Comparative Sequence Analysis and Patterns of Covariation in RNA Secondary Structures
A novel method of RNA secondary structure prediction based on a comparison of nucleotide sequences is described. This method correctly predicts nearly all evolutionarily conserved secondary structures of five different RNAs: tRNA, 5S rRNA, bacterial ribonuclease P (RNase P) RNA, eukaryotic small sub...
Gespeichert in:
| Veröffentlicht in: | Genetics (Austin) 2000-02, Vol.154 (2), p.909-921 |
|---|---|
| Hauptverfasser: | , , |
| Format: | Artikel |
| Sprache: | eng |
| Schlagworte: | |
| Online-Zugang: | Volltext |
| Tags: |
Tag hinzufügen
Keine Tags, Fügen Sie den ersten Tag hinzu!
|
| container_end_page | 921 |
|---|---|
| container_issue | 2 |
| container_start_page | 909 |
| container_title | Genetics (Austin) |
| container_volume | 154 |
| creator | Parsch, John Braverman, John M Stephan, Wolfgang |
| description | A novel method of RNA secondary structure prediction based on a comparison of nucleotide sequences is described. This method correctly predicts nearly all evolutionarily conserved secondary structures of five different RNAs: tRNA, 5S rRNA, bacterial ribonuclease P (RNase P) RNA, eukaryotic small subunit rRNA, and the 3' untranslated region (UTR) of the Drosophila bicoid (bcd) mRNA. Furthermore, covariations occurring in the helices of these conserved RNA structures are analyzed. Two physical parameters are found to be important determinants of the evolution of compensatory mutations: the length of a helix and the distance between base-pairing nucleotides. For the helices of bcd 3' UTR mRNA and RNase P RNA, a positive correlation between the rate of compensatory evolution and helix length is found. The analysis of Drosophila bcd 3' UTR mRNA further revealed that the rate of compensatory evolution decreases with the physical distance between base-pairing residues. This result is in qualitative agreement with Kimura's model of compensatory fitness interactions, which assumes that mutations occurring in RNA helices are individually deleterious but become neutral in appropriate combinations. |
| doi_str_mv | 10.1093/genetics/154.2.909 |
| format | Article |
| fullrecord | <record><control><sourceid>proquest_pubme</sourceid><recordid>TN_cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_1460946</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><sourcerecordid>17472491</sourcerecordid><originalsourceid>FETCH-LOGICAL-c553t-80accaefcc4a21fe0e792206487ae15a14601e8dec231a8fddb8199de53c59d63</originalsourceid><addsrcrecordid>eNqFkU9v1DAQxS1ERbeFL8ABRRy4ZetxHCe-IK1WhSJVBVF6tlxnsusqsRfb2VW_PV5t6R8unOYwv_f0Zh4h74HOgcrqbIUOkzXxDGo-Z3NJ5SsyA8mrkokKXpMZpSBK0VRwTE5ivKOUClm3b8gxUFHXjNMZuVn6caODTnaLxTX-ntAZLBZOD_fRxkK7rvihU8LgYuH7Yum3OthMe1dYV_y8WmSR8a7T4b64TmEyaQoY35KjXg8R3z3MU3Lz5fzX8qK8_P7123JxWZq6rlLZUm2Mxt4Yrhn0SLGRjFHB20Yj1Bq4oIBth4ZVoNu-625bkLLDujK17ER1Sj4ffDfT7YidQZeCHtQm2DEHUl5b9XLj7Fqt_FbtnSXfG3x6MAg-3x6TGm00OAzaoZ-iaqhkrZD_B6HhDeMSMvjxH_DOTyH_MyoGHPLTKcsQO0Am-BgD9o-Rgap9t-pvtyp3q5jK3WbRh-fHPpMcynzKuLar9c4GVHHUw5BxULvd7snpD_SusOM</addsrcrecordid><sourcetype>Open Access Repository</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>214124002</pqid></control><display><type>article</type><title>Comparative Sequence Analysis and Patterns of Covariation in RNA Secondary Structures</title><source>MEDLINE</source><source>Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals</source><source>Oxford University Press Journals All Titles (1996-Current)</source><source>Alma/SFX Local Collection</source><creator>Parsch, John ; Braverman, John M ; Stephan, Wolfgang</creator><creatorcontrib>Parsch, John ; Braverman, John M ; Stephan, Wolfgang</creatorcontrib><description>A novel method of RNA secondary structure prediction based on a comparison of nucleotide sequences is described. This method correctly predicts nearly all evolutionarily conserved secondary structures of five different RNAs: tRNA, 5S rRNA, bacterial ribonuclease P (RNase P) RNA, eukaryotic small subunit rRNA, and the 3' untranslated region (UTR) of the Drosophila bicoid (bcd) mRNA. Furthermore, covariations occurring in the helices of these conserved RNA structures are analyzed. Two physical parameters are found to be important determinants of the evolution of compensatory mutations: the length of a helix and the distance between base-pairing nucleotides. For the helices of bcd 3' UTR mRNA and RNase P RNA, a positive correlation between the rate of compensatory evolution and helix length is found. The analysis of Drosophila bcd 3' UTR mRNA further revealed that the rate of compensatory evolution decreases with the physical distance between base-pairing residues. This result is in qualitative agreement with Kimura's model of compensatory fitness interactions, which assumes that mutations occurring in RNA helices are individually deleterious but become neutral in appropriate combinations.</description><identifier>ISSN: 0016-6731</identifier><identifier>ISSN: 1943-2631</identifier><identifier>EISSN: 1943-2631</identifier><identifier>DOI: 10.1093/genetics/154.2.909</identifier><identifier>PMID: 10655240</identifier><identifier>CODEN: GENTAE</identifier><language>eng</language><publisher>United States: Genetics Soc America</publisher><subject>Analysis of Variance ; Animals ; bicoid (bcd) gene ; Drosophila ; Drosophila - genetics ; Genetics ; Nucleic Acid Conformation ; ribonuclease P ; Ribonucleic acid ; RNA ; RNA - chemistry ; rRNA ; rRNA 5S ; tRNA</subject><ispartof>Genetics (Austin), 2000-02, Vol.154 (2), p.909-921</ispartof><rights>Copyright Genetics Society of America Feb 2000</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c553t-80accaefcc4a21fe0e792206487ae15a14601e8dec231a8fddb8199de53c59d63</citedby><cites>FETCH-LOGICAL-c553t-80accaefcc4a21fe0e792206487ae15a14601e8dec231a8fddb8199de53c59d63</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>230,314,777,781,882,27905,27906</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/10655240$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Parsch, John</creatorcontrib><creatorcontrib>Braverman, John M</creatorcontrib><creatorcontrib>Stephan, Wolfgang</creatorcontrib><title>Comparative Sequence Analysis and Patterns of Covariation in RNA Secondary Structures</title><title>Genetics (Austin)</title><addtitle>Genetics</addtitle><description>A novel method of RNA secondary structure prediction based on a comparison of nucleotide sequences is described. This method correctly predicts nearly all evolutionarily conserved secondary structures of five different RNAs: tRNA, 5S rRNA, bacterial ribonuclease P (RNase P) RNA, eukaryotic small subunit rRNA, and the 3' untranslated region (UTR) of the Drosophila bicoid (bcd) mRNA. Furthermore, covariations occurring in the helices of these conserved RNA structures are analyzed. Two physical parameters are found to be important determinants of the evolution of compensatory mutations: the length of a helix and the distance between base-pairing nucleotides. For the helices of bcd 3' UTR mRNA and RNase P RNA, a positive correlation between the rate of compensatory evolution and helix length is found. The analysis of Drosophila bcd 3' UTR mRNA further revealed that the rate of compensatory evolution decreases with the physical distance between base-pairing residues. This result is in qualitative agreement with Kimura's model of compensatory fitness interactions, which assumes that mutations occurring in RNA helices are individually deleterious but become neutral in appropriate combinations.