Abstract
The compact organization of the Saccharomyces cerevisiae genome necessitates that non-coding regulatory sequences reside in close proximity to one another. Here we show there is an intimate association between transcription terminators and DNA replication origins. Four replication origins were analyzed in a reporter gene assay that detects sequences that direct 3' end formation of mRNA transcripts. All four replication origins function as orientation-independent transcription terminators in this system, producing truncated polyadenylated mRNAs. Despite this close association, the cis-acting elements that confer replication origin function are genetically separable from those required for transcription termination. Several models are explored in an attempt to address how and why the signals specifying transcription termination and replication initiation overlap.
Full Text
The Full Text of this article is available as a PDF (160.5 KB).
Selected References
These references are in PubMed. This may not be the complete list of references from this article.
- Bell S. P., Kobayashi R., Stillman B. Yeast origin recognition complex functions in transcription silencing and DNA replication. Science. 1993 Dec 17;262(5141):1844–1849. doi: 10.1126/science.8266072. [DOI] [PubMed] [Google Scholar]
- Bell S. P., Stillman B. ATP-dependent recognition of eukaryotic origins of DNA replication by a multiprotein complex. Nature. 1992 May 14;357(6374):128–134. doi: 10.1038/357128a0. [DOI] [PubMed] [Google Scholar]
- Bouton A. H., Smith M. M. Fine-structure analysis of the DNA sequence requirements for autonomous replication of Saccharomyces cerevisiae plasmids. Mol Cell Biol. 1986 Jul;6(7):2354–2363. doi: 10.1128/mcb.6.7.2354. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Brewer B. J. Intergenic DNA and the sequence requirements for replication initiation in eukaryotes. Curr Opin Genet Dev. 1994 Apr;4(2):196–202. doi: 10.1016/s0959-437x(05)80045-0. [DOI] [PubMed] [Google Scholar]
- Broach J. R., Li Y. Y., Feldman J., Jayaram M., Abraham J., Nasmyth K. A., Hicks J. B. Localization and sequence analysis of yeast origins of DNA replication. Cold Spring Harb Symp Quant Biol. 1983;47(Pt 2):1165–1173. doi: 10.1101/sqb.1983.047.01.132. [DOI] [PubMed] [Google Scholar]
- Buchman A. R., Kornberg R. D. A yeast ARS-binding protein activates transcription synergistically in combination with other weak activating factors. Mol Cell Biol. 1990 Mar;10(3):887–897. doi: 10.1128/mcb.10.3.887. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Connelly S., Manley J. L. RNA polymerase II transcription termination is mediated specifically by protein binding to a CCAAT box sequence. Mol Cell Biol. 1989 Nov;9(11):5254–5259. doi: 10.1128/mcb.9.11.5254. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Conrad-Webb H., Butow R. A. A polymerase switch in the synthesis of rRNA in Saccharomyces cerevisiae. Mol Cell Biol. 1995 May;15(5):2420–2428. doi: 10.1128/mcb.15.5.2420. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Diffley J. F., Cocker J. H. Protein-DNA interactions at a yeast replication origin. Nature. 1992 May 14;357(6374):169–172. doi: 10.1038/357169a0. [DOI] [PubMed] [Google Scholar]
- Dillin A., Rine J. On the origin of a silencer. Trends Biochem Sci. 1995 Jun;20(6):231–235. doi: 10.1016/s0968-0004(00)89023-4. [DOI] [PubMed] [Google Scholar]
- Egli C. M., Springer C., Braus G. H. A complex unidirectional signal element mediates GCN4 mRNA 3' end formation in Saccharomyces cerevisiae. Mol Cell Biol. 1995 May;15(5):2466–2473. doi: 10.1128/mcb.15.5.2466. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Foss M., McNally F. J., Laurenson P., Rine J. Origin recognition complex (ORC) in transcriptional silencing and DNA replication in S. cerevisiae. Science. 1993 Dec 17;262(5141):1838–1844. doi: 10.1126/science.8266071. [DOI] [PubMed] [Google Scholar]
- Gietz R. D., Sugino A. New yeast-Escherichia coli shuttle vectors constructed with in vitro mutagenized yeast genes lacking six-base pair restriction sites. Gene. 1988 Dec 30;74(2):527–534. doi: 10.1016/0378-1119(88)90185-0. [DOI] [PubMed] [Google Scholar]
- Hegemann J. H., Fleig U. N. The centromere of budding yeast. Bioessays. 1993 Jul;15(7):451–460. doi: 10.1002/bies.950150704. [DOI] [PubMed] [Google Scholar]
