ArticleBMC evolutionary biology2014
Motif types, motif locations and base composition patterns around the RNA polyadenylation site in microorganisms, plants and animals.
Article in BMC evolutionary biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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16 citing papers in PubMed, 33 citations in OpenAlex.
- Profiling maize embryonic leaf development and discovering new genes using high-resolution spatial long-read isoform sequencing.Nature plants · 2026Article
- 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
- Evolutionary dynamics of polyadenylation signals and their recognition strategies in protists.Genome research · 2024Article
- Source leaves are regulated by sink strengths through non-coding RNAs and alternative polyadenylation in cucumber (Cucumis sativus L.).BMC plant biology · 2024Article
- A comprehensive analysis of 3'UTRs in Caenorhabditis elegans.Nucleic acids research · 2024Article
- Deep learning the cis-regulatory code for gene expression in selected model plants.Nature communications · 2024Article
- Multifactorial analysis of terminator performance on heterologous gene expression in Physcomitrella.Plant cell reports · 2024Article
- Construction of drought stress regulation networks in potato based on SMRT and RNA sequencing data.BMC plant biology · 2022Article
- Precise gene models using long-read sequencing reveal a unique poly(A) signal inRNA (New York, N.Y.) · 2022Article
- Identification of Alternative Polyadenylation inFrontiers in genetics · 2021Article
- Characterization ofThe Plant cell · 2020Article
- PacBio single-molecule long-read sequencing shed new light on the transcripts and splice isoforms of the perennial ryegrass.Molecular genetics and genomics : MGG · 2020Article
- Genome-Wide Profiling of Polyadenylation Events in Maize Using High-Throughput Transcriptomic Sequences.G3 (Bethesda, Md.) · 2019Article
- Characterization of mRNA polyadenylation in the apicomplexa.PloS one · 2018Article
- Experimental Genome-Wide Determination of RNA Polyadenylation in Chlamydomonas reinhardtii.PloS one · 2016Article
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2 authors at 2 institutions in 1 country.
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No grant is acknowledged in the PubMed record.
Abstract
backgroundThe polyadenylation of RNA is critical for gene functioning, but the conserved sequence motifs (often called signal or signature motifs), motif locations and abundances, and base composition patterns around mRNA polyadenylation [poly(A)] sites are still uncharacterized in most species. The evolutionary tendency for poly(A) site selection is still largely unknown.
resultsWe analyzed the poly(A) site regions of 31 species or phyla. Different groups of species showed different poly(A) signal motifs: UUACUU at the poly(A) site in the parasite Trypanosoma cruzi; UGUAAC (approximately 13 bases upstream of the site) in the alga Chlamydomonas reinhardtii; UGUUUG (or UGUUUGUU) at mainly the fourth base downstream of the poly(A) site in the parasite Blastocystis hominis; and AAUAAA at approximately 16 bases and approximately 19 bases upstream of the poly(A) site in animals and plants, respectively. Polyadenylation signal motifs are usually several hundred times more abundant around poly(A) sites than in whole genomes. These predominant motifs usually had very specific locations, whether upstream of, at, or downstream of poly(A) sites, depending on the species or phylum. The poly(A) site was usually an adenosine (A) in all analyzed species except for B. hominis, and there was weak A predominance in C. reinhardtii. Fungi, animals, plants, and the protist Phytophthora infestans shared a general base abundance pattern (or base composition pattern) of "U-rich-A-rich-U-rich-Poly(A) site-U-rich regions", or U-A-U-A-U for short, with some variation for each kingdom or subkingdom.
conclusionThis study identified the poly(A) signal motifs, motif locations, and base composition patterns around mRNA poly(A) sites in protists, fungi, plants, and animals and provided insight into poly(A) site evolution.
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