Small RNAs: classification, biogenesis, and function.

Eukaryotes produce various types of small RNAs of 19-28 nt in length. With rapidly increasing numbers of small RNAs listed in recent years, we have come to realize how widespread their functions are and how diverse the biogenesis pathways have evolved. At the same time, we are beginning to grasp the common features and rules governing the key steps in small RNA pathways. In this review, I will summarize the current classification, biogenesis, action mechanism and function of these fascinating molecules.

• Publication year

  2005

• Venue

  Molecules and Cells

• Publication date

  2005-02-01

• Fields of study

  Biology, Medicine

• Identifiers
  DOI 10.1016/s1016-8478(23)13130-xPMID 15750334
• External record

  Open on Semantic Scholar

• Source metadata

  Semantic Scholar, PubMed

• No claims are published for this paper.

• No concepts are published for this paper.

• Methylation as a Crucial Step in Plant microRNA Biogenesis

  2005cited by this paper
• RNAi-mediated pathways in the nucleus

  2005cited by this paper
• RNA Polymerase IV Directs Silencing of Endogenous DNA

  2005cited by this paper
• Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets.

  2005cited by this paper
• Endogenous trans-acting siRNAs regulate the accumulation of Arabidopsis mRNAs.

  2004cited by this paper
• SGS3 and SGS2/SDE1/RDR6 are required for juvenile development and the production of trans-acting siRNAs in Arabidopsis.

  2004cited by this paper
• Human embryonic stem cells express a unique set of microRNAs.

  2004cited by this paper
• Dissection of a Natural RNA Silencing Process in the Drosophila melanogaster Germ Line

  2004cited by this paper
• MicroRNA-Directed Cleavage of HOXB8 mRNA

  2004cited by this paper
• What's new about RNAi?

  2004cited by this paper
• Molecular mechanism of RNA silencing suppression mediated by p19 protein of tombusviruses

  2004influential reference
• Nucleic acid 3′-end recognition by the Argonaute2 PAZ domain

  2004cited by this paper
• RISC assembly defects in the Drosophila RNAi mutant armitage.

  2004cited by this paper
• miRNAs on the move: miRNA biogenesis and the RNAi machinery.

  2004cited by this paper
• Role of transposable elements in heterochromatin and epigenetic control

  2004cited by this paper
• Induction of DNA methylation and gene silencing by short interfering RNAs in human cells

  2004cited by this paper
• Arabidopsis micro-RNA biogenesis through Dicer-like 1 protein functions.

  2004influential reference
• RNA Silencing Genes Control de Novo DNA Methylation

  2004cited by this paper
• A MicroRNA as a Translational Repressor of APETALA2 in Arabidopsis Flower Development

  2004cited by this paper
• Argonaute2 Is the Catalytic Engine of Mammalian RNAi

  2004cited by this paper
• Role of Arabidopsis ARGONAUTE4 in RNA-directed DNA methylation triggered by inverted repeats.

  2004cited by this paper
• Human microRNAs are processed from capped, polyadenylated transcripts that can also function as mRNAs.

  2004cited by this paper
• The Microprocessor complex mediates the genesis of microRNAs

  2004cited by this paper
• Unlocking the potential of the human genome with RNA interference

  2004cited by this paper
• The role of RNA interference in heterochromatic silencing

  2004cited by this paper
• RNA silencing in plants

  2004cited by this paper
• Processing of primary microRNAs by the Microprocessor complex

  2004cited by this paper
• MicroRNAs act sequentially and asymmetrically to control chemosensory laterality in the nematode

  2004cited by this paper
• Structural basis for overhang-specific small interfering RNA recognition by the PAZ domain

  2004cited by this paper
• Genetic and Functional Diversification of Small RNA Pathways in Plants

  2004influential reference
• RNAi protects the Caenorhabditis elegans germline against transposition.

  2004cited by this paper
• The nuclear dsRNA binding protein HYL1 is required for microRNA accumulation and plant development, but not posttranscriptional transgene silencing.

  2004cited by this paper
• Crystal Structure of Argonaute and Its Implications for RISC Slicer Activity

  2004cited by this paper
• The functions of animal microRNAs

  2004cited by this paper
• Conjugation-specific small RNAs in Tetrahymena have predicted properties of scan (scn) RNAs involved in genome rearrangement.

