RNA polymerase III promoter and terminator elements affect Alu RNA expression (original) (raw)

Abstract

Promoter elements derived from the 7SL RNA gene stimulate RNA polymerase III (Pol III) directed Alu transcription in vitro. These elements also stimulate expression of Alus transfected into 293 cells, but transcripts from these same constructs are undetectable in HeLa cells. A terminator resembling the terminator for the 7SL RNA gene has no effect on in vitro Alu template activity, but increases expression in vivo in a position independent manner. Alu transcripts generated from templates with and without this terminator have identical half-lives, indicating that this terminator stimulates expression by increasing template activity. Together, these results show that Alu expression may be regulated at multiple levels and can respond to cis-acting elements. This new found ability to express Alu transcripts by transient transfection provides an opportunity to monitor their post-transcriptional fate. Primary Alu transcripts are not extensively adenylated or deadenylated following transcription, but are short-lived compared to 118 nt scAlu RNA. In addition to Alu RNA, transfected templates encode scAlu RNA, but very high levels of Alu RNA expression does not increase the abundance of scAluRNA. ScAluRNA is not merely a transient RNA degradation product, but is instead tightly regulated by factors other than the abundance of primary transcripts.

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  1. Bredow S., Sürig D., Müller J., Kleinert H., Benecke B. J. Activating-transcription-factor (ATF) regulates human 7S L RNA transcription by RNA polymerase III in vivo and in vitro. Nucleic Acids Res. 1990 Dec 11;18(23):6779–6784. doi: 10.1093/nar/18.23.6779. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Chang D. Y., Maraia R. J. A cellular protein binds B1 and Alu small cytoplasmic RNAs in vitro. J Biol Chem. 1993 Mar 25;268(9):6423–6428. [PubMed] [Google Scholar]
  3. Deininger P. L., Batzer M. A., Hutchison C. A., 3rd, Edgell M. H. Master genes in mammalian repetitive DNA amplification. Trends Genet. 1992 Sep;8(9):307–311. doi: 10.1016/0168-9525(92)90262-3. [DOI] [PubMed] [Google Scholar]
  4. Englander E. W., Wolffe A. P., Howard B. H. Nucleosome interactions with a human Alu element. Transcriptional repression and effects of template methylation. J Biol Chem. 1993 Sep 15;268(26):19565–19573. [PubMed] [Google Scholar]
  5. Graham F. L., van der Eb A. J. A new technique for the assay of infectivity of human adenovirus 5 DNA. Virology. 1973 Apr;52(2):456–467. doi: 10.1016/0042-6822(73)90341-3. [DOI] [PubMed] [Google Scholar]
  6. Hickman M. A., Malone R. W., Lehmann-Bruinsma K., Sih T. R., Knoell D., Szoka F. C., Walzem R., Carlson D. M., Powell J. S. Gene expression following direct injection of DNA into liver. Hum Gene Ther. 1994 Dec;5(12):1477–1483. doi: 10.1089/hum.1994.5.12-1477. [DOI] [PubMed] [Google Scholar]
  7. Jang K. L., Latchman D. S. HSV infection induces increased transcription of Alu repeated sequences by RNA polymerase III. FEBS Lett. 1989 Dec 4;258(2):255–258. doi: 10.1016/0014-5793(89)81667-9. [DOI] [PubMed] [Google Scholar]
  8. Kochanek S., Renz D., Doerfler W. DNA methylation in the Alu sequences of diploid and haploid primary human cells. EMBO J. 1993 Mar;12(3):1141–1151. doi: 10.1002/j.1460-2075.1993.tb05755.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Leeflang E. P., Liu W. M., Chesnokov I. N., Schmid C. W. Phylogenetic isolation of a human Alu founder gene: drift to new subfamily identity [corrected]. J Mol Evol. 1993 Dec;37(6):559–565. doi: 10.1007/BF00182741. [DOI] [PubMed] [Google Scholar]
  10. Leeflang E. P., Liu W. M., Hashimoto C., Choudary P. V., Schmid C. W. Phylogenetic evidence for multiple Alu source genes. J Mol Evol. 1992 Jul;35(1):7–16. doi: 10.1007/BF00160256. [DOI] [PubMed] [Google Scholar]
