- Research article
- Open Access
Poly purine.pyrimidine sequences upstream of the beta-galactosidase gene affect gene expression in Saccharomyces cerevisiae
© Maiti and Brahmachari; licensee BioMed Central Ltd. 2001
- Received: 9 April 2001
- Accepted: 8 October 2001
- Published: 8 October 2001
Poly purine.pyrimidine sequences have the potential to adopt intramolecular triplex structures and are overrepresented upstream of genes in eukaryotes. These sequences may regulate gene expression by modulating the interaction of transcription factors with DNA sequences upstream of genes.
A poly purine.pyrimidine sequence with the potential to adopt an intramolecular triplex DNA structure was designed. The sequence was inserted within a nucleosome positioned upstream of the β-galactosidase gene in yeast, Saccharomyces cerevisiae, between the cycl promoter and gal 10 U pstream A ctivating S equences (UASg). Upon derepression with galactose, β-galactosidase gene expression is reduced 12-fold in cells carrying single copy poly purine.pyrimidine sequences. This reduction in expression is correlated with reduced transcription. Furthermore, we show that plasmids carrying a poly purine.pyrimidine sequence are not specifically lost from yeast cells.
We propose that a poly purine.pyrimidine sequence upstream of a gene affects transcription. Plasmids carrying this sequence are not specifically lost from cells and thus no additional effort is needed for the replication of these sequences in eukaryotic cells.
- Transcription Initiation
- Loop Sequence
- Reduce Gene Expression
- Galactose Medium
- Nucleosome Binding
Stretches of poly purine.pyrimidine (poly pur.pyr) sequences are overrepresented in the eukaryotic genome [1, 2] and often positioned upstream of genes [3, 4]. Many eukaryotic genes contain a poly pur.pyr box upstream of the coding region . Transcription factors may interact specifically with those regions as occurs upstream of the Drosophila hsp26 gene [6, 7] where transcription is enhanced during a heat shock.
Under torsional stress poly pur.pyr sequences have the potential to adopt an intramolecular triplex formation as HY-3 and H-Y5 [8–10]. A proposed triplex model fits with the regular poly pur.pyr tract with mirror symmetry  around a loop sequence. Shimizu et al. have shown that base composition in loop sequences affects intramolecular triplex formation while orientation of the insert in supercoiled plasmid has no effect on isomerisation of the two types of triplex DNA. Nonmirror symmetric poly pur.pyr sequences can also adopt an intramolecular triplex structure .
The in vivo existence of poly pur.pyr sequences as an intramolecular triplex has been detected in Escherichia coli[13, 14]. Modulation of gene expression by insertion of designed poly pur.pyr sequences within the E. coli genes [15, 16] and upstream of a gene in mouse cells has been demonstrated . Poly pur.pyr sequences in active regions of transcription form a DNA-RNA hybrid triplex and make the template transcriptionally inert . Poly homo purine.pyrimidine sequences stop in vitro replication and pause in vivo replication when cloned into a plasmid under the control of the SV40 promoter . Peleg et al. showed that the unwinding activity of the SV40 large T-antigen helicase is decreased in the presence of a triple helix in vitro. When the triplex structure is stabilized with BeP1 [benzo(c) pyridoindole], replication elongation is inhibited in plasmids by prokaryotic DNA polymerase . Friedreich Ataxia-associated poly pur.pyr expansion (GAA.TTC) when cloned in plasmids, shows inhibition of transcription and replication in cos-7 cells . However, structural aspects of the poly pur.pyr sequences as intramolecular triplex DNA and their role in different biological processes in transcription regulation, replication, recombination and interaction with the nucleosome in vivo have not been fully determined .