  2004cited by this paper
• MicroRNA profiling reveals distinct signatures in B cell chronic lymphocytic leukemias.

  2004cited by this paper
• A Protein Sensor for siRNA Asymmetry

  2004cited by this paper
• Distinct roles for Drosophila Dicer-1 and Dicer-2 in the siRNA/miRNA silencing pathways.

  2004cited by this paper
• Human Argonaute2 mediates RNA cleavage targeted by miRNAs and siRNAs.

  2004cited by this paper
• MicroRNAs Modulate Hematopoietic Lineage Differentiation

  2004cited by this paper
• Heterochromatic Silencing and HP1 Localization in Drosophila Are Dependent on the RNAi Machinery

  2004cited by this paper
• Nuclear Export of MicroRNA Precursors

  2004cited by this paper
• ReviewMicroRNAs : Genomics , Biogenesis , Mechanism , and Function

  2004cited by this paper
• What's new about RNAi? Meeting on siRNAs and miRNAs.

  2004cited by this paper
• Novel and Stress-Regulated MicroRNAs and Other Small RNAs from Arabidopsis

  2004cited by this paper
• Viral RNA silencing suppressors inhibit the microRNA pathway at an intermediate step.

  2004influential reference
• RNAi-Mediated Targeting of Heterochromatin by the RITS Complex

  2004cited by this paper
• Crystal structure of p19--a universal suppressor of RNA silencing.

  2004influential reference
• High expression of precursor microRNA‐155/BIC RNA in children with Burkitt lymphoma

  2004cited by this paper
• The Drosha-DGCR8 complex in primary microRNA processing.

  2004influential reference
• Distinct roles for Argonaute proteins in small RNA-directed RNA cleavage pathways.

  2004cited by this paper
• Mechanisms of gene silencing by double-stranded RNA

  2004cited by this paper
• The microRNA Registry

  2004cited by this paper
• Identification of Virus-Encoded MicroRNAs

  2004cited by this paper
• The Arabidopsis double-stranded RNA-binding protein HYL1 plays a role in microRNA-mediated gene regulation.

  2004cited by this paper
• Micromanagers of gene expression: the potentially widespread influence of metazoan microRNAs

  2004influential reference
• Exportin 5 is a RanGTP-dependent dsRNA-binding protein that mediates nuclear export of pre-miRNAs.

  2004cited by this paper
• Histone H3 lysine 9 methylation is required for DNA elimination in developing macronuclei in Tetrahymena.

  2004cited by this paper
• A small modulatory dsRNA specifies the fate of adult neural stem cells.

  2004cited by this paper
• MicroRNA genes are transcribed by RNA polymerase II

  2004cited by this paper
• The human DiGeorge syndrome critical region gene 8 and Its D. melanogaster homolog are required for miRNA biogenesis.

  2004cited by this paper
• RITS acts in cis to promote RNA interference–mediated transcriptional and post-transcriptional silencing

  2004cited by this paper
• Small Interfering RNA-Induced Transcriptional Gene Silencing in Human Cells

  2004cited by this paper
• Small RNAs in genome rearrangement in Tetrahymena.

  2004cited by this paper
• RNA silencing: no mercy for viruses?

  2004cited by this paper
• Evidence for Nuclear Processing of Plant Micro RNA and Short Interfering RNA Precursors1[w]

  2003influential reference
• MicroRNAs and other tiny endogenous RNAs in C. elegans.

  2003cited by this paper
• Exportin-5 mediates the nuclear export of pre-microRNAs and short hairpin RNAs.

  2003cited by this paper
• Hairpin RNAs and Retrotransposon LTRs Effect RNAi and Chromatin-Based Gene Silencing

  2003cited by this paper
• Functional siRNAs and miRNAs exhibit strand bias.

  2003cited by this paper
• The small RNA profile during Drosophila melanogaster development.

  2003cited by this paper
• Recognition of small interfering RNA by a viral suppressor of RNA silencing

  2003influential reference
• The nuclear RNase III Drosha initiates microRNA processing

  2003cited by this paper
• Regulation of Flowering Time and Floral Organ Identity by a MicroRNA and Its APETALA2-Like Target Genes Article, publication date, and citation information can be found at www.plantcell.org/cgi/doi/10.1105/tpc.016238.

