ArticleGenetics2008
Unique features of nuclear mRNA poly(A) signals and alternative polyadenylation in Chlamydomonas reinhardtii.
Article in Genetics, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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Who cites it
37 citing papers in PubMed, 67 citations in OpenAlex.
- PolyAseqTrap: a universal tool for genome-wide identification and quantification of polyadenylation sites from different 3' end sequencing data.Genome biology · 2026Article
- Comprehensive genome annotation of the model ciliate Tetrahymena thermophila by in-depth epigenetic and transcriptomic profiling.Nucleic acids research · 2025Article
- Evolutionary dynamics of polyadenylation signals and their recognition strategies in protists.Genome research · 2024Article
- Subscaling of a cytosolic RNA binding protein governs cell size homeostasis in the multiple fission alga Chlamydomonas.PLoS genetics · 2024Article
- Multifactorial analysis of terminator performance on heterologous gene expression in Physcomitrella.Plant cell reports · 2024Article
- Exploring the Impact of Terminators on Transgene Expression inLife (Basel, Switzerland) · 2021Article
- Widespread polycistronic gene expression in green algae.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Identification of Alternative Polyadenylation inFrontiers in genetics · 2021Article
- Plant 3' Regulatory Regions From mRNA-Encoding Genes and Their Uses to Modulate Expression.Frontiers in plant science · 2020Review
- PlantAPAdb: A Comprehensive Database for Alternative Polyadenylation Sites in Plants.Plant physiology · 2020Article
- DeeReCT-PolyA: a robust and generic deep learning method for PAS identification.Bioinformatics (Oxford, England) · 2019Article
- Genome-Wide Comparative Analyses of Polyadenylation Signals in Eukaryotes Suggest a Possible Origin of the AAUAAA Signal.International journal of molecular sciences · 2019Article
- Biolistic Transformation ofFrontiers in microbiology · 2019Article
- The mThe Plant cell · 2018Article
- Characterization of mRNA polyadenylation in the apicomplexa.PloS one · 2018Article
- Horizontal Gene Transfer of Phytochelatin Synthases from Bacteria to Extremophilic Green Algae.Microbial ecology · 2017Article
- A new class of cyclin dependent kinase in Chlamydomonas is required for coupling cell size to cell division.eLife · 2016Article
- Experimental Genome-Wide Determination of RNA Polyadenylation in Chlamydomonas reinhardtii.PloS one · 2016Article
- PlantAPA: A Portal for Visualization and Analysis of Alternative Polyadenylation in Plants.Frontiers in plant science · 2016Article
- Genome-wide characterization of intergenic polyadenylation sites redefines gene spaces in Arabidopsis thaliana.BMC genomics · 2015Article
Corrections and comments
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
To understand nuclear mRNA polyadenylation mechanisms in the model alga Chlamydomonas reinhardtii, we generated a data set of 16,952 in silico-verified poly(A) sites from EST sequencing traces based on Chlamydomonas Genome Assembly v.3.1. Analysis of this data set revealed a unique and complex polyadenylation signal profile that is setting Chlamydomonas apart from other organisms. In contrast to the high-AU content in the 3'-UTRs of other organisms, Chlamydomonas shows a high-guanylate content that transits to high-cytidylate around the poly(A) site. The average length of the 3'-UTR is 595 nucleotides (nt), significantly longer than that of Arabidopsis and rice. The dominant poly(A) signal, UGUAA, was found in 52% of the near-upstream elements, and its occurrence may be positively correlated with higher gene expression levels. The UGUAA signal also exists in Arabidopsis and in some mammalian genes but mainly in the far-upstream elements, suggesting a shift in function. The C-rich region after poly(A) sites with unique signal elements is a characteristic downstream element that is lacking in higher plants. We also found a high level of alternative polyadenylation in the Chlamydomonas genome, with a range of up to 33% of the 4057 genes analyzed having at least two unique poly(A) sites and approximately 1% of these genes having poly(A) sites residing in predicted coding sequences, introns, and 5'-UTRs. These potentially contribute to transcriptome diversity and gene expression regulation.
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