Skip to main content
PMC home page
Molecular and Cellular Biology logoLink to Molecular and Cellular Biology
. 1987 Dec;7(12):4185–4193. doi: 10.1128/mcb.7.12.4185

Multiple functional motifs in the chicken U1 RNA gene enhancer.

K A Roebuck 1, R J Walker 1, W E Stumph 1
PMCID: PMC368099  PMID: 3437887

Abstract

The DNA sequence requirements of chicken U1 RNA gene expression have been examined in an oocyte transcription system. An enhancer region, which was required for efficient U1 RNA gene expression, is contained within a region of conserved DNA sequences spanning nucleotide positions -230 to -183, upstream of the transcriptional initiation site. These DNA sequences can be divided into at least two distinct subregions or domains that acted synergistically to provide a greater than 20-fold stimulation of U1 RNA synthesis. The first domain contains the octamer sequence ATGCAAAT and was recognized by a DNA-binding factor present in HeLa cell extracts. The second domain (the SPH domain) consists of conserved sequences immediately downstream of the octamer and is an essential component of the enhancer. In the oocyte, the DNA sequences of the SPH domain were able to enhance gene expression at least 10-fold in the absence of the octamer domain. In contrast, the octamer domain, although required for full U1 RNA gene activity, was unable to stimulate expression in the absence of the adjacent downstream DNA sequences. These findings imply that sequences 3' of the octamer play a major role in the function of the chicken U1 RNA gene enhancer. This concept was supported by transcriptional competition studies in which a cloned chicken U4B RNA gene was used to compete for limiting transcription factors in oocytes. Multiple sequence motifs that can function in a variety of cis-linked configurations may be a general feature of vertebrate small nuclear RNA gene enhancers.

