View in EDS PDF Full Text

Alternative isoform regulation in human tissue transcriptomes.

Saved in:
Bibliographic Details
Title: Alternative isoform regulation in human tissue transcriptomes.
Authors: Wang, Eric T., Sandberg, Rickard, Luo, Shujun, Khrebtukova, Irina, Zhang, Lu, Mayr, Christine, Kingsmore, Stephen F., Schroth, Gary P., Burge, Christopher B.
Source: Nature. 11/27/2008, Vol. 456 Issue 7221, p470-476. 7p. 1 Diagram, 1 Chart, 3 Graphs.
Subjects: Messenger RNA, Genetic polymorphisms, Cell lines, Tissue extracts, Nucleotide sequence, Gene mapping, RNA splicing, Scission (Chemistry)
Abstract: Through alternative processing of pre-messenger RNAs, individual mammalian genes often produce multiple mRNA and protein isoforms that may have related, distinct or even opposing functions. Here we report an in-depth analysis of 15 diverse human tissue and cell line transcriptomes on the basis of deep sequencing of complementary DNA fragments, yielding a digital inventory of gene and mRNA isoform expression. Analyses in which sequence reads are mapped to exon–exon junctions indicated that 92–94% of human genes undergo alternative splicing, ∼86% with a minor isoform frequency of 15% or more. Differences in isoform-specific read densities indicated that most alternative splicing and alternative cleavage and polyadenylation events vary between tissues, whereas variation between individuals was approximately twofold to threefold less common. Extreme or ‘switch-like’ regulation of splicing between tissues was associated with increased sequence conservation in regulatory regions and with generation of full-length open reading frames. Patterns of alternative splicing and alternative cleavage and polyadenylation were strongly correlated across tissues, suggesting coordinated regulation of these processes, and sequence conservation of a subset of known regulatory motifs in both alternative introns and 3′ untranslated regions suggested common involvement of specific factors in tissue-level regulation of both splicing and polyadenylation. [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
Header DbId: pbh
DbLabel: Psychology and Behavioral Sciences Collection
An: 35483673
AccessLevel: 6
PubType: Academic Journal
PubTypeId: academicJournal
PreciseRelevancyScore: 0
IllustrationInfo
Items – Name: Title
  Label: Title
  Group: Ti
  Data: Alternative isoform regulation in human tissue transcriptomes.
– Name: Author
  Label: Authors
  Group: Au
  Data: <searchLink fieldCode="AR" term="%22Wang%2C+Eric+T%2E%22">Wang, Eric T.</searchLink><br /><searchLink fieldCode="AR" term="%22Sandberg%2C+Rickard%22">Sandberg, Rickard</searchLink><br /><searchLink fieldCode="AR" term="%22Luo%2C+Shujun%22">Luo, Shujun</searchLink><br /><searchLink fieldCode="AR" term="%22Khrebtukova%2C+Irina%22">Khrebtukova, Irina</searchLink><br /><searchLink fieldCode="AR" term="%22Zhang%2C+Lu%22">Zhang, Lu</searchLink><br /><searchLink fieldCode="AR" term="%22Mayr%2C+Christine%22">Mayr, Christine</searchLink><br /><searchLink fieldCode="AR" term="%22Kingsmore%2C+Stephen+F%2E%22">Kingsmore, Stephen F.</searchLink><br /><searchLink fieldCode="AR" term="%22Schroth%2C+Gary+P%2E%22">Schroth, Gary P.</searchLink><br /><searchLink fieldCode="AR" term="%22Burge%2C+Christopher+B%2E%22">Burge, Christopher B.</searchLink>
– Name: TitleSource
  Label: Source
  Group: Src
  Data: <searchLink fieldCode="JN" term="%22Nature%22">Nature</searchLink>. 11/27/2008, Vol. 456 Issue 7221, p470-476. 7p. 1 Diagram, 1 Chart, 3 Graphs.