Poly pur.pyr sequences affect gene expression in yeast cells
We have taken advantage of the induction system of the β-galactosidase gene under the control of gall-gal 10 UASg. Upon derepression with galactose, enzyme expression is reduced about 12–50 fold (Fig. 3b and table 3c) in cells carrying single to multiple copies of poly pur.pyr inserts containing plasmids compared with duplex-carrying plasmids. No marked differences were observed in the enzyme activities in cells containing pLGSDS36 (480 units) and pAMDC61 (485 units) (i.e. insertion of extra DNA sequences of the same length as the poly pur.pyr sequence or separation of adjacent DNA sequences around the Xho1 site has no effect on β-galactosidase expression). Therefore, the presence of the poly pur.pyr sequence in the plasmid causes a reduction in β-galactosidase expression during derepression.
Reduced gene expression is correlated with reduced transcription
Poly pur.pyr insert carrying plasmids are not specifically lost from the cells
To determine whether plasmids carrying the poly pur.pyr sequence are specifically lost from cells after subsequent generations of growth in nonselective medium, plasmid stabilities and copy numbers were measured. Yeast cells do not maintain  these minichromosome vectors in 100% efficiency and typically 80–90% of cells carry these plasmids in high copy number (20–30 copies/cell) after transformation. Cells loose plasmids slowly during subsequent generations of growth in nonselective medium. However, it has been shown that when replication is impaired at the plasmid origin, copy number/cell rapidly decreases during subsequent culture (within 10–25 generations) and cells completely loose the plasmid . The percentage of cells maintaining plasmids is denoted as % stability. The % stability of each plasmid could be quantitated by the loss of a marker (ura3) from the cells, which will not grow in minimal medium devoid of uracil (CM-URA).
If replication of poly pur.pyr sequences in the plasmid were affected, a reduction in stability as well as in copy number would be expected  typically within 15–20 generations of growth. Figure 4a shows little difference in stabilities. Almost equal stability has been observed in both the cases after 20 generations of growth (i.e. cells are not preferentially loosing plasmids carrying a poly pur.pyr sequence). The copy number (Fig. 4c) of plasmids carrying a poly pur.pyr sequence (copy number, 2.6) compared with those carrying a duplex (copy number, 2.2) after 20 generations of growth does not differ significantly. If replication of the plasmid is impaired, a marked decrease in copy number of plasmids carrying a poly pur.pyr sequence would have been observed. These results suggest that plasmid replication may not be significantly reduced or affected by the presence of a poly pur.pyr sequence.
Poly pur.pyr sequences affect β-galactosidase expression
The yeast expression system has been used to illustrate the role of poly pur.pyr sequences in gene expression where the β-galactosidase gene is under the control of the cycl promoter and gall-gal 10 UASg.
The poly pur.pyr sequence designed has the potential to form an intramolecular triplex DNA structure and mimic sequences present naturally in the upstream region of various genes in yeast genome. Reduced β-galactosidase expression is due to reduced transcription initiation and poly pur.pyr sequences are involved in transcription initiation in vivo. The 61-mer sequence containing the poly pur.pyr sequence is S1 nuclease sensitive in supercoiled plasmid in vitro. In addition to their presence in the S. cerevisiae genome, loop sequences containing poly pur.pyr stretches are also known to be present upstream of various genes in eukaryotes [4, 28, 29] and are implicated to be involved in gene regulation.
No large decrease in stability and copy number of plasmids carrying the poly pur.pyr sequence was observed during subsequent generations of growth suggesting that the presence of this sequence does not affect replication in eukaryotic cells unlike the observation of Duval-Valentine et al. where prokaryotic DNA polymerases pause during replication in vitro. This supports the suggestion that no extra effort is needed by DNA polymerases to replicate such sequences that are abundant in the genome of eukaryotes. A plausible explanation is that the intramolecular triplex structure does not exist on naked DNA in eukaryotes rather such looped structure exists on the nucleosomal surface  and as replication proceeds, the nucleosome makes way  for the DNA polymerase, the intramolecular triplex structure resolves into duplex DNA and facilitates replication. It is possible that extra replication machinery in eukaryotic cells could resolve the intramolecular structure during replication. It has been observed that the SV40 large T-antigen has the unwinding capacity of intramolecular triplex during replication in vitro and replication termination in poly dT tract is relieved by mitochondrial single-strand binding proteins . It would be interesting to investigate whether these sequences form an intramolecular triplex structure at the nucleosomal surface in vivo. Further characterization of superhelical stress and other conditions of adopting an intramolecular triplex structure in the chromosome of eukaryotes are under investigation .
