Sequence-Dependent Kinks Induced in Curved DNA

McNamara, Peter; Bolshoy, Alexander; Trifonov, Edward N.; Harrington, R. M.

doi:10.1080/07391102.1990.10507827

Cited by 84 publications

(45 citation statements)

References 41 publications

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“…Another possibility is that this sequence is important for allowing a particular structure of the DNA and/or proteins in the P'Q-MCM1-otl complex necessary for stable complex formation. Given that TA dinucleotides have been implicated as a preferred kink site in DNA (28), an intriguing possibility is that residues 20A and 21T are important for bending of the DNA in this region.…”

Section: Discussionmentioning

confidence: 99%

Transcription of alpha-specific genes in Saccharomyces cerevisiae: DNA sequence requirements for activity of the coregulator alpha 1.

et al. 1993

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Transcription activation of a-specific genes in Saccharomyces cerevisiae is regulated by two proteins, MCM1 and al, which bind to DNA sequences, called P'Q elements, found upstream of a-specific genes. Neither MCM1 nor al alone binds efficiently to P'Q elements. Together, however, they bind cooperatively in a manner that requires both the P' sequence, which is a weak binding site for MCM1, and the Q sequence, which has been postulated to be the binding site for al. We analyzed a collection of point mutations in the P'Q element of the STE3 gene to determine the importance of individual base pairs for a-specific gene transcription. Within the 10-bp conserved Q sequence, mutations at only three positions strongly affected transcription activation in vivo.These same mutations did not affect the weak binding to P'Q displayed by MCM1 alone. In vitro DNA binding assays showed a direct correlation between the ability of the mutant sequences to form ternary P'Q-MCM1-al complexes and the degree to which transcription was activated in vivo. Thus, the ability of al and MCM1 to bind cooperatively to P'Q elements is critical for activation of a-specific genes. In all natural a-specific genes the Q sequence is adjacent to the degenerate side of P'. To test the significance of this geometry, we created several novel juxtapositions of P, P', and Q sequences. When the Q sequence was opposite the degenerate side, the composite QP' element was inactive as a promoter element in vivo and unable to form stable ternary QP'-MCM1-al complexes in vitro. We also found that addition of a Q sequence to a strong MCM1 binding site allows the addition of ad to the complex. This finding, together with the observation that Q-element point mutations affected ternary complex formation but not the weak binding of MCM1 alone, supports the idea that the Q sequence serves as a binding site for al.The a and a cell types of the yeast Saccharomyces cerevisiae express distinct sets of genes: a cells transcribe a-specific genes, and a cells transcribe a-specific genes. This differential transcription is achieved by a combinatorial strategy involving three proteins, MCM1, which is expressed in all cell types, and al and a2, which are expressed exclusively in a cells. At each gene set, unique regulatory complexes are formed by the binding of subsets of the three proteins to specific sites within the transcriptional control regions. Two complexes serve to activate transcription, and a third serves to repress transcription. The sum of their activities limits transcription of a-and a-specific genes to the appropriate cell type (for a review, see references 6, 16, and 45).Cell-type-specific transcription of a-specific genes is achieved by the action of MCM1 and a2 (Fig. 1). The upstream control regions of a-specific genes contain nearly perfect versions of the palindromic MCM1-binding site, the P box, flanked by a2-binding sites. MCM1 binds to these P boxes and is essential for transcription activation of the gene set in a cells (Fig. 1) (2,8,17,20,21,25,32). In ...

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Section: Discussionmentioning

confidence: 99%

Transcription of alpha-specific genes in Saccharomyces cerevisiae: DNA sequence requirements for activity of the coregulator alpha 1.

et al. 1993

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“…Dinucleotide sequences VOL. 21,2001 TELOMERIC REPEAT-SPECIFIC ENDONUCLEASE 105 such as TA, CA, and TG are known as specific DNA sites where kinks may occur under bending constraints (22). DNA kinks are defined as abrupt deflection of the double helical structure, leading to unstacking of two neighboring base pairs.…”

Section: Discussionmentioning

confidence: 99%

Sequence-Specific Recognition and Cleavage of Telomeric Repeat (TTAGG)_nby Endonuclease of Non-Long Terminal Repeat Retrotransposon TRAS1

