ArticleProceedings of the National Academy of Sciences of the United States of America2014
Dicer-like 3 produces transposable element-associated 24-nt siRNAs that control agricultural traits in rice.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 97 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
97 citing papers in PubMed, 237 citations in OpenAlex.
- Presence and function of small RNAs during plant reproduction.RNA biology · 2026Review
- Enhanced exonuclease-Cas9 systems promote multiple nucleotide deletions with higher efficiency and broader targeting scope in plants.Journal of integrative plant biology · 2026Article
- Regulatory Logic and Transposable Element Dynamics in Caenorhabditis Genomes.Genome biology and evolution · 2026Article
- Article
- Epigenetic control of seed development and dormancy in cereals.Plant signaling & behavior · 2025Review
- Transcription factors instruct DNA methylation patterns in plant reproductive tissues.Nature cell biology · 2025Article
- Origin of a self-compatibility associated MITE in Petota and its application in hybrid potato breeding.The New phytologist · 2025Article
- Transposon-Associated Small RNAs Involved in Plant Defense in Poplar.Plants (Basel, Switzerland) · 2025Article
- MADS31 supports female germline development by repressing the post-fertilization programme in cereal ovules.Nature plants · 2025Article
- Identification and characterization of DICER-LIKE genes and their roles in Marchantia polymorpha development and salt stress response.The Plant journal : for cell and molecular biology · 2025Article
- Biochemical Defence of Plants against Parasitic Nematodes.Plants (Basel, Switzerland) · 2024Review
- Epigenetics and plant hormone dynamics: a functional and methodological perspective.Journal of experimental botany · 2024Review
- Genetic variability of aquaporin expression in maize: From eQTLs to a MITE insertion regulating PIP2;5 expression.Plant physiology · 2024Article
- Exploring Cereal Metagenomics: Unravelling Microbial Communities for Improved Food Security.Microorganisms · 2024Review
- Miniature-inverted-repeat transposable elements contribute to phenotypic variation regulation of rice induced by space environment.Frontiers in plant science · 2024Article
- Foliar application of melatonin improve the number of secondary branches and secondary branch grains quality of rice.PloS one · 2024Article
- Phased secondary small interfering RNAs inNAR genomics and bioinformatics · 2023Article
- Transcriptional Profiling Reveals the Wheat Defences against Fusarium Head Blight Disease Regulated by a NAC Transcription Factor.Plants (Basel, Switzerland) · 2023Article
- Beyond transcription: compelling open questions in plant RNA biology.The Plant cell · 2023Article
- Plant polymerase IV sensitizes chromatin through histone modifications to preclude spread of silencing into protein-coding domains.Genome research · 2023Article
37 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
11 authors at 6 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Transposable elements (TEs) and repetitive sequences make up over 35% of the rice (Oryza sativa) genome. The host regulates the activity of different TEs by different epigenetic mechanisms, including DNA methylation, histone H3K9 methylation, and histone H3K4 demethylation. TEs can also affect the expression of host genes. For example, miniature inverted repeat TEs (MITEs), dispersed high copy-number DNA TEs, can influence the expression of nearby genes. In plants, 24-nt small interfering RNAs (siRNAs) are mainly derived from repeats and TEs. However, the extent to which TEs, particularly MITEs associated with 24-nt siRNAs, affect gene expression remains elusive. Here, we show that the rice Dicer-like 3 homolog OsDCL3a is primarily responsible for 24-nt siRNA processing. Impairing OsDCL3a expression by RNA interference caused phenotypes affecting important agricultural traits; these phenotypes include dwarfism, larger flag leaf angle, and fewer secondary branches. We used small RNA deep sequencing to identify 535,054 24-nt siRNA clusters. Of these clusters, ∼82% were OsDCL3a-dependent and showed significant enrichment of MITEs. Reduction of OsDCL3a function reduced the 24-nt siRNAs predominantly from MITEs and elevated expression of nearby genes. OsDCL3a directly targets genes involved in gibberellin and brassinosteroid homeostasis; OsDCL3a deficiency may affect these genes, thus causing the phenotypes of dwarfism and enlarged flag leaf angle. Our work identifies OsDCL3a-dependent 24-nt siRNAs derived from MITEs as broadly functioning regulators for fine-tuning gene expression, which may reflect a conserved epigenetic mechanism in higher plants with genomes rich in dispersed repeats or TEs.
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.