ArticleNucleic acids research1994
Use of a selection technique to identify the diversity of binding sites for the yeast RAP1 transcription factor.
Article in Nucleic acids research, 1994. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed, 61 citations in OpenAlex.
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- DNA binding modes influence Rap1 activity in the regulation of telomere length and MRX functions at DNA ends.Nucleic acids research · 2020Article
- A sharp Pif1-dependent threshold separates DNA double-strand breaks from critically short telomeres.eLife · 2017Article
- Bug mapping and fitness testing of chemically synthesized chromosome X.Science (New York, N.Y.) · 2017Article
- The wrapping loop and Rap1 C-terminal (RCT) domain of yeast Rap1 modulate access to different DNA binding modes.The Journal of biological chemistry · 2015Article
- Alternative arrangements of telomeric recognition sites regulate the binding mode of the DNA-binding domain of yeast Rap1.Biophysical chemistry · 2015Article
- The DNA-binding domain of yeast Rap1 interacts with double-stranded DNA in multiple binding modes.Biochemistry · 2014Article
- The orientation of the C-terminal domain of the Saccharomyces cerevisiae Rap1 protein is determined by its binding to DNA.Nucleic acids research · 2012Article
- High resolution structure of the HDGF PWWP domain: a potential DNA binding domain.Protein science : a publication of the Protein Society · 2006Article
- Global nucleosome occupancy in yeast.Genome biology · 2004Article
- The different (sur)faces of Rap1p.Molecular genetics and genomics : MGG · 2003Review
- An algorithm for finding protein-DNA binding sites with applications to chromatin-immunoprecipitation microarray experiments.Nature biotechnology · 2002Article
- Telomere formation by rap1p binding site arrays reveals end-specific length regulation requirements and active telomeric recombination.Molecular and cellular biology · 2001Article
- Molecular basis for telomere repeat divergence in budding yeast.Molecular and cellular biology · 2001Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We have used the technique known as selected and amplified binding (SAAB) to isolate binding sites for the yeast transcription factor RAP1 from a degenerate pool of oligonucleotides. A total of 47 sequences were isolated, of which two were shown to be contaminating non-RAP1 binding sites. After excluding these two sequences the remainder of the sequences were used to derive a new consensus binding site for RAP1. The new consensus 5' A/G T A/G C A C C C A N N C C/A C C 3' is a significant extension of the existing consensus (4). It is longer by two base pairs at the 5' end and is significantly more constrained at the 3' end. An analysis of the combinations of mis-matches in individual SAAB sequences, compared to the consensus RAP1 binding site, has allowed us to analyse the structure of the RAP1 binding site in some detail. The binding site can be sub-divided into three regions; a core binding site, a 5' flanking region and a 3' flanking region. The core binding site, consisting of the sequence 5'CACCCA3', is critical for recognition by RAP1. The less conserved flanking regions are not as important. Interactions between RAP1 and these regions probably stabilise the interaction between RAP1 and the core binding site. Each of the sequences isolated in the SAAB analysis was used to search release 78 of the EMBL+GenBank DNA data base. The searches identified 102 potential binding sites for RAP1 within promoters of yeast genes.
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