The effect of the fungal metabolite radicicol analog A on mRNA degradation
The AU-rich element (ARE) is a stability determinant found in the 3′ UTR of a number of short-lived mRNAs. The best characterized ARE is the Shaw–Kamen (SK) box or AUUUA motif. Previously, a fungal metabolite, radicicol analog A (RAA), was shown to destabilize SK box-containing mRNAs based on 16 mRN...
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| Veröffentlicht in: | Genomics (San Diego, Calif.) Calif.), 2007-12, Vol.90 (6), p.723-732 |
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| creator | Mak, Isabella W.Y. Liu, Lin Ling, Victor Kastelic, Tania |
| description | The AU-rich element (ARE) is a stability determinant found in the 3′ UTR of a number of short-lived mRNAs. The best characterized ARE is the Shaw–Kamen (SK) box or AUUUA motif. Previously, a fungal metabolite, radicicol analog A (RAA), was shown to destabilize SK box-containing mRNAs based on 16 mRNAs examined [T. Kastelic et al., Cytokine 8 (1996) 751–761]. Using serial analysis of gene expression (SAGE) to examine the global effect of RAA on mRNA expression in interferon-γ/lipopolysaccharide-stimulated THP-1 human monocytes, we observed that the expression level of greater than 99% of the SAGE tags was unchanged by RAA treatment and only 34 of the 17,608 unique tags annotated were reduced (
p
≤
0.0001). RAA destabilized approximately half of the down-regulated transcripts. Whereas all the destabilized mRNAs possessed at least one SK box, for transcripts not destabilized but nonetheless down-regulated, RAA appears to function by a SK box-independent mechanism not currently understood. |
| doi_str_mv | 10.1016/j.ygeno.2007.08.002 |
| format | Article |
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p
≤
0.0001). RAA destabilized approximately half of the down-regulated transcripts. Whereas all the destabilized mRNAs possessed at least one SK box, for transcripts not destabilized but nonetheless down-regulated, RAA appears to function by a SK box-independent mechanism not currently understood.</description><identifier>ISSN: 0888-7543</identifier><identifier>EISSN: 1089-8646</identifier><identifier>DOI: 10.1016/j.ygeno.2007.08.002</identifier><identifier>PMID: 17936575</identifier><language>eng</language><publisher>San Diego, CA: Elsevier Inc</publisher><subject>3' Untranslated Regions ; AU-rich element ; Base Sequence ; Biological and medical sciences ; Cell Line ; DNA Primers - genetics ; Down-Regulation - drug effects ; Fundamental and applied biological sciences. Psychology ; Fungi - metabolism ; Gene Expression - drug effects ; Gene expression profiling ; Genes. Genome ; Genetics of eukaryotes. Biological and molecular evolution ; Human ; Humans ; Interferon-gamma - pharmacology ; Lipopolysaccharides - pharmacology ; Macrolides - chemistry ; Macrolides - metabolism ; Macrolides - pharmacology ; Molecular and cellular biology ; Molecular genetics ; Monocyte/macrophage ; Monocytes - drug effects ; Monocytes - metabolism ; mRNA stability ; Radicicol analog ; Reverse Transcriptase Polymerase Chain Reaction ; RNA Stability - drug effects ; RNA, Messenger - genetics ; RNA, Messenger - metabolism ; SAGE ; SK box ; THP-1 cells</subject><ispartof>Genomics (San Diego, Calif.), 2007-12, Vol.90 (6), p.723-732</ispartof><rights>2007 Elsevier Inc.</rights><rights>2008 INIST-CNRS</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c387t-5325f6db93189eb04c71d4f87d2d6c6c430f2036d3094f34118e5753e8f404293</citedby><cites>FETCH-LOGICAL-c387t-5325f6db93189eb04c71d4f87d2d6c6c430f2036d3094f34118e5753e8f404293</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktohtml>$$Uhttps://dx.doi.org/10.1016/j.ygeno.2007.08.002$$EHTML$$P50$$Gelsevier$$Hfree_for_read</linktohtml><link.rule.ids>314,780,784,3548,27922,27923,45993</link.rule.ids><backlink>$$Uhttp://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=19912516$$DView record in Pascal Francis$$Hfree_for_read</backlink><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/17936575$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Mak, Isabella W.Y.</creatorcontrib><creatorcontrib>Liu, Lin</creatorcontrib><creatorcontrib>Ling, Victor</creatorcontrib><creatorcontrib>Kastelic, Tania</creatorcontrib><title>The effect of the fungal metabolite radicicol analog A on mRNA degradation</title><title>Genomics (San Diego, Calif.)