ArticleMolecular biology and evolution2015
Ancient Origin and Recent Innovations of RNA Polymerase IV and V.
Article in Molecular biology and evolution, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 49 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
49 citing papers in PubMed, 93 citations in OpenAlex.
- Atypical epigenetic and small RNA control of degenerated transposons and their fragments in clonally reproducingGenome research · 2025Article
- CLSY docking to Pol IV requires a conserved domain critical for small RNA biogenesis and transposon silencing.Nature communications · 2024Article
- BEAN and HABAS: Polyphyletic insertions in the DNA-directed RNA polymerase.Protein science : a publication of the Protein Society · 2024Article
- An RdDM-independent function of Pol V transcripts in gene regulation and plant defence.Nature plants · 2024Article
- Charophytic Green Algae Encode Ancestral Polymerase IV/Polymerase V Subunits and a CLSY/DRD1 Homolog.Genome biology and evolution · 2024Article
- SPT6L, a newly discovered ancestral component of the plant RNA-directed DNA methylation pathway.Frontiers in plant science · 2024Article
- A critical role of a plant-specific TFIIB-related protein, BRP1, in salicylic acid-mediated immune response.Frontiers in plant science · 2024Article
- Article
- Conserved and non-conserved RNA-target modules in plants: lessons for a better understanding of Marchantia development.Plant molecular biology · 2023Review
- DNA-dependent RNA polymerases in plants.The Plant cell · 2023Article
- Article
- The renaissance and enlightenment of Marchantia as a model system.The Plant cell · 2022Article
- The Mediator Complex: A Central Coordinator of Plant Adaptive Responses to Environmental Stresses.International journal of molecular sciences · 2022Review
- Gene duplication and rate variation in the evolution of plastid ACCase and Clp genes in angiosperms.Molecular phylogenetics and evolution · 2022Article
- Evolution of CG Methylation Maintenance Machinery in Plants.Epigenomes · 2021Review
- Atypical DNA methylation, sRNA-size distribution, and female gametogenesis in Utricularia gibba.Scientific reports · 2021Article
- Genome-wide analyses across Viridiplantae reveal the origin and diversification of small RNA pathway-related genes.Communications biology · 2021Article
- The visual story of data storage: From storage properties to user interfaces.Computational and structural biotechnology journal · 2021Review
- Eukaryotic RNA Polymerases: The Many Ways to Transcribe a Gene.Frontiers in molecular biosciences · 2021Review
- Several Isoforms for Each Subunit Shared by RNA Polymerases are Differentially Expressed in the Cultivated Olive Tree (Frontiers in molecular biosciences · 2021Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
10 authors at 5 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Small RNA-mediated chromatin modification is a conserved feature of eukaryotes. In flowering plants, the short interfering (si)RNAs that direct transcriptional silencing are abundant and subfunctionalization has led to specialized machinery responsible for synthesis and action of these small RNAs. In particular, plants possess polymerase (Pol) IV and Pol V, multi-subunit homologs of the canonical DNA-dependent RNA Pol II, as well as specialized members of the RNA-dependent RNA Polymerase (RDR), Dicer-like (DCL), and Argonaute (AGO) families. Together these enzymes are required for production and activity of Pol IV-dependent (p4-)siRNAs, which trigger RNA-directed DNA methylation (RdDM) at homologous sequences. p4-siRNAs accumulate highly in developing endosperm, a specialized tissue found only in flowering plants, and are rare in nonflowering plants, suggesting that the evolution of flowers might coincide with the emergence of specialized RdDM machinery. Through comprehensive identification of RdDM genes from species representing the breadth of the land plant phylogeny, we describe the ancient origin of Pol IV and Pol V, suggesting that a nearly complete and functional RdDM pathway could have existed in the earliest land plants. We also uncover innovations in these enzymes that are coincident with the emergence of seed plants and flowering plants, and recent duplications that might indicate additional subfunctionalization. Phylogenetic analysis reveals rapid evolution of Pol IV and Pol V subunits relative to their Pol II counterparts and suggests that duplicates were retained and subfunctionalized through Escape from Adaptive Conflict. Evolution within the carboxy-terminal domain of the Pol V largest subunit is particularly striking, where illegitimate recombination facilitated extreme sequence divergence.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.