ArticleNature structural & molecular biology2012
Direct sequencing of Arabidopsis thaliana RNA reveals patterns of cleavage and polyadenylation.
Article in Nature structural & molecular biology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 91 papers.
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Who cites it
91 citing papers in PubMed.
- Benchmarking computational methods for identifying and quantifying polyadenylation sites from 3' tag-based single-cell RNA-seq data.Nucleic acids research · 2026Article
- PolyAseqTrap: a universal tool for genome-wide identification and quantification of polyadenylation sites from different 3' end sequencing data.Genome biology · 2026Article
- The general transcription factors (GTFs) of RNA polymerase II and their roles in plant development and stress responses.Critical reviews in biochemistry and molecular biology · 2024Review
- The Arabidopsis U1 snRNP regulates mRNA 3'-end processing.Nature plants · 2024Article
- Light regulates widespread plant alternative polyadenylation through the chloroplast.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- A data-driven genome annotation approach for cassava.The Plant journal : for cell and molecular biology · 2024Article
- Multiple strategies, including 6mA methylation, affecting plant alternative splicing in allopolyploid peanut.Plant biotechnology journal · 2024Article
- Comprehensive Profiling of Alternative Splicing and Alternative Polyadenylation during Fruit Ripening in Watermelon (International journal of molecular sciences · 2023Article
- Plant terminators: the unsung heroes of gene expression.Journal of experimental botany · 2023Review
- A Survey on Methods for Predicting Polyadenylation Sites from DNA Sequences, Bulk RNA-seq, and Single-cell RNA-seq.Genomics, proteomics & bioinformatics · 2023Review
- 3' Untranslated Regions Are Modular Entities That Determine Polyadenylation Profiles.Molecular and cellular biology · 2022Article
- Drought induces epitranscriptome and proteome changes in stem-differentiating xylem of Populus trichocarpa.Plant physiology · 2022Article
- Construction of drought stress regulation networks in potato based on SMRT and RNA sequencing data.BMC plant biology · 2022Article
- A high-resolution single-molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis.Genome biology · 2022Article
- Bookend: precise transcript reconstruction with end-guided assembly.Genome biology · 2022Article
- CONSTITUTIVE EXPRESSER OF PATHOGENESIS-RELATED GENES 5 is an RNA-binding protein controlling plant immunity via an RNA processing complex.The Plant cell · 2022Article
- Full-length transcriptome reconstruction reveals genetic differences in hybrids of Oryza sativa and Oryza punctata with different ploidy and genome compositions.BMC plant biology · 2022Article
- An improved repertoire of splicing variants and their potential roles in Arabidopsis photomorphogenic development.Genome biology · 2022Article
- High-quality reference transcriptome construction improves RNA-seq quantification inFrontiers in genetics · 2022Article
- Identification and characterization of histones inNAR genomics and bioinformatics · 2021Article
31 more citing papers are in PubMed but not listed here.
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Authors and funding
9 authors.
Funding
Abstract
It has recently been shown that RNA 3'-end formation plays a more widespread role in controlling gene expression than previously thought. To examine the impact of regulated 3'-end formation genome-wide, we applied direct RNA sequencing to A. thaliana. Here we show the authentic transcriptome in unprecedented detail and describe the effects of 3'-end formation on genome organization. We reveal extreme heterogeneity in RNA 3' ends, discover previously unrecognized noncoding RNAs and propose widespread reannotation of the genome. We explain the origin of most poly(A)(+) antisense RNAs and identify cis elements that control 3'-end formation in different registers. These findings are essential to understanding what the genome actually encodes, how it is organized and how regulated 3'-end formation affects these processes.
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