ArticleRNA (New York, N.Y.)2012
Known and novel post-transcriptional regulatory sequences are conserved across plant families.
Article in RNA (New York, N.Y.), 2012. 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, 66 citations in OpenAlex.
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- Improved super-resolution ribosome profiling reveals prevalent translation of upstream ORFs and small ORFs in Arabidopsis.The Plant cell · 2024Article
- The identification of conserved sequence features of co-translationally decayed mRNAs and upstream open reading frames in angiosperm transcriptomes.Plant direct · 2023Article
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- Genome and gene evolution of seahorse species revealed by the chromosome-level genome of Hippocampus abdominalis.Molecular ecology resources · 2022Article
- Plants utilise ancient conserved peptide upstream open reading frames in stress-responsive translational regulation.Plant, cell & environment · 2022Article
- Genome-wide identification and characterization of functionally relevant microsatellite markers from transcription factor genes of Tea (Camellia sinensis (L.) O. Kuntze).Scientific reports · 2022Article
- Brassinosteroid homeostasis is critical for the functionality of the Medicago truncatula pulvinus.Plant physiology · 2021Article
- Translational gene regulation in plants: A green new deal.Wiley interdisciplinary reviews. RNA · 2020Review
- Exhaustive identification of conserved upstream open reading frames with potential translational regulatory functions from animal genomes.Scientific reports · 2020Article
- Prevalence of alternative AUG and non-AUG translation initiators and their regulatory effects across plants.Genome research · 2020Article
- uORF Shuffling Fine-Tunes Gene Expression at a Deep Level of the Process.Plants (Basel, Switzerland) · 2020Review
- Comprehensive genome-wide identification of angiosperm upstream ORFs with peptide sequences conserved in various taxonomic ranges using a novel pipeline, ESUCA.BMC genomics · 2020Article
- Metabolite Control of Translation by Conserved Peptide uORFs: The Ribosome as a Metabolite Multisensor.Plant physiology · 2020Article
- uORFlight: a vehicle toward uORF-mediated translational regulation mechanisms in eukaryotes.Database : the journal of biological databases and curation · 2020Article
- Identification and in silico characterization of3 Biotech · 2019Article
- Novel pipeline identifies new upstream ORFs and non-AUG initiating main ORFs with conserved amino acid sequences in the 5' leader of mRNAs inRNA (New York, N.Y.) · 2019Article
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Authors and funding
4 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The sequence elements that mediate post-transcriptional gene regulation often reside in the 5' and 3' untranslated regions (UTRs) of mRNAs. Using six different families of dicotyledonous plants, we developed a comparative transcriptomics pipeline for the identification and annotation of deeply conserved regulatory sequences in the 5' and 3' UTRs. Our approach was robust to confounding effects of poor UTR alignability and rampant paralogy in plants. In the 3' UTR, motifs resembling PUMILIO-binding sites form a prominent group of conserved motifs. Additionally, Expansins, one of the few plant mRNA families known to be localized to specific subcellular sites, possess a core conserved RCCCGC motif. In the 5' UTR, one major subset of motifs consists of purine-rich repeats. A distinct and substantial fraction possesses upstream AUG start codons. Half of the AUG containing motifs reveal hidden protein-coding potential in the 5' UTR, while the other half point to a peptide-independent function related to translation. Among the former, we added four novel peptides to the small catalog of conserved-peptide uORFs. Among the latter, our case studies document patterns of uORF evolution that include gain and loss of uORFs, switches in uORF reading frame, and switches in uORF length and position. In summary, nearly three hundred post-transcriptional elements show evidence of purifying selection across the eudicot branch of flowering plants, indicating a regulatory function spanning at least 70 million years. Some of these sequences have experimental precedent, but many are novel and encourage further exploration.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.