English
 
User Manual Privacy Policy Disclaimer Contact us
  Advanced SearchBrowse

Item

ITEM ACTIONSEXPORT
  Short ultraconserved promoter regions delineate a class of preferentially expressed alternatively spliced transcripts.

Rödelsperger, C., Köhler, S., Schulz, M. H., Manke, T., Bauer, S., & Robinson, P. N. (2009). Short ultraconserved promoter regions delineate a class of preferentially expressed alternatively spliced transcripts. Genomics, 94(5), 308-316. doi:10.1016/j.ygeno.2009.07.005.

Item is

Basic

show hide
Item Permalink: http://hdl.handle.net/11858/00-001M-0000-0010-7D3C-2 Version Permalink: http://hdl.handle.net/11858/00-001M-0000-0010-7D3D-F
Genre: Journal Article
Alternative Title : Genomics

Files

show Files
hide Files
:
sdarticle.pdf (Any fulltext), 748KB
 
File Permalink:
-
Name:
sdarticle.pdf
Description:
-
Visibility:
Restricted (Max Planck Institute for Molecular Genetics, MBMG; )
MIME-Type / Checksum:
application/pdf
Technical Metadata:
Copyright Date:
-
Copyright Info:
eDoc_access: MPG
License:
-

Locators

show

Creators

show
hide
 Creators:
Rödelsperger, Christian1, Author              
Köhler, Sebastian, Author
Schulz, Marcel H.2, Author
Manke, Thomas3, Author              
Bauer, Sebastian, Author
Robinson, Peter N.1, Author              
Affiliations:
1Research Group Development & Disease (Head: Stefan Mundlos), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1433557              
2Max Planck Society, ou_persistent13              
3Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1433547              

Content

show
hide
Free keywords: Promoter; Ultraconservation; Alternative splicing; Digital gene expression; Genomics
 Abstract: Ultraconservation has been variously defined to describe sequences that have remained identical or nearly so over long periods of evolution to a degree that is higher than expected for sequences under typical constraints associated with protein-coding sequences, splice sites, or transcription factor binding sites. Most intergenic ultraconserved elements (UCE) appear to be tissue-specific enhancers, whereas another class of intragenic UCEs is involved in regulation of gene expression by means of alternative splicing. In this study we define a set of 2827 short ultraconserved promoter regions (SUPR) in 5 kb upstream regions of 1268 human protein-coding genes using a definition of 98% identity for at least 30 bp in 7 mammalian species. Our analysis shows that SUPRs are enriched in genes playing a role in regulation and development. Many of the genes having a SUPR-containing promoter have additional alternative promoters that do not contain SUPRs. Comparison of such promoters by CAGE tag, EST, and Solexa read analysis revealed that SUPR-associated transcripts show a significantly higher mean expression than transcripts associated with non-SUPR-containing promoters. The same was true for the comparison between all SUPR-associated and non-SUPR-associated transcripts on a genome-wide basis. SUPR-associated genes show a highly significant tendency to occur in regions that are also enriched for intergenic short ultraconserved elements (SUE) in the vicinity of developmental genes. A number of predicted transcription factor binding sites (TFBS) are overrepresented in SUPRs and SUEs, including those for transcription factors of the homeodomain family, but in contrast to SUEs, SUPRs are also enriched in core-promoter motifs. These observations suggest that SUPRs delineate a distinct class of ultraconserved sequences.

Details

show
hide
Language(s): eng - English
 Dates: 2009-08-04
 Publication Status: Published in print
 Pages: -
 Publishing info: -
 Table of Contents: -
 Rev. Method: -
 Degree: -

Event

show

Legal Case

show

Project information

show

Source 1

show
hide
Title: Genomics
  Alternative Title : Genomics
Source Genre: Journal
 Creator(s):
Affiliations:
Publ. Info: -
Pages: - Volume / Issue: 94 (5) Sequence Number: - Start / End Page: 308 - 316 Identifier: ISSN: 0888-7543