</title><addtitle>Genomics</addtitle><description>The AU-rich element (ARE) is a stability determinant found in the 3′ UTR of a number of short-lived mRNAs. The best characterized ARE is the Shaw–Kamen (SK) box or AUUUA motif. Previously, a fungal metabolite, radicicol analog A (RAA), was shown to destabilize SK box-containing mRNAs based on 16 mRNAs examined [T. Kastelic et al., Cytokine 8 (1996) 751–761]. Using serial analysis of gene expression (SAGE) to examine the global effect of RAA on mRNA expression in interferon-γ/lipopolysaccharide-stimulated THP-1 human monocytes, we observed that the expression level of greater than 99% of the SAGE tags was unchanged by RAA treatment and only 34 of the 17,608 unique tags annotated were reduced (
p
≤
0.0001). RAA destabilized approximately half of the down-regulated transcripts. Whereas all the destabilized mRNAs possessed at least one SK box, for transcripts not destabilized but nonetheless down-regulated, RAA appears to function by a SK box-independent mechanism not currently understood.</description><subject>3' Untranslated Regions</subject><subject>AU-rich element</subject><subject>Base Sequence</subject><subject>Biological and medical sciences</subject><subject>Cell Line</subject><subject>DNA Primers - genetics</subject><subject>Down-Regulation - drug effects</subject><subject>Fundamental and applied biological sciences. Psychology</subject><subject>Fungi - metabolism</subject><subject>Gene Expression - drug effects</subject><subject>Gene expression profiling</subject><subject>Genes. Genome</subject><subject>Genetics of eukaryotes. Biological and molecular evolution</subject><subject>Human</subject><subject>Humans</subject><subject>Interferon-gamma - pharmacology</subject><subject>Lipopolysaccharides - pharmacology</subject><subject>Macrolides - chemistry</subject><subject>Macrolides - metabolism</subject><subject>Macrolides - pharmacology</subject><subject>Molecular and cellular biology</subject><subject>Molecular genetics</subject><subject>Monocyte/macrophage</subject><subject>Monocytes - drug effects</subject><subject>Monocytes - metabolism</subject><subject>mRNA stability</subject><subject>Radicicol analog</subject><subject>Reverse Transcriptase Polymerase Chain Reaction</subject><subject>RNA Stability - drug effects</subject><subject>RNA, Messenger - genetics</subject><subject>RNA, Messenger - metabolism</subject><subject>SAGE</subject><subject>SK box</subject><subject>THP-1 cells</subject><issn>0888-7543</issn><issn>1089-8646</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2007</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNp9kE1r3DAQhkVIabZpf0Eg6JLe7I4sWZYOOSwh_SK0UNKz0EqjjRbbSiRvIf--Sncht56GYZ73ZXgIuWDQMmDy06593uKc2g5gaEG1AN0JWTFQulFSyFOyAqVUM_SCn5F3pewAQHPVvSVnbNBc9kO_It_vH5BiCOgWmgJd6hb289aOdMLFbtIYF6TZ-uiiSyO1sx3Tlq5pmun068eaetzWq11imt-TN8GOBT8c5zn5_fn2_uZrc_fzy7eb9V3juBqWpuddH6TfaM6Uxg0INzAvghp856WTTnAIHXDpOWgRuGBMYX2VowoCRKf5Ofl46H3M6WmPZTFTLA7H0c6Y9sUwXSHWQwX5AXQ5lZIxmMccJ5ufDQPzotDszD-F5kWhAWWqwpq6PNbvNxP618zRWQWujoAtzo4h29nF8sppzbqeycpdHzisMv5EzKa4iLNDH3PVbXyK_33kLwhmji4</recordid><startdate>20071201</startdate><enddate>20071201</enddate><creator>Mak, Isabella W.Y.</creator><creator>Liu, Lin</creator><creator>Ling, Victor</creator><creator>Kastelic, Tania</creator><general>Elsevier Inc</general><general>Elsevier</general><scope>6I.</scope><scope>AAFTH</scope><scope>IQODW</scope><scope>CGR</scope><scope>CUY</scope><scope>CVF</scope><scope>ECM</scope><scope>EIF</scope><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7TM</scope><scope>8FD</scope><scope>FR3</scope><scope>M7N</scope><scope>P64</scope><scope>RC3</scope></search><sort><creationdate>20071201</creationdate><title>The effect of the fungal metabolite radicicol analog A on mRNA degradation</title><author>Mak, Isabella W.Y. ; Liu, Lin ; Ling, Victor ; Kastelic, Tania</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c387t-5325f6db93189eb04c71d4f87d2d6c6c430f2036d3094f34118e5753e8f404293</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2007</creationdate><topic>3' Untranslated Regions</topic><topic>AU-rich element</topic><topic>Base Sequence</topic><topic>Biological and medical sciences</topic><topic>Cell Line</topic><topic>DNA Primers - genetics</topic><topic>Down-Regulation - drug effects</topic><topic>Fundamental and applied biological sciences. Psychology</topic><topic>Fungi - metabolism</topic><topic>Gene Expression - drug