ArticleBMC genomics2014
Genome-wide determination of poly(A) sites in Medicago truncatula: evolutionary conservation of alternative poly(A) site choice.
Article in BMC genomics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Reduced Usage ofPhenomics (Cham, Switzerland) · 2025Article
- Nucleotide-resolution Mapping of RNA N6-Methyladenosine (m6A) modifications and comprehensive analysis of global polyadenylation events in mRNA 3' end processing in malaria pathogenbioRxiv : the preprint server for biology · 2025Article
- Stress responses of plants through transcriptome plasticity by mRNA alternative polyadenylation.Molecular horticulture · 2023Review
- stAPAminer: Mining Spatial Patterns of Alternative Polyadenylation for Spatially Resolved Transcriptomic Studies.Genomics, proteomics & bioinformatics · 2023Article
- Divergence in the Regulation of the Salt Tolerant Response BetweenFrontiers in plant science · 2022Article
- Article
- PlantAPAdb: A Comprehensive Database for Alternative Polyadenylation Sites in Plants.Plant physiology · 2020Article
- Plant 3' Regulatory Regions From mRNA-Encoding Genes and Their Uses to Modulate Expression.Frontiers in plant science · 2020Review
- Profiling Alternative 3' Untranslated Regions in Sorghum using RNA-seq Data.Frontiers in genetics · 2020Article
- A GmSIN1/GmNCED3s/GmRbohBs Feed-Forward Loop Acts as a Signal Amplifier That Regulates Root Growth in Soybean Exposed to Salt Stress.The Plant cell · 2019Article
- Genome-Wide Profiling of Polyadenylation Events in Maize Using High-Throughput Transcriptomic Sequences.G3 (Bethesda, Md.) · 2019Article
- Genome-wide atlas of alternative polyadenylation in the forage legume red clover.Scientific reports · 2018Article
- Capturing the Alternative Cleavage and Polyadenylation Sites of 14 NAC Genes in Populus Using a Combination of 3'-RACE and High-Throughput Sequencing.Molecules (Basel, Switzerland) · 2018Article
- Noncanonical Alternative Polyadenylation Contributes to Gene Regulation in Response to Hypoxia.The Plant cell · 2017Article
- PlantAPA: A Portal for Visualization and Analysis of Alternative Polyadenylation in Plants.Frontiers in plant science · 2016Article
- Experimental Genome-Wide Determination of RNA Polyadenylation in Chlamydomonas reinhardtii.PloS one · 2016Article
- Genome-wide characterization of intergenic polyadenylation sites redefines gene spaces in Arabidopsis thaliana.BMC genomics · 2015Article
- CPSF30 at the Interface of Alternative Polyadenylation and Cellular Signaling in Plants.Biomolecules · 2015Review
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundAlternative polyadenylation (APA) plays an important role in the post-transcriptional regulation of gene expression. Little is known about how APA sites may evolve in homologous genes in different plant species. To this end, comparative studies of APA sites in different organisms are needed. In this study, a collection of poly(A) sites in Medicago truncatula, a model system for legume plants, has been generated and compared with APA sites in Arabidopsis thaliana.
resultsThe poly(A) tags from a deep-sequencing protocol were mapped to the annotated M. truncatula genome, and the identified poly(A) sites used to update the annotations of 14,203 genes. The results show that 64% of M. truncatula genes possess more than one poly(A) site, comparable to the percentages reported for Arabidopsis and rice. In addition, the poly(A) signals associated with M. truncatula genes were similar to those seen in Arabidopsis and other plants. The 3'-UTR lengths are correlated in pairs of orthologous genes between M. truncatula and Arabidopsis. Very little conservation of intronic poly(A) sites was found between Arabidopsis and M. truncatula, which suggests that such sites are likely to be species-specific in plants. In contrast, there is a greater conservation of CDS-localized poly(A) sites in these two species. A sizeable number of M. truncatula antisense poly(A) sites were found. A high percentage of the associated target genes possess Arabidopsis orthologs that are also associated with antisense sites. This is suggestive of important roles for antisense regulation of these target genes.
conclusionsOur results reveal some distinct patterns of sense and antisense poly(A) sites in Arabidopsis and M. truncatula. In so doing, this study lends insight into general evolutionary trends of alternative polyadenylation in plants.
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