Abstract
The 3′ ends of mRNAs terminate with a poly(A) tail. This post-transcriptional modification is directed by sequence features present in the 3′-untranslated region (3′-UTR). We have undertaken a computational analysis of 3′ end formation in Caenorhabditis elegans. By aligning cDNAs that diverge from genomic sequence at the poly(A) tract, we accurately identified a large set of true cleavage sites. When there are many transcripts aligned to a particular locus, local variation of the cleavage site over a span of a few bases is frequently observed. We find that in addition to the well-known AAUAAA motif there are several regions with distinct nucleotide compositional biases. We propose a generalized hidden Markov model that describes sequence features in C.elegans 3′-UTRs. We find that a computer program employing this model accurately predicts experimentally observed 3′ ends even when there are multiple AAUAAA motifs and multiple cleavage sites. We have made available a complete set of polyadenylation site predictions for the C.elegans genome, including a subset of 6570 supported by aligned transcripts.
| Original language | English (US) |
|---|---|
| Pages (from-to) | 3392-3399 |
| Number of pages | 8 |
| Journal | Nucleic Acids Research |
| Volume | 32 |
| Issue number | 11 |
| DOIs | |
| State | Published - 2004 |
| Externally published | Yes |
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ASJC Scopus subject areas
- Genetics
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A probabilistic model of 3′ end formation in Caenorhabditis elegans. / Hajarnavis, Ashwin; Korf, Ian F; Durbin, Richard.
In: Nucleic Acids Research, Vol. 32, No. 11, 2004, p. 3392-3399.Research output: Contribution to journal › Article
}
TY - JOUR
T1 - A probabilistic model of 3′ end formation in Caenorhabditis elegans
AU - Hajarnavis, Ashwin
AU - Korf, Ian F
AU - Durbin, Richard
PY - 2004
Y1 - 2004
N2 - The 3′ ends of mRNAs terminate with a poly(A) tail. This post-transcriptional modification is directed by sequence features present in the 3′-untranslated region (3′-UTR). We have undertaken a computational analysis of 3′ end formation in Caenorhabditis elegans. By aligning cDNAs that diverge from genomic sequence at the poly(A) tract, we accurately identified a large set of true cleavage sites. When there are many transcripts aligned to a particular locus, local variation of the cleavage site over a span of a few bases is frequently observed. We find that in addition to the well-known AAUAAA motif there are several regions with distinct nucleotide compositional biases. We propose a generalized hidden Markov model that describes sequence features in C.elegans 3′-UTRs. We find that a computer program employing this model accurately predicts experimentally observed 3′ ends even when there are multiple AAUAAA motifs and multiple cleavage sites. We have made available a complete set of polyadenylation site predictions for the C.elegans genome, including a subset of 6570 supported by aligned transcripts.
AB - The 3′ ends of mRNAs terminate with a poly(A) tail. This post-transcriptional modification is directed by sequence features present in the 3′-untranslated region (3′-UTR). We have undertaken a computational analysis of 3′ end formation in Caenorhabditis elegans. By aligning cDNAs that diverge from genomic sequence at the poly(A) tract, we accurately identified a large set of true cleavage sites. When there are many transcripts aligned to a particular locus, local variation of the cleavage site over a span of a few bases is frequently observed. We find that in addition to the well-known AAUAAA motif there are several regions with distinct nucleotide compositional biases. We propose a generalized hidden Markov model that describes sequence features in C.elegans 3′-UTRs. We find that a computer program employing this model accurately predicts experimentally observed 3′ ends even when there are multiple AAUAAA motifs and multiple cleavage sites. We have made available a complete set of polyadenylation site predictions for the C.elegans genome, including a subset of 6570 supported by aligned transcripts.
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U2 - 10.1093/nar/gkh656
DO - 10.1093/nar/gkh656
M3 - Article
C2 - 15247332
AN - SCOPUS:3242672609
VL - 32
SP - 3392
EP - 3399
JO - Nucleic Acids Research
JF - Nucleic Acids Research
SN - 0305-1048
IS - 11
ER -