ArticleThe Plant cell2015
Comprehensive Annotation of Physcomitrella patens Small RNA Loci Reveals That the Heterochromatic Short Interfering RNA Pathway Is Largely Conserved in Land Plants.
Article in The Plant cell, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 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
27 citing papers in PubMed, 54 citations in OpenAlex.
- Molecular basis of plant DCL4 action that outcompetes DCL2.Nature plants · 2026Article
- Accurate cross-species 5mC detection for Oxford Nanopore sequencing in plants with DeepPlant.Nature communications · 2025Article
- CLSY docking to Pol IV requires a conserved domain critical for small RNA biogenesis and transposon silencing.Nature communications · 2024Article
- Conserved and non-conserved RNA-target modules in plants: lessons for a better understanding of Marchantia development.Plant molecular biology · 2023Review
- Plant polymerase IV sensitizes chromatin through histone modifications to preclude spread of silencing into protein-coding domains.Genome research · 2023Article
- The emerging role of small RNAs in ovule development, a kind of magic.Plant reproduction · 2021Review
- Deciphering the role of microRNAs duringPhysiology and molecular biology of plants : an international journal of functional plant biology · 2021Article
- Integrated annotations and analyses of small RNA-producing loci from 47 diverse plants.Genome research · 2020Article
- Agrobacterium-mediated Tnt1 mutagenesis of moss protonemal filaments and generation of stable mutants with impaired gametophyte.Molecular genetics and genomics : MGG · 2019Article
- Identification of miRNAs and Their Response to Cold Stress inBiomolecules · 2019Article
- RdDM-independent de novo and heterochromatin DNA methylation by plant CMT and DNMT3 orthologs.Nature communications · 2019Article
- Characterization of siRNAs clusters in Arabidopsis thaliana galls induced by the root-knot nematode Meloidogyne incognita.BMC genomics · 2018Article
- Metagenomic sequencing suggests a diversity of RNA interference-like responses to viruses across multicellular eukaryotes.PLoS genetics · 2018Article
- Threshold-dependent repression of SPL gene expression by miR156/miR157 controls vegetative phase change in Arabidopsis thaliana.PLoS genetics · 2018Article
- Revisiting Criteria for Plant MicroRNA Annotation in the Era of Big Data.The Plant cell · 2018Review
- Genome re-annotation of the wild strawberry Fragaria vesca using extensive Illumina- and SMRT-based RNA-seq datasets.DNA research : an international journal for rapid publication of reports on genes and genomes · 2018Article
- Gene body DNA methylation in plants.Current opinion in plant biology · 2017Review
- A Lin28 homologue reprograms differentiated cells to stem cells in the moss Physcomitrella patens.Nature communications · 2017Article
- Article
- Assessing the Gene Content of the Megagenome: Sugar Pine (Pinus lambertiana).G3 (Bethesda, Md.) · 2016Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors at 2 institutions in 1 country.
Funding
Abstract
Many plant small RNAs are sequence-specific negative regulators of target mRNAs and/or chromatin. In angiosperms, the two most abundant endogenous small RNA populations are usually 21-nucleotide microRNAs (miRNAs) and 24-nucleotide heterochromatic short interfering RNAs (siRNAs). Heterochromatic siRNAs are derived from repetitive regions and reinforce DNA methylation at targeted loci. The existence and extent of heterochromatic siRNAs in other land plant lineages has been unclear. Using small RNA-sequencing (RNA-seq) of the moss Physcomitrella patens, we identified 1090 loci that produce mostly 23- to 24-nucleotide siRNAs. These loci are mostly in intergenic regions with dense DNA methylation. Accumulation of siRNAs from these loci depends upon P. patens homologs of DICER-LIKE3 (DCL3), RNA-DEPENDENT RNA POLYMERASE2, and the largest subunit of DNA-DEPENDENT RNA POLYMERASE IV, with the largest subunit of a Pol V homolog contributing to expression at a smaller subset of the loci. A MINIMAL DICER-LIKE (mDCL) gene, which lacks the N-terminal helicase domain typical of DCL proteins, is specifically required for 23-nucleotide siRNA accumulation. We conclude that heterochromatic siRNAs, and their biogenesis pathways, are largely identical between angiosperms and P. patens, with the notable exception of the P. patens-specific use of mDCL to produce 23-nucleotide siRNAs.
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.