{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,6]],"date-time":"2026-02-06T20:51:08Z","timestamp":1770411068831,"version":"3.49.0"},"reference-count":20,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2016,10,1]],"date-time":"2016-10-01T00:00:00Z","timestamp":1475280000000},"content-version":"vor","delay-in-days":2536,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.0\/uk\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2010,1,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: \u00a0Prochlorococcus possesses the smallest genome of all sequenced photoautotrophs. Although the number of regulatory proteins in the genome is very small, the relative number of small regulatory RNAs is comparable with that of other bacteria. The compact genome size of Prochlorococcus offers an ideal system to search for targets of small RNAs (sRNAs) and to refine existing target prediction algorithms.<\/jats:p>\n               <jats:p>Results: Target predictions for the cyanobacterial sRNA Yfr1 were carried out with INTARNA in Prochlorococcus MED4. The ultraconserved Yfr1 sequence motif was defined as the putative interaction seed. To study the impact of Yfr1 on its predicted mRNA targets, a reporter system based on green fluorescent protein (GFP) was applied. We show that Yfr1 inhibits the translation of two predicted targets. We used mutation analysis to confirm that Yfr1 directly regulates its targets by an antisense interaction sequestering the ribosome binding site, and to assess the importance of interaction site accessibility.<\/jats:p>\n               <jats:p>Contact: \u00a0backofen@informatik.uni-freiburg.de; claudia.steglich@biologie.uni-freiburg.de<\/jats:p>\n               <jats:p>Supplementary information: \u00a0Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btp609","type":"journal-article","created":{"date-parts":[[2009,10,23]],"date-time":"2009-10-23T01:53:19Z","timestamp":1256262799000},"page":"1-5","source":"Crossref","is-referenced-by-count":59,"title":["Seed-based I<scp>nta<\/scp>RNA prediction combined with GFP-reporter system identifies mRNA targets of the small RNA Yfr1"],"prefix":"10.1093","volume":"26","author":[{"given":"Andreas S.","family":"Richter","sequence":"first","affiliation":[{"name":"1 Bioinformatics Group, University of Freiburg, Georges-K\u00f6hler-Allee 106, Freiburg D-79110, 2 Department of Pharmaceutical Biology and Biotechnology, University of Freiburg, Stefan-Meier-Str. 19 and 3 Genetics & Experimental Bioinformatics, University of Freiburg, Sch\u00e4nzlestr. 1, Freiburg D-79104, Germany"}]},{"given":"Christian","family":"Schleberger","sequence":"additional","affiliation":[{"name":"1 Bioinformatics Group, University of Freiburg, Georges-K\u00f6hler-Allee 106, Freiburg D-79110, 2 Department of Pharmaceutical Biology and Biotechnology, University of Freiburg, Stefan-Meier-Str. 19 and 3 Genetics & Experimental Bioinformatics, University of Freiburg, Sch\u00e4nzlestr. 1, Freiburg D-79104, Germany"}]},{"given":"Rolf","family":"Backofen","sequence":"additional","affiliation":[{"name":"1 Bioinformatics Group, University of Freiburg, Georges-K\u00f6hler-Allee 106, Freiburg D-79110, 2 Department of Pharmaceutical Biology and Biotechnology, University of Freiburg, Stefan-Meier-Str. 19 and 3 Genetics & Experimental Bioinformatics, University of Freiburg, Sch\u00e4nzlestr. 1, Freiburg D-79104, Germany"}]},{"given":"Claudia","family":"Steglich","sequence":"additional","affiliation":[{"name":"1 Bioinformatics Group, University of Freiburg, Georges-K\u00f6hler-Allee 106, Freiburg D-79110, 2 Department of Pharmaceutical Biology and Biotechnology, University of Freiburg, Stefan-Meier-Str. 19 and 3 Genetics & Experimental Bioinformatics, University of Freiburg, Sch\u00e4nzlestr. 1, Freiburg D-79104, Germany"}]}],"member":"286","published-online":{"date-parts":[[2009,10,22]]},"reference":[{"key":"2023012507531568400_B1","doi-asserted-by":"crossref","first-page":"134","DOI":"10.1016\/j.mib.2007.03.010","article-title":"Mechanism of RNA silencing by Hfq-binding small RNAs","volume":"10","author":"Aiba","year":"2007","journal-title":"Curr. 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