Full text

PDF
4185

Images in this article

4187Image
on p.4187
4188Image
on p.4188
4189Image
on p.4189
4190Image
on p.4190

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Ares M., Jr, Mangin M., Weiner A. M. Orientation-dependent transcriptional activator upstream of a human U2 snRNA gene. Mol Cell Biol. 1985 Jul;5(7):1560–1570. doi: 10.1128/mcb.5.7.1560. [DOI] [PMC free article] [PubMed] [Google Scholar]
  2. Bark C., Weller P., Zabielski J., Pettersson U. Genes for human U4 small nuclear RNA. Gene. 1986;50(1-3):333–344. doi: 10.1016/0378-1119(86)90337-9. [DOI] [PubMed] [Google Scholar]
  3. Berget S. M., Robberson B. L. U1, U2, and U4/U6 small nuclear ribonucleoproteins are required for in vitro splicing but not polyadenylation. Cell. 1986 Aug 29;46(5):691–696. doi: 10.1016/0092-8674(86)90344-2. [DOI] [PubMed] [Google Scholar]
  4. Black D. L., Chabot B., Steitz J. A. U2 as well as U1 small nuclear ribonucleoproteins are involved in premessenger RNA splicing. Cell. 1985 Oct;42(3):737–750. doi: 10.1016/0092-8674(85)90270-3. [DOI] [PubMed] [Google Scholar]
  5. Black D. L., Steitz J. A. Pre-mRNA splicing in vitro requires intact U4/U6 small nuclear ribonucleoprotein. Cell. 1986 Aug 29;46(5):697–704. doi: 10.1016/0092-8674(86)90345-4. [DOI] [PubMed] [Google Scholar]
  6. Bohmann D., Keller W., Dale T., Schöler H. R., Tebb G., Mattaj I. W. A transcription factor which binds to the enhancers of SV40, immunoglobulin heavy chain and U2 snRNA genes. Nature. 1987 Jan 15;325(6101):268–272. doi: 10.1038/325268a0. [DOI] [PubMed] [Google Scholar]
  7. Chabot B., Black D. L., LeMaster D. M., Steitz J. A. The 3' splice site of pre-messenger RNA is recognized by a small nuclear ribonucleoprotein. Science. 1985 Dec 20;230(4732):1344–1349. doi: 10.1126/science.2933810. [DOI] [PubMed] [Google Scholar]
  8. Choi O. R., Engel J. D. A 3' enhancer is required for temporal and tissue-specific transcriptional activation of the chicken adult beta-globin gene. Nature. 1986 Oct 23;323(6090):731–734. doi: 10.1038/323731a0. [DOI] [PubMed] [Google Scholar]
  9. Ciliberto G., Buckland R., Cortese R., Philipson L. Transcription signals in embryonic Xenopus laevis U1 RNA genes. EMBO J. 1985 Jun;4(6):1537–1543. doi: 10.1002/j.1460-2075.1985.tb03814.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Ciliberto G., Dathan N., Frank R., Philipson L., Mattaj I. W. Formation of the 3' end on U snRNAs requires at least three sequence elements. EMBO J. 1986 Nov;5(11):2931–2937. doi: 10.1002/j.1460-2075.1986.tb04589.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Ciliberto G., Palla F., Tebb G., Mattaj I. W., Philipson L. Properties of a U1 RNA enhancer-like sequence. Nucleic Acids Res. 1987 Mar 25;15(6):2403–2416. doi: 10.1093/nar/15.6.2403. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Davidson I., Fromental C., Augereau P., Wildeman A., Zenke M., Chambon P. Cell-type specific protein binding to the enhancer of simian virus 40 in nuclear extracts. Nature. 1986 Oct 9;323(6088):544–548. doi: 10.1038/323544a0. [DOI] [PubMed] [Google Scholar]
  13. Earley J. M., 3rd, Roebuck K. A., Stumph W. E. Three linked chicken U1 RNA genes have limited flanking DNA sequence homologies that reveal potential regulatory signals. Nucleic Acids Res. 1984 Oct 11;12(19):7411–7421. doi: 10.1093/nar/12.19.7411. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Falkner F. G., Zachau H. G. Correct transcription of an immunoglobulin kappa gene requires an upstream fragment containing conserved sequence elements. Nature. 1984 Jul 5;310(5972):71–74. doi: 10.1038/310071a0. [DOI] [PubMed] [Google Scholar]
  15. Gargiulo G., Razvi F., Worcel A. Assembly of transcriptionally active chromatin in Xenopus oocytes requires specific DNA binding factors. Cell. 1984 Sep;38(2):511–521. doi: 10.1016/0092-8674(84)90506-3. [DOI] [PubMed] [Google Scholar]
  16. Gerster T., Matthias P., Thali M., Jiricny J., Schaffner W. Cell type-specificity elements of the immunoglobulin heavy chain gene enhancer. EMBO J. 1987 May;6(5):1323–1330. doi: 10.1002/j.1460-2075.1987.tb02371.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Hernandez N., Weiner A. M. Formation of the 3' end of U1 snRNA requires compatible snRNA promoter elements. Cell. 1986 Oct 24;47(2):249–258. doi: 10.1016/0092-8674(86)90447-2. [DOI] [PubMed] [Google Scholar]