  11. Liu W. M., Chu W. M., Choudary P. V., Schmid C. W. Cell stress and translational inhibitors transiently increase the abundance of mammalian SINE transcripts. Nucleic Acids Res. 1995 May 25;23(10):1758–1765. doi: 10.1093/nar/23.10.1758. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Liu W. M., Maraia R. J., Rubin C. M., Schmid C. W. Alu transcripts: cytoplasmic localisation and regulation by DNA methylation. Nucleic Acids Res. 1994 Mar 25;22(6):1087–1095. doi: 10.1093/nar/22.6.1087. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. Liu W. M., Schmid C. W. Proposed roles for DNA methylation in Alu transcriptional repression and mutational inactivation. Nucleic Acids Res. 1993 Mar 25;21(6):1351–1359. doi: 10.1093/nar/21.6.1351. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Maraia R. J., Chang D. Y., Wolffe A. P., Vorce R. L., Hsu K. The RNA polymerase III terminator used by a B1-Alu element can modulate 3' processing of the intermediate RNA product. Mol Cell Biol. 1992 Apr;12(4):1500–1506. doi: 10.1128/mcb.12.4.1500. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Maraia R. J., Driscoll C. T., Bilyeu T., Hsu K., Darlington G. J. Multiple dispersed loci produce small cytoplasmic Alu RNA. Mol Cell Biol. 1993 Jul;13(7):4233–4241. doi: 10.1128/mcb.13.7.4233. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Maraia R. J., Kenan D. J., Keene J. D. Eukaryotic transcription termination factor La mediates transcript release and facilitates reinitiation by RNA polymerase III. Mol Cell Biol. 1994 Mar;14(3):2147–2158. doi: 10.1128/mcb.14.3.2147. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Matera A. G., Hellmann U., Hintz M. F., Schmid C. W. Recently transposed Alu repeats result from multiple source genes. Nucleic Acids Res. 1990 Oct 25;18(20):6019–6023. doi: 10.1093/nar/18.20.6019. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Matera A. G., Hellmann U., Schmid C. W. A transpositionally and transcriptionally competent Alu subfamily. Mol Cell Biol. 1990 Oct;10(10):5424–5432. doi: 10.1128/mcb.10.10.5424. [DOI] [PMC free article] [PubMed] [Google Scholar]
  19. Panning B., Smiley J. R. Activation of RNA polymerase III transcription of human Alu repetitive elements by adenovirus type 5: requirement for the E1b 58-kilodalton protein and the products of E4 open reading frames 3 and 6. Mol Cell Biol. 1993 Jun;13(6):3231–3244. doi: 10.1128/mcb.13.6.3231. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Sakamoto K., Fordis C. M., Corsico C. D., Howard T. H., Howard B. H. Modulation of HeLa cell growth by transfected 7SL RNA and Alu gene sequences. J Biol Chem. 1991 Feb 15;266(5):3031–3038. [PubMed] [Google Scholar]
  21. Schmid C., Maraia R. Transcriptional regulation and transpositional selection of active SINE sequences. Curr Opin Genet Dev. 1992 Dec;2(6):874–882. doi: 10.1016/s0959-437x(05)80110-8. [DOI] [PubMed] [Google Scholar]
  22. Sinnett D., Richer C., Deragon J. M., Labuda D. Alu RNA transcripts in human embryonal carcinoma cells. Model of post-transcriptional selection of master sequences. J Mol Biol. 1992 Aug 5;226(3):689–706. doi: 10.1016/0022-2836(92)90626-u. [DOI] [PubMed] [Google Scholar]
  23. Ullu E., Weiner A. M. Human genes and pseudogenes for the 7SL RNA component of signal recognition particle. EMBO J. 1984 Dec 20;3(13):3303–3310. doi: 10.1002/j.1460-2075.1984.tb02294.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Ullu E., Weiner A. M. Upstream sequences modulate the internal promoter of the human 7SL RNA gene. 1985 Nov 28-Dec 4Nature. 318(6044):371–374. doi: 10.1038/318371a0. [DOI] [PubMed] [Google Scholar]
  25. Weiner A. M., Deininger P. L., Efstratiadis A. Nonviral retroposons: genes, pseudogenes, and transposable elements generated by the reverse flow of genetic information. Annu Rev Biochem. 1986;55:631–661. doi: 10.1146/annurev.bi.55.070186.003215. [DOI] [PubMed] [Google Scholar]