Heterogeneity in polyadenylation cleavage sites in mammalian mRNA sequences: implications for SAGE analysis

The analysis of a human thyroid serial analysis of gene expression (SAGE) library shows the presence of an abundant SAGE tag corresponding to the mRNA of thyroglobulin (TG). Additional, less abundant tags are present that can not be linked to any other known gene, but show considerable homology to t...

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Bibliographic Details
Published in:Nucleic acids research 2001-04, Vol.29 (8), p.1690-1694
Main Authors: Pauws, E, van Kampen, A H, van de Graaf, S A, de Vijlder, J J, Ris-Stalpers, C
Format: Article
Language:English
Subjects:
Animals
Base Sequence
Cloning, Molecular
Consensus Sequence - genetics
Databases as Topic
Exons - genetics
Gene Library
Humans
Mice
Molecular Sequence Data
Poly A - genetics
Poly A - metabolism
Rats
Regulatory Sequences, Nucleic Acid - genetics
RNA Processing, Post-Transcriptional
RNA, Messenger - analysis
RNA, Messenger - genetics
RNA, Messenger - metabolism
Sequence Analysis, DNA
thyroglobulin
Thyroglobulin - genetics
Thyroid Gland - metabolism
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Summary:The analysis of a human thyroid serial analysis of gene expression (SAGE) library shows the presence of an abundant SAGE tag corresponding to the mRNA of thyroglobulin (TG). Additional, less abundant tags are present that can not be linked to any other known gene, but show considerable homology to the wild-type TG tag. To determine whether these tags represent TG mRNA molecules with alternative cleavage, 3'-RACE clones were sequenced. The results show that the three putative TG SAGE tags can be attributed to TG transcripts and reflect the use of alternative polyadenylation cleavage sites downstream of a single polyadenylation signal in vivo. By screening more than 300 000 sequences corresponding to human, mouse and rat transcripts for this phenomenon we show that a considerable percentage of mRNA transcripts (44% human, 22% mouse and 22% rat) show cleavage site heterogeneity. When analyzing SAGE-generated expression data, this phenomenon should be considered, since, according to our calculations, 2.8% of human transcripts show two or more different SAGE tags corresponding to a single gene because of alternative cleavage site selection. Both experimental and in silico data show that the selection of the specific cleavage site for poly(A) addition using a given polyadenylation signal is more variable than was previously thought.
ISSN:1362-4962
0305-1048
1362-4962
DOI:10.1093/nar/29.8.1690