Document Detail


Tissue-specific transcript annotation and expression profiling with complementary next-generation sequencing technologies.
MedLine Citation:
PMID:  20615900     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
Next-generation sequencing is excellently suited to evaluate the abundance of mRNAs to study gene expression. Here we compare two alternative technologies, cap analysis of gene expression (CAGE) and serial analysis of gene expression (SAGE), for the same RNA samples. Along with quantifying gene expression levels, CAGE can be used to identify tissue-specific transcription start sites, while SAGE monitors 3'-end usage. We used both methods to get more insight into the transcriptional control of myogenesis, studying differential gene expression in differentiated and proliferating C2C12 myoblast cells with statistical evaluation of reproducibility and differential gene expression. Both CAGE and SAGE provided highly reproducible data (Pearson's correlations >0.92 among biological triplicates). With both methods we found around 10,000 genes expressed at levels >2 transcripts per million (approximately 0.3 copies per cell), with an overlap of 86%. We identified 4304 and 3846 genes differentially expressed between proliferating and differentiated C2C12 cells by CAGE and SAGE, respectively, with an overlap of 2144. We identified 196 novel regulatory regions with preferential use in proliferating or differentiated cells. Next-generation sequencing of CAGE and SAGE libraries provides consistent expression levels and can enrich current genome annotations with tissue-specific promoters and alternative 3'-UTR usage.
Authors:
Matthew S Hestand; Andreas Klingenhoff; Matthias Scherf; Yavuz Ariyurek; Yolande Ramos; Wilbert van Workum; Makoto Suzuki; Thomas Werner; Gert-Jan B van Ommen; Johan T den Dunnen; Matthias Harbers; Peter A C 't Hoen
Publication Detail:
Type:  Evaluation Studies; Journal Article; Research Support, Non-U.S. Gov't     Date:  2010-07-07
Journal Detail:
Title:  Nucleic acids research     Volume:  38     ISSN:  1362-4962     ISO Abbreviation:  Nucleic Acids Res.     Publication Date:  2010 Sep 
Date Detail:
Created Date:  2010-09-13     Completed Date:  2010-10-13     Revised Date:  2013-05-29    
Medline Journal Info:
Nlm Unique ID:  0411011     Medline TA:  Nucleic Acids Res     Country:  England    
Other Details:
Languages:  eng     Pagination:  e165     Citation Subset:  IM    
Affiliation:
The Center for Human and Clinical Genetics, Leiden University Medical Center, 2300 RC Leiden, The Netherlands.
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MeSH Terms
Descriptor/Qualifier:
3' Untranslated Regions
Animals
Cell Line
Gene Expression Profiling / methods*
Mice
Models, Biological
Muscle Development / genetics
Myoblasts / metabolism*
Oligonucleotide Array Sequence Analysis
Reproducibility of Results
Sequence Alignment
Sequence Analysis, RNA*
Transcription Initiation Site
Chemical
Reg. No./Substance:
0/3' Untranslated Regions
Comments/Corrections

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