{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,21]],"date-time":"2026-05-21T06:30:40Z","timestamp":1779345040488,"version":"3.51.4"},"reference-count":47,"publisher":"Elsevier BV","issue":"2","license":[{"start":{"date-parts":[[2002,4,1]],"date-time":"2002-04-01T00:00:00Z","timestamp":1017619200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Journal of Molecular Biology"],"published-print":{"date-parts":[[2002,4]]},"DOI":"10.1016\/s0022-2836(02)00110-9","type":"journal-article","created":{"date-parts":[[2002,10,10]],"date-time":"2002-10-10T22:35:05Z","timestamp":1034289305000},"page":"333-349","source":"Crossref","is-referenced-by-count":14,"title":["In Vivo Topography of Rap1p\u2013DNA Complex at Saccharomyces cerevisiae TEF2 UASRPG During Transcriptional Regulation"],"prefix":"10.1016","volume":"318","author":[{"given":"Veronica","family":"De Sanctis","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sabrina","family":"La Terra","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alessandro","family":"Bianchi","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"David","family":"Shore","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Luciano","family":"Burderi","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ernesto","family":"Di Mauro","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rodolfo","family":"Negri","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"78","reference":[{"key":"10.1016\/S0022-2836(02)00110-9_BIB1","doi-asserted-by":"crossref","first-page":"437","DOI":"10.1016\/S0968-0004(99)01460-7","article-title":"The economics of ribosome biosynthesis in yeast","volume":"24","author":"Warner","year":"1999","journal-title":"Trends Biochem. Sci."},{"key":"10.1016\/S0022-2836(02)00110-9_BIB2","doi-asserted-by":"crossref","first-page":"1063","DOI":"10.1093\/nar\/26.4.1063","article-title":"The C-terminal silencing domain of Rap1p is essential for the repression of the ribosomal protein genes in response to a defect in the secretory pathway","volume":"26","author":"Mizuta","year":"1998","journal-title":"Nucl. Acids Res."},{"key":"10.1016\/S0022-2836(02)00110-9_BIB3","doi-asserted-by":"crossref","first-page":"408","DOI":"10.1016\/0168-9525(94)90058-2","article-title":"RAP1: a protean regulator in yeast","volume":"10","author":"Shore","year":"1994","journal-title":"Trends Genet."},{"key":"10.1016\/S0022-2836(02)00110-9_BIB4","doi-asserted-by":"crossref","unstructured":"Lieb, J. L., Liu, X., & Brown, P. O. (2001). Promoter-specific binding of Rap1 revealed by genome-wide maps of protein\u2013DNA association. Nature Genetics Published Online: 16 July 2001, DOI:10.1038\/ng569.","DOI":"10.1038\/ng569"},{"key":"10.1016\/S0022-2836(02)00110-9_BIB5","doi-asserted-by":"crossref","first-page":"125","DOI":"10.1016\/S0092-8674(00)81088-0","article-title":"The crystal structure of the DNA-binding domain of yeast RAP1 in complex with telomeric DNA","volume":"85","author":"Konig","year":"1996","journal-title":"Cell"},{"key":"10.1016\/S0022-2836(02)00110-9_BIB6","doi-asserted-by":"crossref","first-page":"693","DOI":"10.1006\/jmbi.2000.4161","article-title":"How the multifunctional yeast Rap1p discriminates between DNA target sites: a crystallographic analysis","volume":"303","author":"Taylor","year":"2000","journal-title":"J. Mol. Biol."},{"key":"10.1016\/S0022-2836(02)00110-9_BIB7","doi-asserted-by":"crossref","first-page":"267","DOI":"10.1093\/bioinformatics\/15.4.267","article-title":"DNA-binding requirements of the yeast protein RAP1p as selected in silico from ribosomal protein gene promoter sequences","volume":"15","author":"Lascaris","year":"1999","journal-title":"Bioinformatics"},{"key":"10.1016\/S0022-2836(02)00110-9_BIB8","doi-asserted-by":"crossref","first-page":"2493","DOI":"10.1128\/MCB.14.4.2493","article-title":"Continued functioning of the secretory pathway is essential for ribosome synthesis","volume":"14","author":"Mizuta","year":"1994","journal-title":"Mol. Cell. Biol."},{"key":"10.1016\/S0022-2836(02)00110-9_BIB9","doi-asserted-by":"crossref","first-page":"5279","DOI":"10.1128\/MCB.19.8.5279","article-title":"Chromatin opening as transactivator potentiation by RAP1 in Saccharomyces cerevisiae","volume":"19","author":"Yu","year":"1999","journal-title":"Mol. Cell. Biol."