Saccaromyces cerevisiae strains  8534-10A (Cir+ mat a ura3-52, leu2-3 his 4Õ34) and (cir ° Mat a ura3-52, leu2-3 his 4534) were used in the study. Escherichia coli strain HB101 was used in all cloning procedures.
Design and cloning of poly pur.pyr stretch with a loop sequence
pLGSD5 [22, 25] is a yeast expression vector containing the β-galactosidase gene under the control of the upstream activating sequence of gall-gal 10 (UASg) and the cycl promoter. A multiple cloning site containing a 36 bp poly linker is cloned at the BamH1 site in the 5' of β-galactosidase gene to create pLGSDS36.
The 61-mer sequence containing a 58-mer poly pur.pyr sequence flanked by a Xho I site was synthesized and cloned at the Xho I site (-154 bp from translation start site; -130 bp from transcription initiation site) of pLGSDS36 at the junction of UASg and the CYC1 promoter to create pAMTS61 (single copy), pAMTM61 (a and b; multiple tandemly repeated; 4 and 5 copies) and pAMTMR61 (3 copies tandemly and 1 copy reversibly repeated) (Fig. 3a). The status and copy numbers were confirmed by restriction mapping and sequencing. A 61-mer duplex sequence flanked by a XhoI site was also synthesized and cloned at the Xho I site of pLGSDS36 to create pAMDC61.
β-galactosidase expression was measured in transformants grown in glucose medium (repressed state) and in galactose medium (derepressed state). Yeast cells transformants carrying the plasmids were grown in 10 mL of complete medium (YEPD) in the presence of glucose (2%) as the carbon source. After exponential growth, cells were centrifuged and resuspended in medium (500 mL) containing galactose (2%) as a carbon source to activate transcription. At specific time intervals during exponential growth beginning when the cells were transferred to galactose medium (OD600 about 0–0.04), (β-galactosidase expression was measured in aliquots of culture. Fewer cells (10 mL, OD600 = 2) were transferred to a large volume (500 mL) to allow the cells more divisions in galactose medium to attain subsequent growth to deplete the internal cellular glucose, which may partially repress transcription in their initial phase of growth in galactose. (β-galactosidase expression was measured as described by Reynolds and Lundablad  and expressed in Miller's unit . An aliquot of culture was plated on complete medium (YEPD) and replica plated onto minimal medium (CM-URA) to determine the percentage of cells carrying plasmids (% stability). Actual (β-galactosidase activities were obtained by multiplying average (β-galactosidase activity with the stability factor of each plasmid.
Stability and copy number determination
Plasmid stabilities and copy numbers were determined essentially as described earlier . Transformants carrying plasmids containing the poly pur.pyr sequence and the duplex sequence were grown in YEPD (rich medium) from a single colony to saturation and plated on YEPD plates after dilution. After sufficient growth, plates were replica plated onto CM-URA synthetic medium.
% Stability = (Number of colonies grown in CM-URA / number of colonies grown in YEPD) × 100.
Plasmid copy number was determined by quantifying ura3, which is present in single copy in yeast genome and presence of it in the multicopy plasmids. Total celullar DNA from yeast transformants was digested with Hind lll. A Southern blot was performed on the digested DNA using a 1.1 kb ura3 fragment as a probe. Autoradiograms were scanned using an Ultroscan Broma Laser Densitometer and average plasmid copy number was determined as the ratio of the area of ura3 on the plasmid band (8.2 kb coming from the multicopy plasmid) to the chromosomal band (2.0 kb; single copy). Actual copy number was determined by multiplying with the stability factor of each plasmid maintenance (actual number of cells carrying the plasmid).
