RAP1/YNL216W Summary

Standard Name	RAP1 (see Nomenclature conflict Note)
Systematic Name	YNL216W
Alias	GRF1 1 , TBA1 , TUF1
Feature Type	ORF, Verified
Description	Essential DNA-binding transcription regulator that binds at many loci; involved in either transcription activation or repression, chromatin silencing, and telomere length maintenance; conserved protein with an N-terminal BRCT domain, a central region with homology to the Myb DNA binding domain, and a C-terminal Rap1-specific protein-interaction domain (RCT domain) (2, 3, 4, 5, 6 and see Summary Paragraph)
Name Description	Repressor Activator Protein

Chromosomal Location	ChrXIV:241689 to 244172 \| ORF Map \| GBrowse

	Genetic position: -148 cM

Gene Ontology Annotations All RAP1 GO evidence and references

	View Computational GO annotations for RAP1
Molecular Function
Manually curated	core promoter proximal region sequence-specific DNA binding (IDA) DNA binding, bending (IDA) G-quadruplex DNA binding (IDA) nucleosomal DNA binding (IDA) RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity (IDA) RNA polymerase II transcription factor binding transcription factor activity (IDA) TBP-class protein binding RNA polymerase II transcription factor activity (IDA) telomeric DNA binding (IDA) TFIID-class transcription factor binding (IDA)
High-throughput	sequence-specific DNA binding (IDA)
Biological Process
Manually curated	chromatin silencing at silent mating-type cassette (IGI) chromatin silencing at telomere (IGI) establishment of chromatin silencing at telomere (IPI) establishment of protein localization to chromatin (IPI) establishment of protein localization to telomere (IPI) negative regulation of chromatin silencing (IDA) negative regulation of transcription from RNA polymerase II promoter (IMP) positive regulation of transcription from RNA polymerase II promoter (IMP) protection from non-homologous end joining at telomere (IMP) regulation of glycolysis by positive regulation of transcription from RNA polymerase II promoter (IGI) regulation of transcription by chromatin organization (IDA) telomere maintenance (IMP) telomere maintenance via telomere lengthening (IDA, IMP)
Cellular Component
Manually curated	nuclear chromosome (IDA) nuclear chromosome, telomeric region (IDA) nuclear nucleosome (IDA) nuclear telomere cap complex (IDA)

Regulatory Role

Binding motifs	Predicted RAP1 Binding Site Locations
	CACCCRWACA 15 [Search intergenic regions for CACCCRWACA] CAYCCRTRCA 16 [Search intergenic regions for CAYCCRTRCA] KGGTGTACNG 17 [Search intergenic regions for KGGTGTACNG] WRMACCCATACAYY 18 [Search intergenic regions for WRMACCCATACAYY]

Resources	ScerTF \| UniProbe \| YEASTRACT \| YeTFaSCo

Mutant phenotypes All RAP1 Phenotype evidence and references

Classical genetics
unspecified	silencing: increased telomere length: increased
Large-scale survey
null	competitive fitness: decreased haploinsufficient haploproficient inviable
overexpression	vegetative growth: decreased vegetative growth: decreased rate
reduction of function	competitive fitness: decreased resistance to methyl methanesulfonate: decreased
Resources	PROPHECY \| PhenoM \| SCMD \| ScreenTroll \| Yeast Fitness Database

interactions All RAP1 Interaction evidence and references

	356 total interaction(s) for 275 unique genes/features.
Physical Interactions	Affinity Capture-MS: 11 Affinity Capture-RNA: 1 Affinity Capture-Western: 20 Co-crystal Structure: 1 Co-localization: 2 Far Western: 2 PCA: 4 Reconstituted Complex: 15 Two-hybrid: 17
Genetic Interactions	Dosage Lethality: 3 Dosage Rescue: 4 Negative Genetic: 160 Phenotypic Enhancement: 3 Phenotypic Suppression: 7 Positive Genetic: 81 Synthetic Growth Defect: 6 Synthetic Lethality: 2 Synthetic Rescue: 17
Resources	BioGRID \| BOND \| BioPIXIE \| CYC2008 (complexes) \| Complexome \| DIP \| DRYGIN \| GeneMANIA \| InterologFinder

Expression Summary


Resources	Expression Summary \| Cell cycle and metabolic oscillation \| Cell cycle transcript profile \| Cyclebase \| Genevestigator \| GermOnline \| SPELL \| YMGV \| YeastFunc

Protein Information All RAP1 Protein evidence and references

Localization	YeastRC \| Organelle DB (UMich) \| YPL+ \| YeastGFP
Phosphorylation	PhosphoGRID \| PhosphoPep Database
Structure	GPMDB \| SCOP \| YeastRC
Homologs	Ashbya (AGD) \| Fungal Orthogroups Repository \| P-POD \| PDB Homologs \| PhylomeDB \| YGOB \| YOGY

sequence information

ChrXIV:241689 to 244172 | |

: -148 cM

Last Update

Coordinates: 2011-02-03 | Sequence: 1996-07-31

Subfeature details

	Relative Coordinates	Chromosomal Coordinates	Most Recent Updates
	Relative Coordinates	Chromosomal Coordinates	Coordinates	Sequence
CDS	1..2484	241689..244172	2011-02-03	1996-07-31