- Heidmann S., Obermaier B., Vogel K., Domdey H. Identification of pre-mRNA polyadenylation sites in Saccharomyces cerevisiae. Mol Cell Biol. 1992 Sep;12(9):4215–4229. doi: 10.1128/mcb.12.9.4215. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Hieter P., Mann C., Snyder M., Davis R. W. Mitotic stability of yeast chromosomes: a colony color assay that measures nondisjunction and chromosome loss. Cell. 1985 Feb;40(2):381–392. doi: 10.1016/0092-8674(85)90152-7. [DOI] [PubMed] [Google Scholar]
- Huang R. Y., Kowalski D. A DNA unwinding element and an ARS consensus comprise a replication origin within a yeast chromosome. EMBO J. 1993 Dec;12(12):4521–4531. doi: 10.1002/j.1460-2075.1993.tb06141.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Huang R. Y., Kowalski D. Multiple DNA elements in ARS305 determine replication origin activity in a yeast chromosome. Nucleic Acids Res. 1996 Mar 1;24(5):816–823. doi: 10.1093/nar/24.5.816. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Hyman L. E., Seiler S. H., Whoriskey J., Moore C. L. Point mutations upstream of the yeast ADH2 poly(A) site significantly reduce the efficiency of 3'-end formation. Mol Cell Biol. 1991 Apr;11(4):2004–2012. doi: 10.1128/mcb.11.4.2004. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Irniger S., Egli C. M., Braus G. H. Different classes of polyadenylation sites in the yeast Saccharomyces cerevisiae. Mol Cell Biol. 1991 Jun;11(6):3060–3069. doi: 10.1128/mcb.11.6.3060. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Irniger S., Sanfaçon H., Egli C. M., Braus G. H. Different sequence elements are required for function of the cauliflower mosaic virus polyadenylation site in Saccharomyces cerevisiae compared with in plants. Mol Cell Biol. 1992 May;12(5):2322–2330. doi: 10.1128/mcb.12.5.2322. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Jeong S. W., Lang W. H., Reeder R. H. The release element of the yeast polymerase I transcription terminator can function independently of Reb1p. Mol Cell Biol. 1995 Nov;15(11):5929–5936. doi: 10.1128/mcb.15.11.5929. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Keller W. No end yet to messenger RNA 3' processing! Cell. 1995 Jun 16;81(6):829–832. doi: 10.1016/0092-8674(95)90001-2. [DOI] [PubMed] [Google Scholar]
- Lang W. H., Morrow B. E., Ju Q., Warner J. R., Reeder R. H. A model for transcription termination by RNA polymerase I. Cell. 1994 Nov 4;79(3):527–534. doi: 10.1016/0092-8674(94)90261-5. [DOI] [PubMed] [Google Scholar]
- Li J. J., Herskowitz I. Isolation of ORC6, a component of the yeast origin recognition complex by a one-hybrid system. Science. 1993 Dec 17;262(5141):1870–1874. doi: 10.1126/science.8266075. [DOI] [PubMed] [Google Scholar]
- Marahrens Y., Stillman B. A yeast chromosomal origin of DNA replication defined by multiple functional elements. Science. 1992 Feb 14;255(5046):817–823. doi: 10.1126/science.1536007. [DOI] [PubMed] [Google Scholar]
- Micklem G., Rowley A., Harwood J., Nasmyth K., Diffley J. F. Yeast origin recognition complex is involved in DNA replication and transcriptional silencing. Nature. 1993 Nov 4;366(6450):87–89. doi: 10.1038/366087a0. [DOI] [PubMed] [Google Scholar]
- Miller C. A., Kowalski D. cis-acting components in the replication origin from ribosomal DNA of Saccharomyces cerevisiae. Mol Cell Biol. 1993 Sep;13(9):5360–5369. doi: 10.1128/mcb.13.9.5360. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Natale D. A., Umek R. M., Kowalski D. Ease of DNA unwinding is a conserved property of yeast replication origins. Nucleic Acids Res. 1993 Feb 11;21(3):555–560. doi: 10.1093/nar/21.3.555. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Newlon C. S., Collins I., Dershowitz A., Deshpande A. M., Greenfeder S. A., Ong L. Y., Theis J. F. Analysis of replication origin function on chromosome III of Saccharomyces cerevisiae. Cold Spring Harb Symp Quant Biol. 1993;58:415–423. doi: 10.1101/sqb.1993.058.01.048. [DOI] [PubMed] [Google Scholar]
- Oliver S. G., van der Aart Q. J., Agostoni-Carbone M. L., Aigle M., Alberghina L., Alexandraki D., Antoine G., Anwar R., Ballesta J. P., Benit P. The complete DNA sequence of yeast chromosome III. Nature. 1992 May 7;357(6373):38–46. doi: 10.1038/357038a0. [DOI] [PubMed] [Google Scholar]