Isolation of total RNA and northern hybridisation
Total celullar RNA was isolated by the hot phenol method  from each culture (grown in selective media with 2% galactose) of cells carrying pAMTS61 and pAMDC61. An equal amount of RNA was run in a MOPS-formaldehyde agarose gel and transferred to a nylon membrane with 20 × SSC. A 4.8 kb EcoR1 fragment carrying the entire lacZ and ura3 genes of pLGSDS36 was labeled with alpha-32P dATP by random priming and used as a probe for hybridization at 42°C in 5 × SSC, 50% formamide. Filters were washed twice with 2 × SSC (37°C) for 15 min and twice with 0.5 × SSC (42°C) and autoradiographed. Autoradiograms were scanned and the ratio of the intensities of lacZ transcripts to ura3 transcripts was calculated.
We thank Dr. P. S. Sarkar for designing poly pur.pyr sequences. Dr. L. Guarante for generous gift of plasmid, pLGSD5 and K. Usha for synthesizing oligonucleotides. We are thankful to "Sciencemanager" for careful editing of this manuscript. AKM is supported by DBT postdoctoral fellowship (R (1A) RA (NBTB)/ MBUAKM/92–777). SKB is supported by a grant from DBT, Govt of India. We are grateful to anonymous reviewers for their helpful comments to improve this manuscript.
- Tripathy J, Brahmachari SK: Distribution of simple repetative (TG/CA) n and (CT/AG) n sequences in human and Rodent genomes. J Biomol Struc & Dyn. 1991, 9: 387-397.View ArticleGoogle Scholar
- Behe MJ: An overabundance of long oligopurine tracts occurs in the genome of simple and complex eukaryotes. Nucl Acids Res. 1995, 23: 689-95.PubMed CentralView ArticlePubMedGoogle Scholar
- Wells RD, Collier DA, Hanvey JC, Shimizu M, Wohlrab F: The chemistry and biology of unusual DNA structures adopted by oligopurine. oligopyrimidine sequences. FASEB J. 1988, 2: 2939-49.PubMedGoogle Scholar
- Raghavan S, Burma PK, Brahmachari SK: Positional preferences of polypurine/polypyrimidine tracts in Saccharomyces cerevisiae genome: implications for cis regulation of gene expression. J Mol Evol. 1997, 45: 485-98.View ArticlePubMedGoogle Scholar
- De Martinoff G, Pohl V, Mercken L, van Ommen GJ, Vassert G: Structural organization of the bovine thyroglobulin gene and its 5'-flanking region. Eur J Biochem. 1987, 164: 591-599.View ArticleGoogle Scholar
- Glaser RL, Thomas GH, Siegfried E, Elgin SC, Lis JT: Optimal heat-induced expression of the Drosophila hsp26 gene requires a promoter sequence containing (CT) n. (GA) n repeats. J Mol Biol. 1990, 211: 751-61.View ArticlePubMedGoogle Scholar
- Lu Q, Wallrath LL, Granok H, Elgin SC: (CT) n (GA) n repeats and heat shock elements have distinct roles in chromatin structure and transcriptional activation of the Drosophila hsp26 gene. Mol Cell Biol. 1993, 5: 2802-2814.View ArticleGoogle Scholar
- Htun H, Dahlberg JE: Topology and formation of triple-stranded H-DNA. Science. 1989, 243: 1571-6.View ArticlePubMedGoogle Scholar
- Johnston BH: The S1-sensitive form of d(C-T)n.d(A-G)n: chemical evidence for a three-stranded structure in plasmids. Science. 1988, 241: 1800-4.View ArticlePubMedGoogle Scholar