effects</topic><topic>Gene expression profiling</topic><topic>Genes. Genome</topic><topic>Genetics of eukaryotes. Biological and molecular evolution</topic><topic>Human</topic><topic>Humans</topic><topic>Interferon-gamma - pharmacology</topic><topic>Lipopolysaccharides - pharmacology</topic><topic>Macrolides - chemistry</topic><topic>Macrolides - metabolism</topic><topic>Macrolides - pharmacology</topic><topic>Molecular and cellular biology</topic><topic>Molecular genetics</topic><topic>Monocyte/macrophage</topic><topic>Monocytes - drug effects</topic><topic>Monocytes - metabolism</topic><topic>mRNA stability</topic><topic>Radicicol analog</topic><topic>Reverse Transcriptase Polymerase Chain Reaction</topic><topic>RNA Stability - drug effects</topic><topic>RNA, Messenger - genetics</topic><topic>RNA, Messenger - metabolism</topic><topic>SAGE</topic><topic>SK box</topic><topic>THP-1 cells</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Mak, Isabella W.Y.</creatorcontrib><creatorcontrib>Liu, Lin</creatorcontrib><creatorcontrib>Ling, Victor</creatorcontrib><creatorcontrib>Kastelic, Tania</creatorcontrib><collection>ScienceDirect Open Access Titles</collection><collection>Elsevier:ScienceDirect:Open Access</collection><collection>Pascal-Francis</collection><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Nucleic Acids Abstracts</collection><collection>Technology Research Database</collection><collection>Engineering Research Database</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><jtitle>Genomics (San Diego, Calif.)</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Mak, Isabella W.Y.</au><au>Liu, Lin</au><au>Ling, Victor</au><au>Kastelic, Tania</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>The effect of the fungal metabolite radicicol analog A on mRNA degradation</atitle><jtitle>Genomics (San Diego, Calif.)</jtitle><addtitle>Genomics</addtitle><date>2007-12-01</date><risdate>2007</risdate><volume>90</volume><issue>6</issue><spage>723</spage><epage>732</epage><pages>723-732</pages><issn>0888-7543</issn><eissn>1089-8646</eissn><abstract>The AU-rich element (ARE) is a stability determinant found in the 3′ UTR of a number of short-lived mRNAs. The best characterized ARE is the Shaw–Kamen (SK) box or AUUUA motif. Previously, a fungal metabolite, radicicol analog A (RAA), was shown to destabilize SK box-containing mRNAs based on 16 mRNAs examined [T. Kastelic et al., Cytokine 8 (1996) 751–761]. Using serial analysis of gene expression (SAGE) to examine the global effect of RAA on mRNA expression in interferon-γ/lipopolysaccharide-stimulated THP-1 human monocytes, we observed that the expression level of greater than 99% of the SAGE tags was unchanged by RAA treatment and only 34 of the 17,608 unique tags annotated were reduced (
p
≤
0.0001). RAA destabilized approximately half of the down-regulated transcripts. Whereas all the destabilized mRNAs possessed at least one SK box, for transcripts not destabilized but nonetheless down-regulated, RAA appears to function by a SK box-independent mechanism not currently understood.</abstract><cop>San Diego, CA</cop><pub>Elsevier Inc</pub><pmid>17936575</pmid><doi>10.1016/j.ygeno.2007.08.002</doi><tpages>10</tpages><oa>free_for_read</oa></addata></record> |
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| source | MEDLINE; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; ScienceDirect Journals (5 years ago - present) |
| subjects | 3' Untranslated Regions AU-rich element Base Sequence Biological and medical sciences Cell Line DNA Primers - genetics Down-Regulation - drug effects Fundamental and applied biological sciences. Psychology Fungi - metabolism Gene Expression - drug effects Gene expression profiling Genes. Genome Genetics of eukaryotes. Biological and molecular evolution Human Humans Interferon-gamma - pharmacology Lipopolysaccharides - pharmacology Macrolides - chemistry Macrolides - metabolism Macrolides - pharmacology Molecular and cellular biology Molecular genetics Monocyte/macrophage Monocytes - drug effects Monocytes - metabolism mRNA stability Radicicol analog Reverse Transcriptase Polymerase Chain Reaction RNA Stability - drug effects RNA, Messenger - genetics RNA, Messenger - metabolism SAGE SK box THP-1 cells |
| title | The effect of the fungal metabolite radicicol analog A on mRNA degradation |
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