  2003cited by this paper
• A uniform system for microRNA annotation.

  2003cited by this paper
• Asymmetry in the Assembly of the RNAi Enzyme Complex

  2003cited by this paper
• ARGONAUTE4 Control of Locus-Specific siRNA Accumulation and DNA and Histone Methylation

  2003cited by this paper
• Size selective recognition of siRNA by an RNA silencing suppressor.

  2003cited by this paper
• The crystal structure of the Argonaute2 PAZ domain reveals an RNA binding motif in RNAi effector complexes

  2003cited by this paper
• bantam encodes a developmentally regulated microRNA that controls cell proliferation and regulates the proapoptotic gene hid in Drosophila.

  2003cited by this paper
• Arabidopsis HEN1: a genetic link between endogenous miRNA controlling development and siRNA controlling transgene silencing and virus resistance.

  2003cited by this paper
• Embryonic stem cell-specific MicroRNAs.

  2003cited by this paper
• HASTY, the Arabidopsis ortholog of exportin 5/MSN5, regulates phase change and morphogenesis

  2003cited by this paper
• R2D2, a Bridge Between the Initiation and Effector Steps of the Drosophila RNAi Pathway

  2003cited by this paper
• Structure and conserved RNA binding of the PAZ domain

  2003cited by this paper
• Asymmetry in the assembly of the RNAi enzyme complex.

  2003cited by this paper
• Methylation of histone h3 at lysine 9 targets programmed DNA elimination in tetrahymena.

  2002cited by this paper
• miRNPs: a novel class of ribonucleoproteins containing numerous microRNAs.

  2002influential reference
• RNAi related mechanisms affect both transcriptional and posttranscriptional transgene silencing in Drosophila.

  2002cited by this paper
• Non-Mendelian inheritance and homology-dependent effects in ciliates.

  2002cited by this paper
• CARPEL FACTORY, a Dicer homolog, and HEN1, a novel protein, act in microRNA metabolism in Arabidopsis thaliana.

  2002influential reference
• A viral protein suppresses RNA silencing and binds silencing‐generated, 21‐ to 25‐nucleotide double‐stranded RNAs

  2002cited by this paper
• Two classes of short interfering RNA in RNA silencing

  2002cited by this paper
• A Drosophila fragile X protein interacts with components of RNAi and ribosomal proteins.

  2002cited by this paper
• Fragile X-related protein and VIG associate with the RNA interference machinery.

  2002cited by this paper
• Endogenous and Silencing-Associated Small RNAs in Plants Online version contains Web-only data. Article, publication date, and citation information can be found at www.plantcell.org/cgi/doi/10.1105/tpc.003210.

  2002influential reference
• Single-stranded antisense siRNAs guide target RNA cleavage in RNAi.

  2002influential reference
• MicroRNA maturation: stepwise processing and subcellular localization

  2002cited by this paper
• Analysis of gene function in somatic mammalian cells using small interfering RNAs.

  2002cited by this paper
• Establishment and Maintenance of a Heterochromatin Domain

  2002cited by this paper

• The Small RNA Landscape in Azoospermia: Implications for Male Infertility and Sperm Retrieval—A Preliminary Study

  2025cites this paper
• FungiSNC: An integrated database for fungi small non-coding RNAs based on high-throughput sequencing.

  2025cites this paper
• A narrative review on MicroRNA's role in diagnosis and therapy of equine endometritis.

  2025cites this paper
• Implementing RNA Interference to Boost Plant Resistance and Enhance Crop Characteristics: A Review

  2024cites this paper
• Changes in the Repertoire of tRNA-Derived Fragments in Different Blood Cell Populations

  2024cites this paper
• Transcriptional landscape of small non-coding RNAs reveals diversity of categories and functions in molluscs

  2024cites this paper
• CircITGB5 regulates the proliferation and adipogenic differentiation of chicken intramuscular preadipocytes through the miR-181b-5p/CPT1A axis.

  2024cites this paper
• Knockdown of miR-361-5p promotes the induced activation of SHF-stem cells through FOXM1 mediated Wnt/β-catenin pathway in cashmere goats

  2024cites this paper
• High expression of miR-22-3p in chicken hierarchical follicles promotes granulosa cell proliferation, steroidogenesis, and lipid metabolism via PTEN/PI3K/Akt/mTOR signaling pathway.