</description><subject>Analysis of Variance</subject><subject>Animals</subject><subject>bicoid (bcd) gene</subject><subject>Drosophila</subject><subject>Drosophila - genetics</subject><subject>Genetics</subject><subject>Nucleic Acid Conformation</subject><subject>ribonuclease P</subject><subject>Ribonucleic acid</subject><subject>RNA</subject><subject>RNA - chemistry</subject><subject>rRNA</subject><subject>rRNA 5S</subject><subject>tRNA</subject><issn>0016-6731</issn><issn>1943-2631</issn><issn>1943-2631</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2000</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><recordid>eNqFkU9v1DAQxS1ERbeFL8ABRRy4ZetxHCe-IK1WhSJVBVF6tlxnsusqsRfb2VW_PV5t6R8unOYwv_f0Zh4h74HOgcrqbIUOkzXxDGo-Z3NJ5SsyA8mrkokKXpMZpSBK0VRwTE5ivKOUClm3b8gxUFHXjNMZuVn6caODTnaLxTX-ntAZLBZOD_fRxkK7rvihU8LgYuH7Yum3OthMe1dYV_y8WmSR8a7T4b64TmEyaQoY35KjXg8R3z3MU3Lz5fzX8qK8_P7123JxWZq6rlLZUm2Mxt4Yrhn0SLGRjFHB20Yj1Bq4oIBth4ZVoNu-625bkLLDujK17ER1Sj4ffDfT7YidQZeCHtQm2DEHUl5b9XLj7Fqt_FbtnSXfG3x6MAg-3x6TGm00OAzaoZ-iaqhkrZD_B6HhDeMSMvjxH_DOTyH_MyoGHPLTKcsQO0Am-BgD9o-Rgap9t-pvtyp3q5jK3WbRh-fHPpMcynzKuLar9c4GVHHUw5BxULvd7snpD_SusOM</recordid><startdate>20000201</startdate><enddate>20000201</enddate><creator>Parsch, John</creator><creator>Braverman, John M</creator><creator>Stephan, Wolfgang</creator><general>Genetics Soc America</general><general>Genetics Society of America</general><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>4T-</scope><scope>4U-</scope><scope>7QP</scope><scope>7SS</scope><scope>7TK</scope><scope>7TM</scope><scope>8FD</scope><scope>FR3</scope><scope>K9.</scope><scope>M7N</scope><scope>P64</scope><scope>RC3</scope><scope>7X8</scope><scope>5PM</scope></search><sort><creationdate>20000201</creationdate><title>Comparative Sequence Analysis and Patterns of Covariation in RNA Secondary Structures</title><author>Parsch, John ; Braverman, John M ; Stephan, Wolfgang</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c553t-80accaefcc4a21fe0e792206487ae15a14601e8dec231a8fddb8199de53c59d63</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2000</creationdate><topic>Analysis of Variance</topic><topic>Animals</topic><topic>bicoid (bcd) gene</topic><topic>Drosophila</topic><topic>Drosophila - genetics</topic><topic>Genetics</topic><topic>Nucleic Acid Conformation</topic><topic>ribonuclease P</topic><topic>Ribonucleic acid</topic><topic>RNA</topic><topic>RNA - chemistry</topic><topic>rRNA</topic><topic>rRNA 5S</topic><topic>tRNA</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Parsch, John</creatorcontrib><creatorcontrib>Braverman, John M</creatorcontrib><creatorcontrib>Stephan, Wolfgang</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>Docstoc</collection><collection>University Readers</collection><collection>Calcium & Calcified Tissue Abstracts</collection><collection>Entomology Abstracts (Full archive)</collection><collection>Neurosciences Abstracts</collection><collection>Nucleic Acids Abstracts</collection><collection>Technology Research Database</collection><collection>Engineering Research Database</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Algology Mycology and Protozoology Abstracts (Microbiology C)</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Genetics