The disparate nature of “intergenic” polyadenylation sites

Lopez, Fabrice; Granjeaud, Samuel; Ara, Takeshi; Ghattas, Badih; Gautheret, Daniel

doi:10.1261/rna.136206

Cited by 26 publications

(29 citation statements)

References 34 publications

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“…While their authenticity as potentially unannotated gene transcripts remains to be tested, their existence at such a scale (∼23%) requires further investigation. Similarly, previous studies also showed that there were many poly(A) sites in the intergenic regions (Lopez et al 2006;Shepard et al 2011;Derti et al 2012). Concerning the rice data presented herein, additional evidence implies that these are authentic poly(A) sites.…”

Section: Discussionsupporting

confidence: 88%

Genome-wide dynamics of alternative polyadenylation in rice

Yang

et al. 2016

Genome Res.

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Alternative polyadenylation (APA), in which a transcript uses one of the poly(A) sites to define its 3′-end, is a common regulatory mechanism in eukaryotic gene expression. However, the potential of APA in determining crop agronomic traits remains elusive. This study systematically tallied poly(A) sites of 14 different rice tissues and developmental stages using the poly(A) tag sequencing (PAT-seq) approach. The results indicate significant involvement of APA in developmental and quantitative trait loci (QTL) gene expression. About 48% of all expressed genes use APA to generate transcriptomic and proteomic diversity. Some genes switch APA sites, allowing differentially expressed genes to use alternate 3′ UTRs. Interestingly, APA in mature pollen is distinct where differential expression levels of a set of poly(A) factors and different distributions of APA sites are found, indicating a unique mRNA 3′-end formation regulation during gametophyte development. Equally interesting, statistical analyses showed that QTL tends to use APA for regulation of gene expression of many agronomic traits, suggesting a potential important role of APA in rice production. These results provide thus far the most comprehensive and high-resolution resource for advanced analysis of APA in crops and shed light on how APA is associated with trait formation in eukaryotes.

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Section: Discussionsupporting

confidence: 88%

Genome-wide dynamics of alternative polyadenylation in rice

Yang

et al. 2016

Genome Res.

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“…Therefore, these sequences cannot fully account for the specificity of 3Ј-end processing. Putative poly(A) signals are frequently found within AU-rich sequences, such as introns and intergenic regions (21,37). In addition, bioinformatical studies have determined that the sequence motifs that make the poly(A) signal are, contrary to earlier predictions, not well conserved, even in mammalian genes.…”

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confidence: 92%

Poly(A) Signals Located near the 5′ End of Genes Are Silenced by a General Mechanism That Prevents Premature 3′-End Processing

Guo

Garrett

Micklem

et al. 2011

Molecular and Cellular Biology

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Poly(A) signals located at the 3 end of eukaryotic genes drive cleavage and polyadenylation at the same end of pre-mRNA. Although these sequences are expected only at the 3 end of genes, we found that strong poly(A) signals are also predicted within the 5 untranslated regions (UTRs) of many Drosophila melanogaster mRNAs. Most of these 5 poly(A) signals have little influence on the processing of the endogenous transcripts, but they are very active when placed at the 3 end of reporter genes. In investigating these unexpected observations, we discovered that both these novel poly(A) signals and standard poly(A) signals become functionally silent when they are positioned close to transcription start sites in either Drosophila or human cells. This indicates that the stage when the poly(A) signal emerges from the polymerase II (Pol II) transcription complex determines whether a putative poly(A) signal is recognized as functional. The data suggest that this mechanism, which probably prevents cryptic poly(A) signals from causing premature transcription termination, depends on low Ser2 phosphorylation of the C-terminal domain of Pol II and inefficient recruitment of processing factors.

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“…The prediction tables are based on methodology that improves on earlier EST-based analyses (14)(15)(16)(17)(18)(19) and demonstrates a 97% level of predictive recall on a hand-curated and experimentally supported benchmark transcript set. Exact and comprehensive definition of alternative 3Ј transcript ends will allow for the design of probes that discriminate between alternative forms and thereby support elucidation of the regulatory impact of alternative polyadenylation.…”

Section: Discussionmentioning

confidence: 99%

Identification of gene 3′ ends by automated EST cluster analysis

Muro

Herrington

Janmohamed

et al. 2008

Proc. Natl. Acad. Sci. U.S.A.

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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

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The disparate nature of “intergenic” polyadenylation sites

Cited by 26 publications

References 34 publications

Genome-wide dynamics of alternative polyadenylation in rice

Genome-wide dynamics of alternative polyadenylation in rice

Poly(A) Signals Located near the 5′ End of Genes Are Silenced by a General Mechanism That Prevents Premature 3′-End Processing

Identification of gene 3′ ends by automated EST cluster analysis

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