  18. Herr W., Clarke J. The SV40 enhancer is composed of multiple functional elements that can compensate for one another. Cell. 1986 May 9;45(3):461–470. doi: 10.1016/0092-8674(86)90332-6. [DOI] [PubMed] [Google Scholar]
  19. Hoffman M. L., Korf G. M., McNamara K. J., Stumph W. E. Structural and functional analysis of chicken U4 small nuclear RNA genes. Mol Cell Biol. 1986 Nov;6(11):3910–3919. doi: 10.1128/mcb.6.11.3910. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Howard E. F., Michael S. K., Dahlberg J. E., Lund E. Functional, developmentally expressed genes for mouse U1a and U1b snRNAs contain both conserved and non-conserved transcription signals. Nucleic Acids Res. 1986 Dec 22;14(24):9811–9825. doi: 10.1093/nar/14.24.9811. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Korf G. M., Stumph W. E. Chicken U2 and U1 RNA genes are found in very different genomic environments but have similar promoter structures. Biochemistry. 1986 Apr 22;25(8):2041–2047. doi: 10.1021/bi00356a031. [DOI] [PubMed] [Google Scholar]
  22. Krainer A. R., Maniatis T. Multiple factors including the small nuclear ribonucleoproteins U1 and U2 are necessary for pre-mRNA splicing in vitro. Cell. 1985 Oct;42(3):725–736. doi: 10.1016/0092-8674(85)90269-7. [DOI] [PubMed] [Google Scholar]
  23. Krol A., Lund E., Dahlberg J. E. The two embryonic U1 RNA genes of Xenopus laevis have both common and gene-specific transcription signals. EMBO J. 1985 Jun;4(6):1529–1535. doi: 10.1002/j.1460-2075.1985.tb03813.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Mangin M., Ares M., Jr, Weiner A. M. Human U2 small nuclear RNA genes contain an upstream enhancer. EMBO J. 1986 May;5(5):987–995. doi: 10.1002/j.1460-2075.1986.tb04313.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Marzluff W. F., Brown D. T., Lobo S., Wang S. S. Isolation and characterization of two linked mouse U1b small nuclear RNA genes. Nucleic Acids Res. 1983 Sep 24;11(18):6255–6270. doi: 10.1093/nar/11.18.6255. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Mason J. O., Williams G. T., Neuberger M. S. Transcription cell type specificity is conferred by an immunoglobulin VH gene promoter that includes a functional consensus sequence. Cell. 1985 Jun;41(2):479–487. doi: 10.1016/s0092-8674(85)80021-0. [DOI] [PubMed] [Google Scholar]
  27. Mattaj I. W., Lienhard S., Jiricny J., De Robertis E. M. An enhancer-like sequence within the Xenopus U2 gene promoter facilitates the formation of stable transcription complexes. Nature. 1985 Jul 11;316(6024):163–167. doi: 10.1038/316163a0. [DOI] [PubMed] [Google Scholar]
  28. Mattaj I. W., Zeller R. Xenopus laevis U2 snRNA genes: tandemly repeated transcription units sharing 5' and 3' flanking homology with other RNA polymerase II transcribed genes. EMBO J. 1983;2(11):1883–1891. doi: 10.1002/j.1460-2075.1983.tb01675.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  29. Maxam A. M., Gilbert W. Sequencing end-labeled DNA with base-specific chemical cleavages. Methods Enzymol. 1980;65(1):499–560. doi: 10.1016/s0076-6879(80)65059-9. [DOI] [PubMed] [Google Scholar]
  30. Mocikat R., Falkner F. G., Mertz R., Zachau H. G. Upstream regulatory sequences of immunoglobulin genes are recognized by nuclear proteins which also bind to other gene regions. Nucleic Acids Res. 1986 Nov 25;14(22):8829–8844. doi: 10.1093/nar/14.22.8829. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Murphy J. T., Burgess R. R., Dahlberg J. E., Lund E. Transcription of a gene for human U1 small nuclear RNA. Cell. 1982 May;29(1):265–274. doi: 10.1016/0092-8674(82)90111-8. [DOI] [PubMed] [Google Scholar]
  32. Murphy J. T., Skuzeski J. T., Lund E., Steinberg T. H., Burgess R. R., Dahlberg J. E. Functional elements of the human U1 RNA promoter. Identification of five separate regions required for efficient transcription and template competition. J Biol Chem. 1987 Feb 5;262(4):1795–1803. [PubMed] [Google Scholar]
  33. Ondek B., Shepard A., Herr W. Discrete elements within the SV40 enhancer region display different cell-specific enhancer activities. EMBO J. 1987 Apr;6(4):1017–1025. doi: 10.1002/j.1460-2075.1987.tb04854.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Parslow T. G., Jones S. D., Bond B., Yamamoto K. R. The immunoglobulin octanucleotide: independent activity and selective interaction with enhancers. Science. 1987 Mar 20;235(4795):1498–1501. doi: 10.1126/science.3029871. [DOI] [PubMed] [Google Scholar]
