grillo G, Licciulli F, Liuni S . Structural and functional features of eukaryotic mRNA untranslated regions. Gene. 2001; 276(1-2):73-81. DOI: 10.1016/s0378-1119(01)00674-6. View

18.

Browning V, Bergstrom R, Daigle S, Schimenti J . A haplolethal locus uncovered by deletions in the mouse T complex. Genetics. 2002; 160(2):675-82. PMC: 1461990. DOI: 10.1093/genetics/160.2.675. View

19.

Kawaji H, Kasukawa T, Fukuda S, Katayama S, Kai C, Kawai J . CAGE Basic/Analysis Databases: the CAGE resource for comprehensive promoter analysis. Nucleic Acids Res. 2005; 34(Database issue):D632-6. PMC: 1347397. DOI: 10.1093/nar/gkj034. View

20.

Ruf N, Dunzinger U, Brinckmann A, Haaf T, Nurnberg P, Zechner U . Expression profiling of uniparental mouse embryos is inefficient in identifying novel imprinted genes. Genomics. 2006; 87(4):509-19. DOI: 10.1016/j.ygeno.2005.12.007. View