- Shimizu M, Kubo K, Matsumoto U, Shindo H: The loop sequence plays crucial roles for isomerization of intramolecular DNA triplexes in supercoiled plasmids. J Mol Biol. 1994, 235: 185-97. 10.1006/jmbi.1994.1036View ArticlePubMedGoogle Scholar
- Mirkin SM, Lyamichev VI, Drushlyak KN, Dobrynin VN, Filippov SA, Frank-Kamenetskii MD: DNA H form requires a homopurine-homopyrimidine mirror repeat. Nature. 1987, 330: 495-7. 10.1038/330495a0View ArticlePubMedGoogle Scholar
- Klysic J: An intramolecular triplex structure from non mirror repeated sequence containing both py:pu.py and pu:pu.py triads. J Mol Biol. 1995, 245: 499-507. 10.1006/jmbi.1994.0041View ArticleGoogle Scholar
- Karlovsky P, Pecinka P, Vojtiskova M, Makaturova E, Palecek E: Protonated triplex DNA in E. coli cells as detected by chemical probing. FEES Lett. 1990, 274: 39-42. 10.1016/0014-5793(90)81324-H. 10.1016/0014-5793(90)81324-HView ArticleGoogle Scholar
- Kohwi Y, Malkhosyan SR, Kohwi-Shigematsu T: Intramolecular dG.dG.dC triplex detected in Escherichia coli cells. J Mol Biol. 1992, 223: 817-822.View ArticlePubMedGoogle Scholar
- Sarkar PS, Brahmachari SK: Intramolecular triplex potential sequence within a gene downregulates its expression in vivo. Nucl Acids Res. 1992, 20: 5713-5718.PubMed CentralView ArticlePubMedGoogle Scholar
- Duval-Valentin G, de Bizemont T, Takasugi M, Mergny JL, Bisagni E, Helene C: Triple-helix specific ligands stabilize H-DNA conformation. J Mol Biol. 1995, 247: 847-58. 10.1006/jmbi.1995.0185View ArticlePubMedGoogle Scholar
- Kohwi Y, Kohwi-Shigematsu T: Altered gene expression correlates with DNA structure. Genes Dev. 1991, 5: 2547-54.View ArticlePubMedGoogle Scholar
- Reaban ME, Griffin JA: Induction of RNA stabilized DNA conformers by transcription of an immunoglobulin switch region. Nature. 1990, 348: 342-344. 10.1038/348342a0View ArticlePubMedGoogle Scholar
- Rao BS: Regulation of DNA replication by homopurine/homopyrimidine sequences. Mol Cell Biochem. 1996, 156: 163-8.View ArticlePubMedGoogle Scholar
- Peleg M, Kopel V, Borowiec JA, Manor H: Formation of DNA triple helices inhibits DNA unwinding by the SV40 large T-antigen helicase. Nucleic Acids Res. 1995, 23: 1292-9.PubMed CentralView ArticlePubMedGoogle Scholar
- Ohshima K, Montermini L, Wells RD, Pandolfo M: Inhibitory effects of expanded GAA.TTC triplet repeats from intron I of the Friedreich ataxia gene on transcription and replication in vivo. J Biol Chem. 1998, 273: 14588-95. 10.1074/jbc.273.23.14588View ArticlePubMedGoogle Scholar
- Guarente L, Yocum RR, Gifford P: A GAL10-CYC1 hybrid yeast promoter identifies the GAL4 regulatory region as an upstream site. Proc Natl Acad Sci USA. 1982, 79: 7410-4.PubMed CentralView ArticlePubMedGoogle Scholar
- Fedor MJ, Lue NF, Kornberg RD: Statistical positioning of nucleosomes by specific protein-binding to an upstream activating sequence in yeast. J Mol Biol. 1988, 204: 109-27.View ArticlePubMedGoogle Scholar
- Morse RH: Nucleosome disruption by transcription factor binding in yeast. Science. 1993, 262: 1563-6.View ArticlePubMedGoogle Scholar