},{"key":"10.1016\/S0022-2836(02)00110-9_BIB10","doi-asserted-by":"crossref","first-page":"5847","DOI":"10.1128\/MCB.20.16.5847-5857.2000","article-title":"Artificially recruited TATA-binding protein fails to remodel chromatin and does not activate three promoters that require chromatin remodeling","volume":"20","author":"Ryan","year":"2000","journal-title":"Mol. Cell. Biol."},{"key":"10.1016\/S0022-2836(02)00110-9_BIB11","doi-asserted-by":"crossref","first-page":"51","DOI":"10.1016\/S0168-9525(99)01936-8","article-title":"RAP, RAP, open up! New wrinkles for RAP1 in yeast","volume":"16","author":"Morse","year":"2000","journal-title":"Trends Genet."},{"key":"10.1016\/S0022-2836(02)00110-9_BIB12","doi-asserted-by":"crossref","first-page":"293","DOI":"10.1006\/jmbi.1993.1283","article-title":"Distortion of the DNA double helix by RAP1 at silencers and multiple telomeric binding sites","volume":"231","author":"Gilson","year":"1993","journal-title":"J. Mol. Biol."},{"key":"10.1016\/S0022-2836(02)00110-9_BIB13","doi-asserted-by":"crossref","first-page":"757","DOI":"10.1006\/jmbi.1998.2130","article-title":"Quantitative analysis of multiple-hit footprinting studies to characterize DNA conformational changes in protein\u2013DNA complexes: application to DNA opening by E(70 RNA polymerase","volume":"283","author":"Tsodikov","year":"1998","journal-title":"J. Mol. Biol."},{"key":"10.1016\/S0022-2836(02)00110-9_BIB14","doi-asserted-by":"crossref","first-page":"3166","DOI":"10.1128\/MCB.21.9.3166-3178.2001","article-title":"RNA polymerase III transcription complexes on chromosomal 5S rRNA genes in vivo: TFIIIB occupancy and promoter opening","volume":"21","author":"Costanzo","year":"2001","journal-title":"Mol. Cell. Biol"},{"key":"10.1016\/S0022-2836(02)00110-9_BIB15","doi-asserted-by":"crossref","first-page":"3084","DOI":"10.1016\/S0021-9258(18)89476-5","article-title":"Elongation factor 1\u03b1 from Saccharomyces cerevisiae","volume":"260","author":"Thiele","year":"1985","journal-title":"J. Biol. Chem."},{"key":"10.1016\/S0022-2836(02)00110-9_BIB16","doi-asserted-by":"crossref","first-page":"721","DOI":"10.1016\/0092-8674(87)90095-X","article-title":"Purification and cloning of a DNA binding protein from yeast that binds to both silencer and activator elements","volume":"51","author":"Shore","year":"1987","journal-title":"Cell"},{"key":"10.1016\/S0022-2836(02)00110-9_BIB17","doi-asserted-by":"crossref","first-page":"5086","DOI":"10.1128\/MCB.8.12.5086","article-title":"Connections between transcriptional activators, silencers and telomers as revealed by functional analysis of a yeast DNA-binding protein","volume":"8","author":"Buchman","year":"1988","journal-title":"Mol. Cell. Biol."},{"key":"10.1016\/S0022-2836(02)00110-9_BIB18","doi-asserted-by":"crossref","first-page":"3648","DOI":"10.1073\/pnas.84.11.3648","article-title":"TUF, the DNA-binding factor specific for UASRPG upstream activating sequences: identification of the proteins and its DNA-binding domain","volume":"84","author":"Huet","year":"1987","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"10.1016\/S0022-2836(02)00110-9_BIB19","doi-asserted-by":"crossref","first-page":"14669","DOI":"10.1016\/S0021-9258(18)77354-7","article-title":"Contacts between the factor TUF and RPG sequences","volume":"265","author":"Vignais","year":"1990","journal-title":"J. Biol. Chem."},{"key":"10.1016\/S0022-2836(02)00110-9_BIB20","doi-asserted-by":"crossref","first-page":"2431","DOI":"10.1002\/j.1460-2075.1993.tb05897.x","article-title":"GCR1, a transcriptional activator in Saccharomyces cerevisiae, complexes with RAP1 and can function without its DNA binding domain","volume":"12","author":"Tornow","year":"1993","journal-title":"EMBO J."