ArticleScientific reports2016
A Genome-wide Study of "Non-3UTR" Polyadenylation Sites in Arabidopsis thaliana.
Article in Scientific reports, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed, 31 citations in OpenAlex.
- The Arabidopsis U1 snRNP regulates mRNA 3'-end processing.Nature plants · 2024Article
- Multifactorial analysis of terminator performance on heterologous gene expression in Physcomitrella.Plant cell reports · 2024Article
- Stress responses of plants through transcriptome plasticity by mRNA alternative polyadenylation.Molecular horticulture · 2023Review
- Long-read direct RNA sequencing reveals epigenetic regulation of chimeric gene-transposon transcripts in Arabidopsis thaliana.Nature communications · 2023Article
- ReadZS detects cell type-specific and developmentally regulated RNA processing programs in single-cell RNA-seq.Genome biology · 2022Article
- Unleashing the power within short-read RNA-seq for plant research: Beyond differential expression analysis and toward regulomics.Frontiers in plant science · 2022Review
- Negative charge in the RACK1 loop broadens the translational capacity of the human ribosome.Cell reports · 2021Article
- The DME demethylase regulates sporophyte gene expression, cell proliferation, differentiation, and meristem resurrection.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- The circadian clock shapes theThe Journal of biological chemistry · 2020Article
- Plant 3' Regulatory Regions From mRNA-Encoding Genes and Their Uses to Modulate Expression.Frontiers in plant science · 2020Review
- Discovery of alternative polyadenylation dynamics from single cell types.Computational and structural biotechnology journal · 2020Review
- Genome-Wide Profiling of Polyadenylation Events in Maize Using High-Throughput Transcriptomic Sequences.G3 (Bethesda, Md.) · 2019Article
- RACK1 evolved species-specific multifunctionality in translational control through sequence plasticity within a loop domain.Journal of cell science · 2019Article
- Modeling of Genome-Wide Polyadenylation Signals inFrontiers in genetics · 2019Article
- UTR-Dependent Control of Gene Expression in Plants.Trends in plant science · 2018Review
- Experimental Verification and Evolutionary Origin of 5'-UTR Polyadenylation Sites inFrontiers in plant science · 2018Article
- Genome-Wide Comparative Analysis of Miniature Inverted Repeat Transposable Elements in 19 Arabidopsis thaliana Ecotype Accessions.Scientific reports · 2017Article
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Alternative polyadenylation has been recognized as a key contributor of gene expression regulation by generating different transcript isoforms with altered 3' ends. Although polyadenylation is well known for marking the end of a 3' UTR, an increasing number of studies have reported previously less-addressed polyadenylation events located in other parts of genes in many eukaryotic organisms. These other locations include 5' UTRs, introns and coding sequences (termed herein as non-3UTR), as well as antisense and intergenic polyadenlation. Focusing on the non-3UTR polyadenylation sites (n3PASs), we detected and characterized more than 11000 n3PAS clusters in the Arabidopsis genome using poly(A)-tag sequencing data (PAT-Seq). Further analyses suggested that the occurrence of these n3PASs were positively correlated with certain characteristics of their respective host genes, including the presence of spliced, diminutive or diverse beginning of 5' UTRs, number of introns and whether introns have extreme lengths. The interaction of the host genes with surrounding genetic elements, like a convergently overlapped gene and associated transposable element, may contribute to the generation of a n3PAS as well. Collectively, these results provide a better understanding of n3PASs, and offer some new insights of the underlying mechanisms for non-3UTR polyadenylation and its regulation in plants.
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