Anzai

Takahashi

Fujiwara

2001

Molecular and Cellular Biology

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The telomere of the silkworm Bombyx mori consists of (TTAGG/CCTAA) n repeats and harbors a large number of telomeric repeat-specific non-long terminal repeat retrotransposons, such as TRAS1 and SART1. To understand how these retrotransposons recognize and integrate into the telomeric repeat in a sequence-specific manner, we expressed the apurinic-apryrimidinic endonuclease-like endonuclease domain of TRAS1 (TRAS1 EN), which is supposed to digest the target DNA, and characterized its enzymatic properties. Purified TRAS1 EN could generate specific nicks on both strands of the telomeric repeat sequence between T and A of the (TTAGG) n strand (bottom strand) and between C and T of the (CCTAA) n strand (top strand). These sites are consistent with insertion sites expected from the genomic structure of boundary regions of TRAS1. Time course studies of nicking activities on both strands revealed that the cleavages on the bottom strand preceded those on the top strand, supporting the target-primed reverse transcription model. TRAS1 EN could cleave the telomeric repeats specifically even if it was flanked by longer tracts of nontelomeric sequence, indicating that the target site specificity of the TRAS1 element was mainly determined by its EN domain. Based on mutation analyses, TRAS1 EN recognizes less than 10 bp around the initial cleavage site (upstream 7 bp and downstream 3 bp), and the GTTAG sequence especially is essential for the cleavage reaction on the bottom strand (5. . . TTAGGTT 2 AGG . . . 3). TRAS1 EN, the first identified endonuclease digesting telomeric repeats, may be used as a genetic tool to shorten the telomere in insects and some other organisms.

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“…A second pair of curved and noncurved fragments (the GC curve and GC noncurve) were constructed which did not contain A tracts. The GC curve contains the motif "CCGG" in phase with the pitch of the DNA helix (an average of once every 10.5 bp) and has been shown previously to be curved by anomalous electrophoretic mobility and ligation assays (33)(34)(35). The GC noncurve has a similar base composition to the GC curve but is designed such that the DNA is much less curved.…”

Section: Construction Of Plasmids Containing Synthetic Curved and Nonmentioning

confidence: 99%

DNA Binding Is Not Sufficient for H-NS-mediated Repression ofproU Expression

Jordi¹,

Fielder

Burns

et al. 1997

Journal of Biological Chemistry

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H-NS is a major component of bacterial chromatin and influences the expression of many genes. H-NS has beenshown to exhibit a binding preference for certain ATrich curved DNA elements in vitro. In this study we have addressed the factors that determine the specificity of H-NS action in vitro and in vivo. In bandshift studies, H-NS showed a slight binding preference for all curved sequences tested whether GC-based or AT-based; the specific architecture of the curve also influenced H-NS binding. In filter retention assays little difference in affinity could be detected for any sequence tested, including the downstream regulatory element (DRE) a downstream curved DNA element required for H-NS to repress transcription of the Salmonella typhimurium proU operon in vivo. A K d of 1-2 M was estimated for binding of H-NS to each of these sequences. In vivo, the distance between the proU promoter and the DRE, their relative orientations on the face of the DNA helix, and translation of the DRE had no major effect on proU regulation. None of the synthetic curved sequences tested could functionally replace the DRE in vivo. These data show that differential binding to curved DNA cannot account for the specificity of H-NS action in vivo. Furthermore, binding of H-NS to DNA per se is insufficient to repress the proU promoter. Thus, the DRE does not simply act as an H-NS binding site but must have a more specific role in mediating H-NS regulation of proU transcription.

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Sequence-Dependent Kinks Induced in Curved DNA

Cited by 84 publications

References 41 publications

Transcription of alpha-specific genes in Saccharomyces cerevisiae: DNA sequence requirements for activity of the coregulator alpha 1.

Transcription of alpha-specific genes in Saccharomyces cerevisiae: DNA sequence requirements for activity of the coregulator alpha 1.

Sequence-Specific Recognition and Cleavage of Telomeric Repeat (TTAGG)_nby Endonuclease of Non-Long Terminal Repeat Retrotransposon TRAS1

DNA Binding Is Not Sufficient for H-NS-mediated Repression ofproU Expression

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Sequence-Dependent Kinks Induced in Curved DNA

Cited by 84 publications

References 41 publications

Transcription of alpha-specific genes in Saccharomyces cerevisiae: DNA sequence requirements for activity of the coregulator alpha 1.

Transcription of alpha-specific genes in Saccharomyces cerevisiae: DNA sequence requirements for activity of the coregulator alpha 1.

Sequence-Specific Recognition and Cleavage of Telomeric Repeat (TTAGG)nby Endonuclease of Non-Long Terminal Repeat Retrotransposon TRAS1

DNA Binding Is Not Sufficient for H-NS-mediated Repression ofproU Expression

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Sequence-Specific Recognition and Cleavage of Telomeric Repeat (TTAGG)_nby Endonuclease of Non-Long Terminal Repeat Retrotransposon TRAS1