},{"key":"10.1016\/S0022-2836(02)00110-9_BIB21","doi-asserted-by":"crossref","first-page":"79","DOI":"10.1016\/0378-1119(90)90441-S","article-title":"Efficient expression of the Saccharomyces cerevisiae glycolytic gene ADH1 is dependent upon a cis-acting regulatory element (UASRPG) found initially in genes encoding ribosomal proteins","volume":"90","author":"Tornow","year":"1990","journal-title":"Gene"},{"key":"10.1016\/S0022-2836(02)00110-9_BIB22","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1093\/genetics\/158.1.133","article-title":"Rap1p requires Gcr1p and Gcr2p homodimers to activate ribosomal protein and glycolytic genes, respectively","volume":"158","author":"Deminoff","year":"2001","journal-title":"Genetics"},{"key":"10.1016\/S0022-2836(02)00110-9_BIB23","doi-asserted-by":"crossref","first-page":"5393","DOI":"10.1128\/MCB.19.8.5393","article-title":"Transcriptional elements involved in the repression of the ribosomal protein synthesis","volume":"19","author":"Li","year":"1999","journal-title":"Mol. Cell. Biol."},{"key":"10.1016\/S0022-2836(02)00110-9_BIB24","doi-asserted-by":"crossref","first-page":"143","DOI":"10.1016\/0378-1119(94)90248-8","article-title":"Differential transcription of the two Saccharomyces cerevisiae genes encoding elongation factor 2","volume":"148","author":"Veldman","year":"1994","journal-title":"Gene"},{"key":"10.1016\/S0022-2836(02)00110-9_BIB25","doi-asserted-by":"crossref","first-page":"2723","DOI":"10.1128\/MCB.11.5.2723","article-title":"Association of RAP1 binding sites with stringent control of ribosomal protein gene transcription in Saccharomyces cerevisiae","volume":"11","author":"Moehle","year":"1991","journal-title":"Mol. Cell. Biol."},{"key":"10.1016\/S0022-2836(02)00110-9_BIB26","doi-asserted-by":"crossref","first-page":"7749","DOI":"10.1073\/pnas.88.17.7749","article-title":"Separation of transcriptional activation and silencing functions of the RAP1-encoded repressor\/activator protein 1: isolation of viable mutants affecting both silencing and telomere length","volume":"88","author":"Sussel","year":"1991","journal-title":"Proc. Natl Acad. Sci. USA"},{"key":"10.1016\/S0022-2836(02)00110-9_BIB27","doi-asserted-by":"crossref","first-page":"1146","DOI":"10.1101\/gad.7.7a.1146","article-title":"RAP1 and telomere structure regulate telomere position effects in Saccharomyces cerevisiae","volume":"7","author":"Kyrion","year":"1993","journal-title":"Genes Dev."},{"key":"10.1016\/S0022-2836(02)00110-9_BIB28","doi-asserted-by":"crossref","first-page":"2257","DOI":"10.1101\/gad.8.19.2257","article-title":"Evidence that a complex of SIR proteins interacts with the silencer and telomere-binding protein RAP1","volume":"8","author":"Moretti","year":"1994","journal-title":"Genes Dev."},{"key":"10.1016\/S0022-2836(02)00110-9_BIB29","doi-asserted-by":"crossref","first-page":"1786","DOI":"10.1128\/JVI.66.3.1786-1790.1992","article-title":"EBNA1 distorts oriP, the Epstein\u2013Barr virus latent replication origin","volume":"66","author":"Frappier","year":"1992","journal-title":"J. Virol."},{"key":"10.1016\/S0022-2836(02)00110-9_BIB30","doi-asserted-by":"crossref","first-page":"26090","DOI":"10.1074\/jbc.M101746200","article-title":"Alternative mechanisms of transcriptional activation by Rap1p","volume":"276","author":"Idrissi","year":"2001","journal-title":"J. Biol. Chem."},{"key":"10.1016\/S0022-2836(02)00110-9_BIB31","doi-asserted-by":"crossref","first-page":"616","DOI":"10.1101\/gad.5.4.616","article-title":"RAP1 protein activates and silences transcription of mating type genes in yeast","volume":"5","author":"Kurtz","year":"1991","journal-title":"Genes Dev."},{"key":"10.1016\/S0022-2836(02)00110-9_BIB32","doi-asserted-by":"crossref","first-page":"925","DOI":"10.1006\/jmbi.1998.2215","article-title":"Structural and functional heterogeneity of Rap1p complexes with telomeric and UASRPG-like sequences","volume":"284","author":"Idrissi","year":"1998","journal-title":"J. Mol. Biol."},{"key":"10.1016\/S0022-2836(02)00110-9_BIB33","doi-asserted-by":"crossref","first-page":"477","DOI":"10.1042\/0264-6021:3410477","article-title":"Functional divergence between the half-sites of the DNA binding sequences for the yeast transcriptional regulator Rap1p","volume":"341","author":"Idrissi","year":"1999","journal-title":"Biochem. J."},{"key":"10.1016\/S0022-2836(02)00110-9_BIB34","doi-asserted-by":"crossref","first-page":"1089","DOI":"10.1101\/gad.13.9.1089","article-title":"UASrpg can function as a heterochromatin boundary element in yeast","volume":"13","author":"Bi","year":"1999","journal-title":"Genes Dev."