  2023cites this paper
• Multi-Faceted Role of Luteolin in Cancer Metastasis: EMT, Angiogenesis, ECM Degradation and Apoptosis

  2023cites this paper
• MicroRNAs as potential biomarkers and therapeutic targets in age-related macular degeneration

  2023cites this paper
• MicroRNAs in equine Endometritis: A review of pathophysiology and molecular insights for diagnostic and therapeutic strategies.

  2023cites this paper
• Crucial role of autophagy in propofol-treated neurological diseases: a comprehensive review

  2023cites this paper
• Role of non-coding RNAs in neuroblastoma

  2023cites this paper
• Tweaking the Small Non-Coding RNAs to Improve Desirable Traits in Plant

  2023cites this paper
• Extracellular MicroRNAs as Potential Biomarkers for Frail Kidney Phenotype: Progresses and Precautions

  2023cites this paper
• MicroRNAs: Small Molecules with Significant Functions, Particularly in the Context of Viral Hepatitis B and C Infection

  2023cites this paper
• Prenatal Exposure to Delta-9-tetrahydrocannabinol (THC) Alters the Expression of miR-122-5p and Its Target Igf1r in the Adult Rat Ovary

  2022cites this paper
• Limb Remote Ischemic Conditioning Promotes Neurogenesis after Cerebral Ischemia by Modulating miR-449b/Notch1 Pathway in Mice

  2022cites this paper
• Targeting Genetic Modifiers of HBG Gene Expression in Sickle Cell Disease: The miRNA Option

  2022cites this paper
• Evidence that Transcriptional Alterations in Sarcoptes scabiei Are under Tight Post-Transcriptional (microRNA) Control

  2022cites this paper
• MicroRNA29B induces fetal hemoglobin via inhibition of the HBG repressor protein MYB in vitro and in humanized sickle cell mice

  2022cites this paper
• miR-122-5p regulates proliferation and apoptosis of chicken granulosa cells of hierarchal follicles by targeting MAPK3.

  2022cites this paper
• Effects of scion-rootstock interaction on citrus fruit quality related to differentially expressed small RNAs

  2022cites this paper
• Profiling Secreted miRNA Biomarkers of Chemical-Induced Neurodegeneration in Human iPSC-Derived Neurons

  2022cites this paper
• INVOLVEMENT OF PLANT MICRORNAS IN ABIOTIC STRESS RESPONSES

  2022cites this paper
• Identification of a Potential MiRNA–mRNA Regulatory Network for Osteoporosis by Using Bioinformatics Methods: A Retrospective Study Based on the Gene Expression Omnibus Database

  2022cites this paper
• Nanomaterials and nanotechnology for the delivery of agrochemicals: strategies towards sustainable agriculture

  2022cites this paper
• Emerging biology of noncoding RNAs in malaria parasites

  2022cites this paper
• microRNAs and Their Roles in Plant Development

  2022cites this paper
• MicroRNAs mediate precise control of spinal interneuron populations to exert delicate sensory-to-motor outputs

  2021cites this paper
• Current paradigms in epigenetic anticancer therapeutics and future challenges.

  2021cites this paper
• Exploring epigenetic and microRNA approaches for γ-globin gene regulation

  2021cites this paper
• Harnessing Perks of MiRNA Principles for Betterment of Agriculture and Food Security

  2021cites this paper
• Advances in the application of Let-7 microRNAs in the diagnosis, treatment and prognosis of leukemia

  2021cites this paper
• Zooming in: PAGE-Northern Blot Helps to Analyze Anti-Sense Transcripts Originating from Human rIGS under Transcriptional Stress

  2021cites this paper
• Plant Non-Coding RNAs: Origin, Biogenesis, Mode of Action and Their Roles in Abiotic Stress

  2020cites this paper
• What does it take to be antiviral? An Argonaute-centered perspective on plant antiviral defense.

  2020cites this paper
• Doxorubicin induces cytotoxicity and miR-132 expression in granulosa cells.

