Identification of gene 3′ ends by automated EST cluster analysis

Abstract

The properties and biology of mRNA transcripts can be affected profoundly by the choice of alternative polyadenylation sites, making definition of the 3 ends of transcripts essential for understanding their regulation. Here we show that 22-52% of sequences in commonly used human and murine ''full-length'' transcript databases may not currently end at bona fide polyadenylation sites. To identify probable transcript termini over the entire murine and human genomes, we analyzed the EST databases for positional clustering of EST ends. The analysis yielded 58,282 murine-and 86,410 human-candidate polyadenylation sites, of which 75% mapped to 23,091 known murine transcripts and 22,891 known human transcripts. The murine dataset correctly predicted 97% of the 3 ends in a manually curated and experimentally supported benchmark transcript set. Of currently known genes, 15% had no associated prediction and 25% had only a single predicted termination site. The remaining genes had an average of 3-4 alternative polyadenylation sites predicted for each murine or human transcript, respectively. The results are made available in the form of tables and an interactive web site that can be mined for rapid assessment of the validity of 3 ends in existing collections, enumeration of potential alternative 3 polyadenylation sites of known transcripts, direct retrieval of terminal sequences for design of probes, and detection of polyadenylation sites not currently mapped to known genes.3Ј UTR ͉ gene prediction ͉ alternative polyadenylation ͉ transcriptome ͉ transcript probe design

POLYAR, a new computer program for prediction of poly(A) sites in human sequences

“…However, till date a complete set of full-length cDNAs is not available, clustering and DNA mapping studies of human and murine EST databases reveals that of the currently known genes, 15% have no EST-supported 3'end. In other words, the 3'-termini of a significant portion of known genes from these species remains to be identified [22]. Similar results have been obtained by Lopez et al [23].…”

Comprehensive Polyadenylation Site Maps in Yeast and Human Reveal Pervasive Alternative Polyadenylation

“…We observed rare or no occurrence of internal priming events (Table S1 and Extended Experimental Procedures). Thus, the technology is capable of mapping the extensive 3′ end heterogeneity we and others (Iseli et al, 2002; Lopez et al, 2006; Muro et al, 2008) observed in the majority of yeast and human genes in a genome-wide manner and at nucleotide resolution (Figure 1A–D). …”

Evidence that cleavage factor Im is a heterotetrameric protein complex controlling alternative polyadenylation

“…Recent estimates indicate that ∼60% of human genes are capable of undergoing alternative polyadenylation (Tian et al. 2005; Muro et al. 2008), which gives rise to mRNAs with 3′‐UTRs of different lengths and often affects transcript stability.…”