Poly A- transcripts expressed in HeLa cells

Wu, Q., Kim, Y. C., Lu, J., Xuan, Z. Y., Chen, J., Zheng, Y., Zhou, T., Zhang, M. Q., Wu, C. I., Wang, S. M. (July 2008) Poly A- transcripts expressed in HeLa cells. PLoS ONE, 3 (7). e2803.

[img]
Preview
PDF (Paper)
Zhang PLoS One 2008.pdf - Published Version

Download (323Kb) | Preview
URL: http://www.ncbi.nlm.nih.gov/pubmed/18665230
DOI: 10.1371/journal.pone.0002803

Abstract

BACKGROUND: Transcripts expressed in eukaryotes are classified as poly A+ transcripts or poly A- transcripts based on the presence or absence of the 3' poly A tail. Most transcripts identified so far are poly A+ transcripts, whereas the poly A- transcripts remain largely unknown. METHODOLOGY/PRINCIPAL FINDINGS: We developed the TRD (Total RNA Detection) system for transcript identification. The system detects the transcripts through the following steps: 1) depleting the abundant ribosomal and small-size transcripts; 2) synthesizing cDNA without regard to the status of the 3' poly A tail; 3) applying the 454 sequencing technology for massive 3' EST collection from the cDNA; and 4) determining the genome origins of the detected transcripts by mapping the sequences to the human genome reference sequences. Using this system, we characterized the cytoplasmic transcripts from HeLa cells. Of the 13,467 distinct 3' ESTs analyzed, 24% are poly A-, 36% are poly A+, and 40% are bimorphic with poly A+ features but without the 3' poly A tail. Most of the poly A- 3' ESTs do not match known transcript sequences; they have a similar distribution pattern in the genome as the poly A+ and bimorphic 3' ESTs, and their mapped intergenic regions are evolutionarily conserved. Experiments confirmed the authenticity of the detected poly A- transcripts. CONCLUSION/SIGNIFICANCE: Our study provides the first large-scale sequence evidence for the presence of poly A- transcripts in eukaryotes. The abundance of the poly A- transcripts highlights the need for comprehensive identification of these transcripts for decoding the transcriptome, annotating the genome and studying biological relevance of the poly A- transcripts.

Item Type: Paper
Subjects: bioinformatics > genomics and proteomics > genetics & nucleic acid processing
bioinformatics > genomics and proteomics
Investigative techniques and equipment
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > transcriptomes
CSHL Authors:
Communities: CSHL labs > Zhang lab
Depositing User: Matt Covey
Date: 30 July 2008
Date Deposited: 25 Feb 2013 21:26
Last Modified: 25 Feb 2013 21:26
PMCID: PMC2481391
Related URLs:
URI: http://repository.cshl.edu/id/eprint/27595

Actions (login required)

Administrator's edit/view item Administrator's edit/view item
CSHL HomeAbout CSHLResearchEducationNews & FeaturesCampus & Public EventsCareersGiving