  35. Reddy R., Busch H. Small nuclear RNAs and RNA processing. Prog Nucleic Acid Res Mol Biol. 1983;30:127–162. doi: 10.1016/s0079-6603(08)60685-6. [DOI] [PubMed] [Google Scholar]
  36. Roop D. R., Kristo P., Stumph W. E., Tsai M. J., O'Malley B. W. Structure and expression of a chicken gene coding for U1 RNA. Cell. 1981 Mar;23(3):671–680. doi: 10.1016/0092-8674(81)90430-x. [DOI] [PubMed] [Google Scholar]
  37. Schirm S., Jiricny J., Schaffner W. The SV40 enhancer can be dissected into multiple segments, each with a different cell type specificity. Genes Dev. 1987 Mar;1(1):65–74. doi: 10.1101/gad.1.1.65. [DOI] [PubMed] [Google Scholar]
  38. Sen R., Baltimore D. Multiple nuclear factors interact with the immunoglobulin enhancer sequences. Cell. 1986 Aug 29;46(5):705–716. doi: 10.1016/0092-8674(86)90346-6. [DOI] [PubMed] [Google Scholar]
  39. Singh H., Sen R., Baltimore D., Sharp P. A. A nuclear factor that binds to a conserved sequence motif in transcriptional control elements of immunoglobulin genes. Nature. 1986 Jan 9;319(6049):154–158. doi: 10.1038/319154a0. [DOI] [PubMed] [Google Scholar]
  40. Sive H. L., Heintz N., Roeder R. G. Multiple sequence elements are required for maximal in vitro transcription of a human histone H2B gene. Mol Cell Biol. 1986 Oct;6(10):3329–3340. doi: 10.1128/mcb.6.10.3329. [DOI] [PMC free article] [PubMed] [Google Scholar]
  41. Sive H. L., Roeder R. G. Interaction of a common factor with conserved promoter and enhancer sequences in histone H2B, immunoglobulin, and U2 small nuclear RNA (snRNA) genes. Proc Natl Acad Sci U S A. 1986 Sep;83(17):6382–6386. doi: 10.1073/pnas.83.17.6382. [DOI] [PMC free article] [PubMed] [Google Scholar]
  42. Skuzeski J. M., Lund E., Murphy J. T., Steinberg T. H., Burgess R. R., Dahlberg J. E. Synthesis of human U1 RNA. II. Identification of two regions of the promoter essential for transcription initiation at position +1. J Biol Chem. 1984 Jul 10;259(13):8345–8352. [PubMed] [Google Scholar]
  43. Suh D., Busch H., Reddy R. Isolation and characterization of a human U3 small nucleolar RNA gene. Biochem Biophys Res Commun. 1986 Jun 30;137(3):1133–1140. doi: 10.1016/0006-291x(86)90343-8. [DOI] [PubMed] [Google Scholar]
  44. Watanabe-Nagasu N., Itoh Y., Tani T., Okano K., Koga N., Okada N., Ohshima Y. Structural analysis of gene loci for rat U1 small nuclear RNA. Nucleic Acids Res. 1983 Mar 25;11(6):1791–1801. doi: 10.1093/nar/11.6.1791. [DOI] [PMC free article] [PubMed] [Google Scholar]
  45. Westin G., Lund E., Murphy J. T., Pettersson U., Dahlberg J. E. Human U2 and U1 RNA genes use similar transcription signals. EMBO J. 1984 Dec 20;3(13):3295–3301. doi: 10.1002/j.1460-2075.1984.tb02293.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  46. Wildeman A. G., Zenke M., Schatz C., Wintzerith M., Grundström T., Matthes H., Takahashi K., Chambon P. Specific protein binding to the simian virus 40 enhancer in vitro. Mol Cell Biol. 1986 Jun;6(6):2098–2105. doi: 10.1128/mcb.6.6.2098. [DOI] [PMC free article] [PubMed] [Google Scholar]
  47. Yuo C. Y., Ares M., Jr, Weiner A. M. Sequences required for 3' end formation of human U2 small nuclear RNA. Cell. 1985 Aug;42(1):193–202. doi: 10.1016/s0092-8674(85)80115-x. [DOI] [PubMed] [Google Scholar]
  48. Zenke M., Grundström T., Matthes H., Wintzerith M., Schatz C., Wildeman A., Chambon P. Multiple sequence motifs are involved in SV40 enhancer function. EMBO J. 1986 Feb;5(2):387–397. doi: 10.1002/j.1460-2075.1986.tb04224.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  49. Zhuang Y., Weiner A. M. A compensatory base change in U1 snRNA suppresses a 5' splice site mutation. Cell. 1986 Sep 12;46(6):827–835. doi: 10.1016/0092-8674(86)90064-4. [DOI] [PubMed] [Google Scholar]
  50. de Vegvar H. E., Lund E., Dahlberg J. E. 3' end formation of U1 snRNA precursors is coupled to transcription from snRNA promoters. Cell. 1986 Oct 24;47(2):259–266. doi: 10.1016/0092-8674(86)90448-4. [DOI] [PubMed] [Google Scholar]

Articles from Molecular and Cellular Biology are provided here courtesy of Taylor & Francis

RESOURCES