},{"key":"10.1016\/S0022-2836(02)00110-9_BIB35","doi-asserted-by":"crossref","first-page":"3187","DOI":"10.1128\/MCB.16.6.3187","article-title":"Activation mechanism of the multifunctional transcription factor repressor\u2013activator protein 1","volume":"16","author":"Drazinic","year":"1996","journal-title":"Mol. Cell. Biol."},{"key":"10.1016\/S0022-2836(02)00110-9_BIB36","doi-asserted-by":"crossref","first-page":"1450","DOI":"10.1093\/nar\/22.8.1450","article-title":"A simple in vivo footprinting method to examine DNA-protein interactions over the yeast PYK UAS element","volume":"22","author":"Dumitru","year":"1993","journal-title":"Nucl. Acids Res."},{"key":"10.1016\/S0022-2836(02)00110-9_BIB37","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1016\/S0968-0004(97)01008-6","article-title":"Recognition of telomeric DNA","volume":"22","author":"Konig","year":"1997","journal-title":"Trends Biochem. Sci."},{"key":"10.1016\/S0022-2836(02)00110-9_BIB38","doi-asserted-by":"crossref","first-page":"2292","DOI":"10.1093\/nar\/28.12.2292","article-title":"Saccharomyces cerevisiae RAP1 binds to telomeric sequences with spatial flexibility","volume":"28","author":"Wahlin","year":"2000","journal-title":"Nucl. Acids Res."},{"key":"10.1016\/S0022-2836(02)00110-9_BIB39","doi-asserted-by":"crossref","first-page":"8463","DOI":"10.1016\/S0021-9258(18)81810-5","article-title":"Asymmetric DNA bending induced by the yeast multifunctional factor TUF","volume":"264","author":"Vignais","year":"1989","journal-title":"J. Biol. Chem."},{"key":"10.1016\/S0022-2836(02)00110-9_BIB40","doi-asserted-by":"crossref","first-page":"1297","DOI":"10.1016\/S1097-2765(00)00128-3","article-title":"Coordinate regulation of yeast ribosomal protein genes is associated with targeted recruitment of Esa1 histone acetylase","volume":"6","author":"Reid","year":"2000","journal-title":"Mol. Cell."},{"key":"10.1016\/S0022-2836(02)00110-9_BIB41","unstructured":"Tennant, A. F. 1991. The QDP\/PLT User's Guide. NASA Technical Memorandum 4301."},{"key":"10.1016\/S0022-2836(02)00110-9_BIB42","series-title":"Data Reduction and Error Analysis for the Physical Sciences","author":"Bevington","year":"1969"},{"key":"10.1016\/S0022-2836(02)00110-9_BIB43","doi-asserted-by":"crossref","first-page":"431","DOI":"10.1137\/0111030","article-title":"An algorithm for least squares estimation of non linear parameters","volume":"11","author":"Marquardt","year":"1963","journal-title":"J. Soc. Ind. Appl. Math."},{"key":"10.1016\/S0022-2836(02)00110-9_BIB44","doi-asserted-by":"crossref","first-page":"177","DOI":"10.1086\/154592","article-title":"Parameter estimation in X-ray astronomy","volume":"208","author":"Lampton","year":"1976","journal-title":"Astrophys. J."},{"key":"10.1016\/S0022-2836(02)00110-9_BIB45","first-page":"169","article-title":"Mapping of yeast nucleosomes in vivo","volume":"6","author":"Buttinelli","year":"1995","journal-title":"Methods Mol. Genet."},{"key":"10.1016\/S0022-2836(02)00110-9_BIB46","doi-asserted-by":"crossref","first-page":"261","DOI":"10.1016\/0301-4622(95)00034-U","article-title":"Influence of dynamic fluctuations on DNA curvature","volume":"55","author":"De Santis","year":"1995","journal-title":"Biophys. Chem."},{"key":"10.1016\/S0022-2836(02)00110-9_BIB47","doi-asserted-by":"crossref","first-page":"903","DOI":"10.1006\/jmbi.2001.4458","article-title":"Specific interactions of the telomeric protein Rap1p with nucleosomal binding sites","volume":"306","author":"Rossetti","year":"2001","journal-title":"J. Mol. Biol."}],"container-title":["Journal of Molecular Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0022283602001109?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S0022283602001109?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2021,5,14]],"date-time":"2021-05-14T18:38:54Z","timestamp":1621017534000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S0022283602001109"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2002,4]]},"references-count":47,"journal-issue":{"issue":"2","published-print":{"date-parts":[[2002,4]]}},"alternative-id":["S0022283602001109"],"URL":"https:\/\/doi.org\/10.1016\/s0022-2836(02)00110-9","relation":{},"ISSN":["0022-2836"],"issn-type":[{"value":"0022-2836","type":"print"}],"subject":[],"published":{"date-parts":[[2002,4]]}}}