ArticleBMC bioinformatics2007
Predictive modeling of plant messenger RNA polyadenylation sites.
Article in BMC bioinformatics, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- Multifactorial analysis of terminator performance on heterologous gene expression in Physcomitrella.Plant cell reports · 2024Article
- Alternative Transcripts Diversify Genome Function for Phenome Relevance to Health and Diseases.Genes · 2023Review
- A Survey on Methods for Predicting Polyadenylation Sites from DNA Sequences, Bulk RNA-seq, and Single-cell RNA-seq.Genomics, proteomics & bioinformatics · 2023Review
- Identification of key genes associated with secondary metabolites biosynthesis by system network analysis in Valeriana officinalis.Journal of plant research · 2021Article
- Poly(A)-DG: A deep-learning-based domain generalization method to identify cross-species Poly(A) signal without prior knowledge from target species.PLoS computational biology · 2020Article
- Use of synthetic biology tools to optimize the production of active nitrogenase Fe protein in chloroplasts of tobacco leaf cells.Plant biotechnology journal · 2020Article
- Modeling of Genome-Wide Polyadenylation Signals inFrontiers in genetics · 2019Article
- An intronless form of the tobacco extensin gene terminator strongly enhances transient gene expression in plant leaves.Plant molecular biology · 2018Article
- A Genome-wide Study of "Non-3UTR" Polyadenylation Sites in Arabidopsis thaliana.Scientific reports · 2016Article
- Genome-wide characterization of intergenic polyadenylation sites redefines gene spaces in Arabidopsis thaliana.BMC genomics · 2015Article
- Article
- In silico prediction of mRNA poly(A) sites in Chlamydomonas reinhardtii.Molecular genetics and genomics : MGG · 2012Article
- Isolation of Alcohol Dehydrogenase cDNA and Basal Regulatory Region from Metroxylon sagu.ISRN molecular biology · 2012Article
- Hypomorphic alleles reveal FCA-independent roles for FY in the regulation of FLOWERING LOCUS C.Plant physiology · 2011Article
- Spurious polyadenylation of Norovirus Narita 104 capsid protein mRNA in transgenic plants.Plant molecular biology · 2011Article
- Mining Functional Elements in Messenger RNAs: Overview, Challenges, and Perspectives.Frontiers in plant science · 2011Article
- Riboswitches as hormone receptors: hypothetical cytokinin-binding riboswitches in Arabidopsis thaliana.Biology direct · 2010Article
- Next generation transcriptomes for next generation genomes using est2assembly.BMC bioinformatics · 2009Article
- Effects of the multiple polyadenylation signal AAUAAA on mRNA 3'-end formation and gene expression.Planta · 2009Article
- The frequent transcriptional readthrough of the tobacco Tnt1 retrotransposon and its possible implications for the control of resistance genes.Journal of molecular evolution · 2009Article
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10 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundOne of the essential processing events during pre-mRNA maturation is the post-transcriptional addition of a polyadenine [poly(A)] tail. The 3'-end poly(A) track protects mRNA from unregulated degradation, and indicates the integrity of mRNA through recognition by mRNA export and translation machinery. The position of a poly(A) site is predetermined by signals in the pre-mRNA sequence that are recognized by a complex of polyadenylation factors. These signals are generally tri-part sequence patterns around the cleavage site that serves as the future poly(A) site. In plants, there is little sequence conservation among these signal elements, which makes it difficult to develop an accurate algorithm to predict the poly(A) site of a given gene. We attempted to solve this problem.
resultsBased on our current working model and the profile of nucleotide sequence distribution of the poly(A) signals and around poly(A) sites in Arabidopsis, we have devised a Generalized Hidden Markov Model based algorithm to predict potential poly(A) sites. The high specificity and sensitivity of the algorithm were demonstrated by testing several datasets, and at the best combinations, both reach 97%. The accuracy of the program, called poly(A) site sleuth or PASS, has been demonstrated by the prediction of many validated poly(A) sites. PASS also predicted the changes of poly(A) site efficiency in poly(A) signal mutants that were constructed and characterized by traditional genetic experiments. The efficacy of PASS was demonstrated by predicting poly(A) sites within long genomic sequences.
conclusionBased on the features of plant poly(A) signals, a computational model was built to effectively predict the poly(A) sites in Arabidopsis genes. The algorithm will be useful in gene annotation because a poly(A) site signifies the end of the transcript. This algorithm can also be used to predict alternative poly(A) sites in known genes, and will be useful in the design of transgenes for crop genetic engineering by predicting and eliminating undesirable poly(A) sites.
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