{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,20]],"date-time":"2026-03-20T22:46:08Z","timestamp":1774046768525,"version":"3.50.1"},"reference-count":24,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":2817,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"funder":[{"DOI":"10.13039\/501100001742","name":"United States-Israel Binational Science Foundation","doi-asserted-by":"publisher","award":["2005280"],"award-info":[{"award-number":["2005280"]}],"id":[{"id":"10.13039\/501100001742","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100006492","name":"Division of Intramural Research","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100006492","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000071","name":"NICHD","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000071","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2009,3,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Motivation: The identification of functional cis-acting DNA regulatory elements is a crucial step towards understanding gene regulation. Ab initio motif detection algorithms have been extensively used in search of regulatory elements. Yet, their success in providing experimentally validated regulatory elements in vertebrates has been limited.<\/jats:p><jats:p>Results: Here we report in silico identification and in vivo validation of regulatory elements that determine enhanced gene expression in the pineal gland of zebrafish. Microarray data enabled detection of genes that exhibit high expression in the pineal gland. The promoter regions of these genes were computationally analyzed in order to identify overrepresented motifs. The highest ranking motif identified is a CRX\/OTX binding site, known to govern expression in the pineal gland and retina. The second highest ranking motif was not reported before; we experimentally validated its function in vivo by mutational analysis. The methodology presented here may be applicable as a general scheme for finding regulatory elements that contribute to tissue-specific gene expression.<\/jats:p><jats:p>Contacts: \u00a0yoavg@tauex.tau.ac.il; elieis@post.tau.ac.il<\/jats:p><jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btp031","type":"journal-article","created":{"date-parts":[[2009,1,16]],"date-time":"2009-01-16T01:44:59Z","timestamp":1232070299000},"page":"559-562","source":"Crossref","is-referenced-by-count":14,"title":["A new<i>cis<\/i>-acting regulatory element driving gene expression in the zebrafish pineal gland"],"prefix":"10.1093","volume":"25","author":[{"given":"Shahar","family":"Alon","sequence":"first","affiliation":[{"name":"1 Department of Neurobiology, The George S. Wise Faculty of Life Sciences, 2Raymond and Beverly Sackler School of Physics and Astronomy, 3Cancer Research Center, Sheba Medical Center, Tel Hashomer and Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel, 4Laboratory of Molecular Genetics and 5Program in Developmental Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA"}]},{"given":"Eli","family":"Eisenberg","sequence":"additional","affiliation":[{"name":"1 Department of Neurobiology, The George S. Wise Faculty of Life Sciences, 2Raymond and Beverly Sackler School of Physics and Astronomy, 3Cancer Research Center, Sheba Medical Center, Tel Hashomer and Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel, 4Laboratory of Molecular Genetics and 5Program in Developmental Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA"}]},{"given":"Jasmine","family":"Jacob-Hirsch","sequence":"additional","affiliation":[{"name":"1 Department of Neurobiology, The George S. Wise Faculty of Life Sciences, 2Raymond and Beverly Sackler School of Physics and Astronomy, 3Cancer Research Center, Sheba Medical Center, Tel Hashomer and Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel, 4Laboratory of Molecular Genetics and 5Program in Developmental Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA"}]},{"given":"Gideon","family":"Rechavi","sequence":"additional","affiliation":[{"name":"1 Department of Neurobiology, The George S. Wise Faculty of Life Sciences, 2Raymond and Beverly Sackler School of Physics and Astronomy, 3Cancer Research Center, Sheba Medical Center, Tel Hashomer and Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel, 4Laboratory of Molecular Genetics and 5Program in Developmental Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA"}]},{"given":"Gad","family":"Vatine","sequence":"additional","affiliation":[{"name":"1 Department of Neurobiology, The George S. Wise Faculty of Life Sciences, 2Raymond and Beverly Sackler School of Physics and Astronomy, 3Cancer Research Center, Sheba Medical Center, Tel Hashomer and Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel, 4Laboratory of Molecular Genetics and 5Program in Developmental Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA"}]},{"given":"Reiko","family":"Toyama","sequence":"additional","affiliation":[{"name":"1 Department of Neurobiology, The George S. Wise Faculty of Life Sciences, 2Raymond and Beverly Sackler School of Physics and Astronomy, 3Cancer Research Center, Sheba Medical Center, Tel Hashomer and Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel, 4Laboratory of Molecular Genetics and 5Program in Developmental Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA"}]},{"given":"Steven L.","family":"Coon","sequence":"additional","affiliation":[{"name":"1 Department of Neurobiology, The George S. Wise Faculty of Life Sciences, 2Raymond and Beverly Sackler School of Physics and Astronomy, 3Cancer Research Center, Sheba Medical Center, Tel Hashomer and Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel, 4Laboratory of Molecular Genetics and 5Program in Developmental Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA"}]},{"given":"David C.","family":"Klein","sequence":"additional","affiliation":[{"name":"1 Department of Neurobiology, The George S. Wise Faculty of Life Sciences, 2Raymond and Beverly Sackler School of Physics and Astronomy, 3Cancer Research Center, Sheba Medical Center, Tel Hashomer and Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel, 4Laboratory of Molecular Genetics and 5Program in Developmental Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA"}]},{"given":"Yoav","family":"Gothilf","sequence":"additional","affiliation":[{"name":"1 Department of Neurobiology, The George S. Wise Faculty of Life Sciences, 2Raymond and Beverly Sackler School of Physics and Astronomy, 3Cancer Research Center, Sheba Medical Center, Tel Hashomer and Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel, 4Laboratory of Molecular Genetics and 5Program in Developmental Endocrinology and Genetics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA"}]}],"member":"286","published-online":{"date-parts":[[2009,1,15]]},"reference":[{"key":"2023013110110126200_B1","doi-asserted-by":"crossref","first-page":"1210","DOI":"10.1210\/me.2003-0439","article-title":"Zebrafish serotonin-N-acetyltransferase-2 gene regulation: pineal-restrictive downstream module contains a functional E-box and three photoreceptor conserved elements","volume":"18","author":"Appelbaum","year":"2004","journal-title":"Mol. 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