- Guarente L, Ptashne M: Fusion of Escherichia coli lacZ to the cytochrome c gene of Saccharomyces cerevisiae. Proc Natl Acad Sci USA. 1981, 78: 2199-203.PubMed CentralView ArticlePubMedGoogle Scholar
- Maiti AK, Sinha P: The mcm2 mutation of yeast affects replication, rather than segregation or amplification of the two micron plasmid. J Mol Biol. 1992, 224: 545-558.View ArticlePubMedGoogle Scholar
- Brahmachari SK, Meera G, Sarkar PS, Balagurumoorthy P, Tripathi J, Raghavan S, Shaligram U, Pataskar S: Simple repetitive sequences in the genome: structure and functional significance. Electrophoresis. 1995, 16: 1705-14.View ArticlePubMedGoogle Scholar
- Yagil G: Paranemic structures of DNA and their role in DNA unwinding. Crit Rev Biochem & Mol Biol. 1991, 26: 475-559.View ArticleGoogle Scholar
- Brahmachari SK, Sarkar PS, Raghavan S, Narayan M, Maiti AK: Polypurine/ polypyrimidine sequences as cis-acting transcriptional regulators. Gene. 1997, 190: 17-26. 10.1016/S0378-1119(97)00034-6View ArticlePubMedGoogle Scholar
- Tsukiyama T, Becker PB, Wu C: ATP-dependent nucleosome disruption at a heat-shock promoter mediated by binding of GAGA transcription factor. Nature. 1994, 367: 525-32. 10.1038/367525a0View ArticlePubMedGoogle Scholar
- Chasman DI, Lue NF, Buchman AR, LaPointe JW, Lorch Y, Kornberg RD: A yeast protein that influences the chromatin structure of UASg and functions as a powerful auxiliary gene activator. Genes Dev. 1990, 4: 503-14.View ArticlePubMedGoogle Scholar
- Westin L, Blomquist P, Milligan JF, Wrange O: Triple helix DNA alters nucleosomal histone-DNA interactions and acts as a nucleosome barrier. Nucleic Acids Res. 1995, 23: 2184-91.PubMed CentralView ArticlePubMedGoogle Scholar
- Larsen A, Weintraub H: An altered DNA conformation detected by S1 nuclease occurs at specific regions in active chick globin chromatin. Cell. 1982, 2: 609-622.View ArticleGoogle Scholar
- Bonne-Andrea C, Wong ML, Alberts BM: In vitro replication through nucleosomes without histone displacement. Nature. 1990, 343: 719-26. 10.1038/343719a0View ArticlePubMedGoogle Scholar
- Kopel V, Pozner A, Baran N, Manor H: Unwinding of the third strand of a DNA triple helix, a novel activity of the SV40 large T-antigen helicase. Nucleic Acids Res. 1996, 24: 330-5. 10.1093/nar/24.2.330PubMed CentralView ArticlePubMedGoogle Scholar
- Mikhailov VS, Bogenhagen DF: Termination within oligo(dT) tracts in template DNA by DNA polymerase gamma occurs with formation of a DNA triplex structure and is relieved by mitochondrial single-stranded DNA-binding protein. J Biol Chem. 1996, 271: 30774-80. 10.1074/jbc.271.48.30774View ArticlePubMedGoogle Scholar
- Reynolds A, Lundablad V: In current protocols in Molecular Biology (ed. Ausubel et al; Green publishing associates, inc and John willey and Sons. 1993Google Scholar
- Miller JH: experiments in molecular Genetics. (Cold spring harbour laboratory Press, Cold spring harbour, NY), . 1972Google Scholar
- Collart M, Oliviero S: Preparation of yeast RNA. In current protocols in Molecular Biology (ed. Ausubel et al; Green publishing associates, inc and John willey and Sons). 1993Google Scholar
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