Skip to main content
Log in

Antisense regulation of human gene MAP3K13: True phenomenon or artifact?

  • Genomics. Transcriptomics. Proteomics
  • Published:
Molecular Biology Aims and scope Submit manuscript

Abstract

Antisense regulation of gene expression is a widespread but poorly understood mechanism of gene expression regulation. The potential role of antisense transcripts in tumorigenesis is most intriguing for functional research. Here we experimentally characterize an antisense mRNA asLZK overlapping the human MAP3K13/LZK gene that is involved in the mitogenesis-related JNK/SAPK signal transduction pathway. According to the functional annotation of the human genome, asLZK transcript (LOC647276) is expressed at the relatively high level and overrepresented in tumor samples. To our surprise, experimental study of human asLZK revealed that this sequence is not expressed, but represents a silent pseudogene of ribosomal protein L4 encoding gene RPL4. This pseudogene resulted from relatively recent retroposition of RPL4 mRNA into the first intron of MAP3K13 gene and does not participate in the regulation of MAP3K13 expression. This study stresses that, after initial in silico mapping efforts, experimental verification of the expression landscape is warranted.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Subscribe and save

Springer+ Basic
EUR 32.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or Ebook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Similar content being viewed by others

References

  1. Yelin R., Dahary D., Sorek R., Levanon E.Y., Goldstein O., Shoshan A., Diber A., Biton S., Tamir Y., Khosravi R., Nemzer S., Pinner E., Walach S., Bernstein J., Savitsky K., Rotman G. 2003. Widespread occurrence of antisense transcription in the human genome. Nature Biotechnol. 21, 379–386.

    Article  CAS  Google Scholar 

  2. Numata K., Okada Y., Saito R., Kiyosawa H., Kanai A., Tomita M. 2007. Comparative analysis of cis-encoded antisense RNAs in eukaryotes. Gene. 392, 134–141.

    Article  PubMed  CAS  Google Scholar 

  3. Munroe S.H., Zhu J. 2006. Overlapping transcripts, double-stranded RNA and antisense regulation: A genomic perspective. Cell. Mol. Life Sci. 63, 2102–2118.

    Article  PubMed  CAS  Google Scholar 

  4. Lavorgna G., Dahary D., Lehner B., Sorek R., Sanderson C.M., Casari G. 2004. In search of antisense. Trends Biochem. Sci. 29, 88–94.

    Article  PubMed  CAS  Google Scholar 

  5. Klimov D., Skoblov M., Ryazantzev A., Tyazhelova T., Baranova A. 2006. In silico search for natural antisense transcripts reveals their differential expression in human tumors. J. Bioinform. Comput. Biol. 4, 515–521.

    Article  PubMed  CAS  Google Scholar 

  6. Reis E.M., Nakaya H.I., Louro R., Canavez F.C., Flatschart A.V., Almeida G.T., Egidio C.M., Paquola A.C., Machado A.A., Festa F., Yamamoto D., Alvarenga R., da Silva C.C., Brito G.C., Simon S.D., Moreira-Filho C.A., Leite K.R., Camara-Lopes L.H., Campos F.S., Gimba E., Vignal G.M., El-Dorry H., Sogayar M.C., Barcinski M.A., da Silva A.M., Verjovski-Almeida S. 2004. Antisense intronic non-coding RNA levels correlate to the degree of tumor differentiation in prostate cancer. Oncogene. 23, 6684–6692.

    Article  PubMed  CAS  Google Scholar 

  7. Baranova A.V., Lobashev A.V., Ivanov D.V., Krukovskaya L.L., Yankovsky N.K., Kozlov A.P. 2001. In silico screening for tumour-specific expressed sequences in human genome. FEBS Lett. 508, 143–148.

    Article  PubMed  CAS  Google Scholar 

  8. Krukovskaja L.L., Baranova A., Tyezelova T., Polev D., Kozlov A.P. 2005. Experimental study of human expressed sequences newly identified in silico as tumor specific. Tumour Biol. 26, 17–24.

    Article  PubMed  CAS  Google Scholar 

  9. Merlo L.M., Pepper J.W., Reid B.J., Maley C.C. 2006. Cancer as an evolutionary and ecological process. Nat. Rev. Cancer. 6, 924–935.

    Article  PubMed  CAS  Google Scholar 

  10. Ikeda A., Hasegawa K., Masaki M., Moriguchi T., Nishida E., Kozutsumi Y., Oka S., Kawasaki T. 2001. Mixed lineage kinase LZK forms a functional signaling complex with JIP-1, a scaffold protein of the c-Jun NH2-terminal kinase pathway. J. Biochem. 130, 773–781.

    PubMed  CAS  Google Scholar 

  11. Johnson G.L., Nakamura K. 2007. The c-jun kinase/stress-activated pathway: Regulation, function and role in human disease. Biochim. Biophys. Acta. 1773, 1341–1348.

    Article  PubMed  CAS  Google Scholar 

  12. Vasilevskaya I., O’Dwyer P.J. 2003. Role of Jun and Jun kinase in resistance of cancer cells to therapy. Drug Resist. Update. 6, 147–156.

    Article  CAS  Google Scholar 

  13. Weiner A.M. 1986. Nonviral retroposons: genes, pseudogenes, and transposable elements generated by the reverse flow of genetic information. Annu. Rev. Biochem. 55, 631–661.

    Article  PubMed  CAS  Google Scholar 

  14. The ENCODE Project Consortium. 2004. The ENCODE (ENCyclopedia Of DNA Elements) Project. Science. 306, 636–640.

    Article  CAS  Google Scholar 

  15. Zheng D., Frankish A., Baertsch R., Kapranov P., Reymond A., Choo S.W., Lu Y., Denoeud F., Antonarakis S.E., Snyder M., Ruan Y., Wei C.L., Gingeras T.R., Guigo R., Harrow J., Gerstein M.B. 2007. Pseudogenes in the ENCODE regions: Consensus annotation, analysis of transcription, and evolution. Genome Res. 17, 839–851.

    Article  PubMed  CAS  Google Scholar 

  16. Wang J.P., Lindsay B.G., Leebens-Mack J., Cui L., Wall K., Miller W.C., dePamphilis C.W. 2004. EST clustering error evaluation and correction. Bioinformatics. 20, 2973–2984.

    Article  PubMed  CAS  Google Scholar 

  17. Lindlof A. 2003. Gene identification through large-scale EST sequence processing. Appl. Bioinformatics. 2, 123–129.

    PubMed  Google Scholar 

  18. Harrow J., Denoeud F., Frankish A., Reymond A., Chen C.K., Chrast J., Lagarde J., Gilbert J.G., Storey R., Swarbreck D., Rossier C., Ucla C., Hubbard T., Antonarakis S.E., Guigo R. 2006. GENCODE: Producing a reference annotation for ENCODE. Genome Biol. Suppl 1, S4.1–S4.9.

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to A. V. Marakhonov.

Additional information

Original Russian Text © A.V. Marakhonov, A.V. Baranova, M.Yu. Skoblov, 2008, published in Molekulyarnaya Biologiya, 2008, Vol. 42, No. 4, pp. 581–587.

The text was submitted by the authors in English.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Marakhonov, A.V., Baranova, A.V. & Skoblov, M.Y. Antisense regulation of human gene MAP3K13: True phenomenon or artifact?. Mol Biol 42, 514–520 (2008). https://doi.org/10.1134/S0026893308040055

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1134/S0026893308040055

Key words

Navigation