– Name: Subject
  Label: Subjects
  Group: Su
  Data: <searchLink fieldCode="DE" term="%22Messenger+RNA%22">Messenger RNA</searchLink><br /><searchLink fieldCode="DE" term="%22Genetic+polymorphisms%22">Genetic polymorphisms</searchLink><br /><searchLink fieldCode="DE" term="%22Cell+lines%22">Cell lines</searchLink><br /><searchLink fieldCode="DE" term="%22Tissue+extracts%22">Tissue extracts</searchLink><br /><searchLink fieldCode="DE" term="%22Nucleotide+sequence%22">Nucleotide sequence</searchLink><br /><searchLink fieldCode="DE" term="%22Gene+mapping%22">Gene mapping</searchLink><br /><searchLink fieldCode="DE" term="%22RNA+splicing%22">RNA splicing</searchLink><br /><searchLink fieldCode="DE" term="%22Scission+%28Chemistry%29%22">Scission (Chemistry)</searchLink>
– Name: Abstract
  Label: Abstract
  Group: Ab
  Data: Through alternative processing of pre-messenger RNAs, individual mammalian genes often produce multiple mRNA and protein isoforms that may have related, distinct or even opposing functions. Here we report an in-depth analysis of 15 diverse human tissue and cell line transcriptomes on the basis of deep sequencing of complementary DNA fragments, yielding a digital inventory of gene and mRNA isoform expression. Analyses in which sequence reads are mapped to exon–exon junctions indicated that 92–94% of human genes undergo alternative splicing, ∼86% with a minor isoform frequency of 15% or more. Differences in isoform-specific read densities indicated that most alternative splicing and alternative cleavage and polyadenylation events vary between tissues, whereas variation between individuals was approximately twofold to threefold less common. Extreme or ‘switch-like’ regulation of splicing between tissues was associated with increased sequence conservation in regulatory regions and with generation of full-length open reading frames. Patterns of alternative splicing and alternative cleavage and polyadenylation were strongly correlated across tissues, suggesting coordinated regulation of these processes, and sequence conservation of a subset of known regulatory motifs in both alternative introns and 3′ untranslated regions suggested common involvement of specific factors in tissue-level regulation of both splicing and polyadenylation. [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.)
PLink https://search.ebscohost.com/login.aspx?direct=true&site=eds-live&db=pbh&AN=35483673
RecordInfo BibRecord:
  BibEntity:
    Identifiers:
      – Type: doi
        Value: 10.1038/nature07509
    Languages:
      – Code: eng
        Text: English
    PhysicalDescription:
      Pagination:
        PageCount: 7
        StartPage: 470
    Subjects:
      – SubjectFull: Messenger RNA
        Type: general
      – SubjectFull: Genetic polymorphisms
        Type: general
      – SubjectFull: Cell lines
        Type: general
      – SubjectFull: Tissue extracts
        Type: general
      – SubjectFull: Nucleotide sequence
        Type: general
      – SubjectFull: Gene mapping
        Type: general
      – SubjectFull: RNA splicing
        Type: general
      – SubjectFull: Scission (Chemistry)
        Type: general
    Titles:
      – TitleFull: Alternative isoform regulation in human tissue transcriptomes.
        Type: main
  BibRelationships:
    HasContributorRelationships:
      – PersonEntity:
          Name:
            NameFull: Wang, Eric T.
      – PersonEntity:
          Name:
            NameFull: Sandberg, Rickard
      – PersonEntity:
          Name:
            NameFull: Luo, Shujun
      – PersonEntity:
          Name:
            NameFull: Khrebtukova, Irina
      – PersonEntity:
          Name:
            NameFull: Zhang, Lu
      – PersonEntity:
          Name:
            NameFull: Mayr, Christine
      – PersonEntity:
          Name:
            NameFull: Kingsmore, Stephen F.
      – PersonEntity:
          Name:
            NameFull: Schroth, Gary P.
      – PersonEntity:
          Name:
            NameFull: Burge, Christopher B.
    IsPartOfRelationships:
      – BibEntity:
          Dates:
            – D: 27
              M: 11
              Text: 11/27/2008
              Type: published
              Y: 2008
          Identifiers:
            – Type: issn-print
              Value: 00280836
          Numbering:
            – Type: volume
              Value: 456
            – Type: issue
              Value: 7221
          Titles:
            – TitleFull: Nature
              Type: main
ResultId 1