- Parikh V. S., Conrad-Webb H., Docherty R., Butow R. A. Interaction between the yeast mitochondrial and nuclear genomes influences the abundance of novel transcripts derived from the spacer region of the nuclear ribosomal DNA repeat. Mol Cell Biol. 1989 May;9(5):1897–1907. doi: 10.1128/mcb.9.5.1897. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Pikielny C. W., Teem J. L., Rosbash M. Evidence for the biochemical role of an internal sequence in yeast nuclear mRNA introns: implications for U1 RNA and metazoan mRNA splicing. Cell. 1983 Sep;34(2):395–403. doi: 10.1016/0092-8674(83)90373-2. [DOI] [PubMed] [Google Scholar]
- Proudfoot N. J. How RNA polymerase II terminates transcription in higher eukaryotes. Trends Biochem Sci. 1989 Mar;14(3):105–110. doi: 10.1016/0968-0004(89)90132-1. [DOI] [PubMed] [Google Scholar]
- Rao H., Marahrens Y., Stillman B. Functional conservation of multiple elements in yeast chromosomal replicators. Mol Cell Biol. 1994 Nov;14(11):7643–7651. doi: 10.1128/mcb.14.11.7643. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Reeder R. H., Lang W. The mechanism of transcription termination by RNA polymerase I. Mol Microbiol. 1994 Apr;12(1):11–15. doi: 10.1111/j.1365-2958.1994.tb00989.x. [DOI] [PubMed] [Google Scholar]
- Reines D., Wells D., Chamberlin M. J., Kane C. M. Identification of intrinsic termination sites in vitro for RNA polymerase II within eukaryotic gene sequences. J Mol Biol. 1987 Jul 20;196(2):299–312. doi: 10.1016/0022-2836(87)90691-7. [DOI] [PubMed] [Google Scholar]
- Russo P., Li W. Z., Hampsey D. M., Zaret K. S., Sherman F. Distinct cis-acting signals enhance 3' endpoint formation of CYC1 mRNA in the yeast Saccharomyces cerevisiae. EMBO J. 1991 Mar;10(3):563–571. doi: 10.1002/j.1460-2075.1991.tb07983.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Russo P., Sherman F. Transcription terminates near the poly(A) site in the CYC1 gene of the yeast Saccharomyces cerevisiae. Proc Natl Acad Sci U S A. 1989 Nov;86(21):8348–8352. doi: 10.1073/pnas.86.21.8348. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Shirahige K., Iwasaki T., Rashid M. B., Ogasawara N., Yoshikawa H. Location and characterization of autonomously replicating sequences from chromosome VI of Saccharomyces cerevisiae. Mol Cell Biol. 1993 Aug;13(8):5043–5056. doi: 10.1128/mcb.13.8.5043. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Smith M. M., Andrésson O. S. DNA sequences of yeast H3 and H4 histone genes from two non-allelic gene sets encode identical H3 and H4 proteins. J Mol Biol. 1983 Sep 25;169(3):663–690. doi: 10.1016/s0022-2836(83)80164-8. [DOI] [PubMed] [Google Scholar]
- Snyder M., Buchman A. R., Davis R. W. Bent DNA at a yeast autonomously replicating sequence. Nature. 1986 Nov 6;324(6092):87–89. doi: 10.1038/324087a0. [DOI] [PubMed] [Google Scholar]
- Snyder M., Sapolsky R. J., Davis R. W. Transcription interferes with elements important for chromosome maintenance in Saccharomyces cerevisiae. Mol Cell Biol. 1988 May;8(5):2184–2194. doi: 10.1128/mcb.8.5.2184. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Tanaka S., Halter D., Livingstone-Zatchej M., Reszel B., Thoma F. Transcription through the yeast origin of replication ARS1 ends at the ABFI binding site and affects extrachromosomal maintenance of minichromosomes. Nucleic Acids Res. 1994 Sep 25;22(19):3904–3910. doi: 10.1093/nar/22.19.3904. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Teem J. L., Rosbash M. Expression of a beta-galactosidase gene containing the ribosomal protein 51 intron is sensitive to the rna2 mutation of yeast. Proc Natl Acad Sci U S A. 1983 Jul;80(14):4403–4407. doi: 10.1073/pnas.80.14.4403. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Van Houten J. V., Newlon C. S. Mutational analysis of the consensus sequence of a replication origin from yeast chromosome III. Mol Cell Biol. 1990 Aug;10(8):3917–3925. doi: 10.1128/mcb.10.8.3917. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Wahle E. 3'-end cleavage and polyadenylation of mRNA precursors. Biochim Biophys Acta. 1995 Apr 4;1261(2):183–194. doi: 10.1016/0167-4781(94)00248-2. [DOI] [PubMed] [Google Scholar]
- Walker S. S., Malik A. K., Eisenberg S. Analysis of the interactions of functional domains of a nuclear origin of replication from Saccharomyces cerevisiae. Nucleic Acids Res. 1991 Nov 25;19(22):6255–6262. doi: 10.1093/nar/19.22.6255. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Warner J. R. Synthesis of ribosomes in Saccharomyces cerevisiae. Microbiol Rev. 1989 Jun;53(2):256–271. doi: 10.1128/mr.53.2.256-271.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]