Retrieve sequences

Analyze Sequence

S288C only	BLASTP \| ATCC/WashU Clones \| BLASTN \| Design Primers \| Restriction Fragment Map \| Restriction Fragment Sizes \| Six-Frame Translation
S288C vs. other species	Fungal Alignment \| BLASTN vs. fungi \| BLASTP at NCBI \| BLASTP vs. fungi \| Synteny Viewer
S288C vs. other strains	Strain Alignment

Resources

External Links	All Associated Seq \| Entrez Gene \| Entrez RefSeq Protein \| MIPS \| Search all NCBI (Entrez) \| UniProtKB

Primary SGDID	S000005160

NOMENCLATURE CONFLICT NOTE

Name	Relevance	Description
TUF1	Nomenclature conflict	TUF1 has been used in the literature to refer to both RAP1/YNL216W (Shore, D. and Nasmyth, K. (1987) Cell 51:721; PMID:3315231), which encodes a transcription factor and telomere capping protein, and TUF1/YOR187W (Nagata, S. et al. (1983) Proc. Nat. Acad. Sci. 80:6192; PMID:6353412), which encodes mitochondrial translation elongation factor Tu.

SUMMARY PARAGRAPH for RAP1

RAP1 (Repressor Activator Protein) encodes an essential protein involved in many diverse, some seemingly contradictory, processes in S. cerevisiae, including telomere maintenance, transcriptional silencing (repression) of the silent mating loci HML and HMR, and high level transcriptional activation of genes encoding ribosomal proteins and glycolytic enzymes (7, 8, 9, 2). In these various roles, the underlying function of Rap1p is to bind DNA in a sequence specific manner, often regulating the chromatin structure in the region where it binds (10, 3). Rap1p binds extensively in telomeric regions, where its function is related to both transcriptional silencing and telomere maintenance (11). In its role as a transcription activating factor, the largest group of target genes are those that encode ribosomal proteins (2). In rapidly growing yeast cells, the transcription rate of these genes is extremely high, accounting for about twenty percent of the total mRNA content of the cell (12). Rap1p is known to be required for the transcription of several non-ribosomal protein genes, including HIS4 (13), ENO1 and ENO2 (14), and is implicated in transcriptional regulation of 185 additional genes (2).

Last updated: 2003-01-17

References cited on this page View Complete Literature Guide for RAP1

1)	Elledge SJ and Davis RW (1989) Identification of the DNA damage-responsive element of RNR2 and evidence that four distinct cellular factors bind it. Mol Cell Biol 9(12):5373-86
2)	Lieb JD, et al. (2001) Promoter-specific binding of Rap1 revealed by genome-wide maps of protein-DNA association. Nat Genet 28(4):327-34
3)	Konig P, et al. (1996) The crystal structure of the DNA-binding domain of yeast RAP1 in complex with telomeric DNA. Cell 85(1):125-36
4)	Pina B, et al. (2003) The different (sur)faces of Rap1p. Mol Genet Genomics 268(6):791-8
5)	Zhang W, et al. (2011) Solution structure of Rap1 BRCT domain from Saccharomyces cerevisiae reveals a novel fold. Biochem Biophys Res Commun 404(4):1055-9
6)	Chen Y, et al. (2011) A conserved motif within RAP1 has diversified roles in telomere protection and regulation in different organisms. Nat Struct Mol Biol 18(2):213-21
7)	Shore D and Nasmyth K (1987) Purification and cloning of a DNA binding protein from yeast that binds to both silencer and activator elements. Cell 51(5):721-32
8)	Vignais ML, et al. (1987) Specific binding of TUF factor to upstream activation sites of yeast ribosomal protein genes. EMBO J 6(5):1451-7
9)	Buchman AR, et al. (1988) Connections between transcriptional activators, silencers, and telomeres as revealed by functional analysis of a yeast DNA-binding protein. Mol Cell Biol 8(12):5086-99
10)	Morse RH (2000) RAP, RAP, open up! New wrinkles for RAP1 in yeast. Trends Genet 16(2):51-3
11)	Shore D (1997) Telomere length regulation: getting the measure of chromosome ends. Biol Chem 378(7):591-7
12)	Lascaris RF, et al. (1999) DNA-binding requirements of the yeast protein Rap1p as selected in silico from ribosomal protein gene promoter sequences. Bioinformatics 15(4):267-77
13)	Devlin C, et al. (1991) RAP1 is required for BAS1/BAS2- and GCN4-dependent transcription of the yeast HIS4 gene. Mol Cell Biol 11(7):3642-51
14)	Brindle PK, et al. (1990) Multiple factors bind the upstream activation sites of the yeast enolase genes ENO1 and ENO2: ABFI protein, like repressor activator protein RAP1, binds cis-acting sequences which modulate repression or activation of transcription. Mol Cell Biol 10(9):4872-85
15)	Badis G, et al. (2008) A library of yeast transcription factor motifs reveals a widespread function for Rsc3 in targeting nucleosome exclusion at promoters. Mol Cell 32(6):878-87
16)	Harbison CT, et al. (2004) Transcriptional regulatory code of a eukaryotic genome. Nature 431(7004):99-104
17)	Zhu C, et al. (2009) High-resolution DNA-binding specificity analysis of yeast transcription factors. Genome Res 19(4):556-66
18)	Matys V, et al. (2003) TRANSFAC: transcriptional regulation, from patterns to profiles. Nucleic Acids Res 31(1):374-8