Abstracts</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Genetics (Austin)</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Parsch, John</au><au>Braverman, John M</au><au>Stephan, Wolfgang</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Comparative Sequence Analysis and Patterns of Covariation in RNA Secondary Structures</atitle><jtitle>Genetics (Austin)</jtitle><addtitle>Genetics</addtitle><date>2000-02-01</date><risdate>2000</risdate><volume>154</volume><issue>2</issue><spage>909</spage><epage>921</epage><pages>909-921</pages><issn>0016-6731</issn><issn>1943-2631</issn><eissn>1943-2631</eissn><coden>GENTAE</coden><abstract>A novel method of RNA secondary structure prediction based on a comparison of nucleotide sequences is described. This method correctly predicts nearly all evolutionarily conserved secondary structures of five different RNAs: tRNA, 5S rRNA, bacterial ribonuclease P (RNase P) RNA, eukaryotic small subunit rRNA, and the 3' untranslated region (UTR) of the Drosophila bicoid (bcd) mRNA. Furthermore, covariations occurring in the helices of these conserved RNA structures are analyzed. Two physical parameters are found to be important determinants of the evolution of compensatory mutations: the length of a helix and the distance between base-pairing nucleotides. For the helices of bcd 3' UTR mRNA and RNase P RNA, a positive correlation between the rate of compensatory evolution and helix length is found. The analysis of Drosophila bcd 3' UTR mRNA further revealed that the rate of compensatory evolution decreases with the physical distance between base-pairing residues. This result is in qualitative agreement with Kimura's model of compensatory fitness interactions, which assumes that mutations occurring in RNA helices are individually deleterious but become neutral in appropriate combinations.</abstract><cop>United States</cop><pub>Genetics Soc America</pub><pmid>10655240</pmid><doi>10.1093/genetics/154.2.909</doi><tpages>13</tpages><oa>free_for_read</oa></addata></record> |
| fulltext | fulltext |
| identifier | ISSN: 0016-6731 |
| ispartof | Genetics (Austin), 2000-02, Vol.154 (2), p.909-921 |
| issn | 0016-6731 1943-2631 1943-2631 |
| language | eng |
| recordid | cdi_pubmedcentral_primary_oai_pubmedcentral_nih_gov_1460946 |
| source | MEDLINE; Elektronische Zeitschriftenbibliothek - Frei zugängliche E-Journals; Oxford University Press Journals All Titles (1996-Current); Alma/SFX Local Collection |
| subjects | Analysis of Variance Animals bicoid (bcd) gene Drosophila Drosophila - genetics Genetics Nucleic Acid Conformation ribonuclease P Ribonucleic acid RNA RNA - chemistry rRNA rRNA 5S tRNA |
| title | Comparative Sequence Analysis and Patterns of Covariation in RNA Secondary Structures |
| url | https://sfx.bib-bvb.de/sfx_tum?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-01-20T05%3A23%3A18IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-proquest_pubme&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Comparative%20Sequence%20Analysis%20and%20Patterns%20of%20Covariation%20in%20RNA%20Secondary%20Structures&rft.jtitle=Genetics%20(Austin)&rft.au=Parsch,%20John&rft.date=2000-02-01&rft.volume=154&rft.issue=2&rft.spage=909&rft.epage=921&rft.pages=909-921&rft.issn=0016-6731&rft.eissn=1943-2631&rft.coden=GENTAE&rft_id=info:doi/10.1093/genetics/154.2.909&rft_dat=%3Cproquest_pubme%3E17472491%3C/proquest_pubme%3E%3Curl%3E%3C/url%3E&disable_directlink=true&sfx.directlink=off&sfx.report_link=0&rft_id=info:oai/&rft_pqid=214124002&rft_id=info:pmid/10655240&rfr_iscdi=true |