Formation, regulation and evolution of Caenorhabditis elegans 3?UTRs.
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| Title: | Formation, regulation and evolution of Caenorhabditis elegans 3?UTRs. |
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| Authors: | Jan, Calvin H., Friedman, Robin C., Ruby, J. Graham, Bartel, David P. |
| Source: | Nature. 1/6/2011, Vol. 469 Issue 7328, p97-101. 5p. 1 Diagram, 3 Graphs. |
| Subjects: | Caenorhabditis elegans, Genetic regulation, Messenger RNA, Gene expression, Non-coding RNA |
| Abstract: | Post-transcriptional gene regulation frequently occurs through elements in mRNA 3? untranslated regions (UTRs). Although crucial roles for 3?UTR-mediated gene regulation have been found in Caenorhabditis elegans, most C. elegans genes have lacked annotated 3?UTRs. Here we describe a high-throughput method for reliable identification of polyadenylated RNA termini, and we apply this method, called poly(A)-position profiling by sequencing (3P-Seq), to determine C. elegans 3?UTRs. Compared to standard methods also recently applied to C. elegans UTRs, 3P-Seq identified 8,580 additional UTRs while excluding thousands of shorter UTR isoforms that do not seem to be authentic. Analysis of this expanded and corrected data set suggested that the high A/U content of C. elegans 3?UTRs facilitated genome compaction, because the elements specifying cleavage and polyadenylation, which are A/U rich, can more readily emerge in A/U-rich regions. Indeed, 30% of the protein-coding genes have mRNAs with alternative, partially overlapping end regions that generate another 10,480 cleavage and polyadenylation sites that had gone largely unnoticed and represent potential evolutionary intermediates of progressive UTR shortening. Moreover, a third of the convergently transcribed genes use palindromic arrangements of bidirectional elements to specify UTRs with convergent overlap, which also contributes to genome compaction by eliminating regions between genes. Although nematode 3?UTRs have median length only one-sixth that of mammalian 3?UTRs, they have twice the density of conserved microRNA sites, in part because additional types of seed-complementary sites are preferentially conserved. These findings reveal the influence of cleavage and polyadenylation on the evolution of genome architecture and provide resources for studying post-transcriptional gene regulation. [ABSTRACT FROM AUTHOR] |
| Copyright of Nature is the property of Springer Nature and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.) | |
| Database: | Psychology and Behavioral Sciences Collection |
| FullText | Links: – Type: pdflink Text: Availability: 0 |
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| Header | DbId: pbh DbLabel: Psychology and Behavioral Sciences Collection An: 57144098 AccessLevel: 6 PubType: Academic Journal PubTypeId: academicJournal PreciseRelevancyScore: 0 |
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| Items | – Name: Title Label: Title Group: Ti Data: Formation, regulation and evolution of Caenorhabditis elegans 3?UTRs. – Name: Author Label: Authors Group: Au Data: <searchLink fieldCode="AR" term="%22Jan%2C+Calvin+H%2E%22">Jan, Calvin H.</searchLink><br /><searchLink fieldCode="AR" term="%22Friedman%2C+Robin+C%2E%22">Friedman, Robin C.</searchLink><br /><searchLink fieldCode="AR" term="%22Ruby%2C+J%2E+Graham%22">Ruby, J. Graham</searchLink><br /><searchLink fieldCode="AR" term="%22Bartel%2C+David+P%2E%22">Bartel, David P.</searchLink> – Name: TitleSource Label: Source Group: Src Data: <searchLink fieldCode="JN" term="%22Nature%22">Nature</searchLink>. 1/6/2011, Vol. 469 Issue 7328, p97-101. 5p. 1 Diagram, 3 Graphs. – Name: Subject Label: Subjects Group: Su Data: <searchLink fieldCode="DE" term="%22Caenorhabditis+elegans%22">Caenorhabditis elegans</searchLink><br /><searchLink fieldCode="DE" term="%22Genetic+regulation%22">Genetic regulation</searchLink><br /><searchLink fieldCode="DE" term="%22Messenger+RNA%22">Messenger RNA</searchLink><br /><searchLink fieldCode="DE" term="%22Gene+expression%22">Gene expression</searchLink><br /><searchLink fieldCode="DE" term="%22Non-coding+RNA%22">Non-coding RNA</searchLink> – Name: Abstract Label: Abstract Group: Ab Data: Post-transcriptional gene regulation frequently occurs through elements in mRNA 3? untranslated regions (UTRs). Although crucial roles for 3?UTR-mediated gene regulation have been found in Caenorhabditis elegans, most C. elegans genes have lacked annotated 3?UTRs. Here we describe a high-throughput method for reliable identification of polyadenylated RNA termini, and we apply this method, called poly(A)-position profiling by sequencing (3P-Seq), to determine C. elegans 3?UTRs. Compared to standard methods also recently applied to C. elegans UTRs, 3P-Seq identified 8,580 additional UTRs while excluding thousands of shorter UTR isoforms that do not seem to be authentic. Analysis of this expanded and corrected data set suggested that the high A/U content of C. elegans 3?UTRs facilitated genome compaction, because the elements specifying cleavage and polyadenylation, which are A/U rich, can more readily emerge in A/U-rich regions. Indeed, 30% of the protein-coding genes have mRNAs with alternative, partially overlapping end regions that generate another 10,480 cleavage and polyadenylation sites that had gone largely unnoticed and represent potential evolutionary intermediates of progressive UTR shortening. Moreover, a third of the convergently transcribed genes use palindromic arrangements of bidirectional elements to specify UTRs with convergent overlap, which also contributes to genome compaction by eliminating regions between genes. Although nematode 3?UTRs have median length only one-sixth that of mammalian 3?UTRs, they have twice the density of conserved microRNA sites, in part because additional types of seed-complementary sites are preferentially conserved. These findings reveal the influence of cleavage and polyadenylation on the evolution of genome architecture and provide resources for studying post-transcriptional gene regulation. [ABSTRACT FROM AUTHOR] – Name: AbstractSuppliedCopyright Label: Group: Ab Data: <i>Copyright of Nature is the property of Springer Nature and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract.</i> (Copyright applies to all Abstracts.) |
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| RecordInfo | BibRecord: BibEntity: Identifiers: – Type: doi Value: 10.1038/nature09616 Languages: – Code: eng Text: English PhysicalDescription: Pagination: PageCount: 5 StartPage: 97 Subjects: – SubjectFull: Caenorhabditis elegans Type: general – SubjectFull: Genetic regulation Type: general – SubjectFull: Messenger RNA Type: general – SubjectFull: Gene expression Type: general – SubjectFull: Non-coding RNA Type: general Titles: – TitleFull: Formation, regulation and evolution of Caenorhabditis elegans 3?UTRs. Type: main BibRelationships: HasContributorRelationships: – PersonEntity: Name: NameFull: Jan, Calvin H. – PersonEntity: Name: NameFull: Friedman, Robin C. – PersonEntity: Name: NameFull: Ruby, J. Graham – PersonEntity: Name: NameFull: Bartel, David P. IsPartOfRelationships: – BibEntity: Dates: – D: 06 M: 01 Text: 1/6/2011 Type: published Y: 2011 Identifiers: – Type: issn-print Value: 00280836 Numbering: – Type: volume Value: 469 – Type: issue Value: 7328 Titles: – TitleFull: Nature Type: main |
| ResultId | 1 |