  2020cites this paper
• Small Interfering RNAs Are Highly Effective Inhibitors of Crimean-Congo Hemorrhagic Fever Virus Replication In Vitro

  2020cites this paper
• Identification of small non-coding RNAs responsive to GUN1 and GUN5 related retrograde signals in Arabidopsis thaliana.

  2020cites this paper
• Global expression of noncoding RNome reveals dysregulation of small RNAs in patients with HTLV-1–associated adult T-cell leukemia: a pilot study

  2020cites this paper
• Role of sRNAs in abiotic stress tolerance

  2020cites this paper
• Interest of blood biomarkers to predict lesions in medical imaging in the context of mild traumatic brain injury.

  2020cites this paper
• High Expression of miR-204 in Chicken Atrophic Ovaries Promotes Granulosa Cell Apoptosis and Inhibits Autophagy

  2020influential citation
• Overexpression of a RNA silencing suppressor, B2 protein encoded by Flock House virus, in tobacco plants results in tolerance to salt stress

  2020cites this paper
• Overexpression of a RNA silencing suppressor, B2 protein encoded by Flock House virus, in tobacco plants results in tolerance to salt stress

  2020cites this paper
• Aldosterone‐induced microRNAs act as feedback regulators of mineralocorticoid receptor signaling in kidney epithelia

  2020cites this paper
• Epigenetic Molecular Mechanisms in Insects

  2020cites this paper
• Interest of blood biomarkers to predict lesions in medical imaging in the context of mild traumatic brain injury.

  2020cites this paper
• Relationship between Sphk1/S1P and microRNAs in human cancers

  2020cites this paper
• Discovery and functional understanding of MiRNAs in molluscs: a genome-wide profiling approach

  2020cites this paper
• Differential microRNA and metabolic expressions in neuroendocrine and cervical carcinomas

  2020cites this paper
• Genome-wide identification of miRNAs and their targets during early somatic embryogenesis in Dimocarpus longan Lour.

  2020cites this paper
• Plant growth regulation by small RNA-mediated plant-biotic interactions

  2020cites this paper
• NOL6, a new founding oncogene in human prostate cancer and targeted by miR-590-3p

  2020cites this paper
• Non-coding RNAs and the mineralocorticoid receptor in the kidney.

  2020cites this paper
• LIPUS promotes FOXO1 accumulation by downregulating miR-182 to enhance osteogenic differentiation in hPDLCs.

  2019cites this paper
• Noncoding RNAs in Parasite-Vector-Host Interactions.

  2019cites this paper
• Pharmacoepigenetics of Memantine in Dementia

  2019cites this paper
• Visualization and quantification of cellular RNA production and degradation using a combined fluorescence and mass spectrometry characterization assay.

  2019cites this paper
• Genome-wide association study of vitamin E using genotyping by sequencing in sesame (Sesamum indicum)

  2019cites this paper
• MicroRNA‐195 suppresses the progression of lung adenocarcinoma by directly targeting apelin

  2019cites this paper
• Identification of novel and conserved microRNAs involved in fruit development and ripening in Fragaria vesca

  2019cites this paper
• Three new circulating microRNAs may be associated with wet age-related macular degeneration

  2019cites this paper
• Regulation of hepatic microRNAs in response to early stage Echinococcus multilocularis egg infection in C57BL/6 mice

  2019cites this paper
• Rôle du microARN miR-124 dans la plasticité homéostatique via le contrôle de l’expression de la synaptopodine et des récepteurs AMPA dans les neurones de l'hippocampe

  2019cites this paper
• The Role of Noncoding RNAs in Gene Regulation

  2019cites this paper
• Deregulation of SATB2 in carcinogenesis with emphasis on miRNA-mediated control.

  2019cites this paper
• The accumulation of chloroplast small RNAs in unicellular alga Chlamydomonas reinhardtii is affected by nitrogen deprivation

  2019cites this paper
• Impact of small RNAs in retrograde signalling pathways in Arabidopsis thaliana

  2019influential citation
• Estimating time since deposition using quantification of RNA degradation in body fluid-specific markers.

  2019cites this paper
• Plant Regulomics Portal (PRP): a comprehensive integrated regulatory information and analysis portal for plant genomes

  2019cites this paper
• Drought and heat stress-related proteins: an update about their functional relevance in imparting stress tolerance in agricultural crops

  2019cites this paper
• Disease gene recognition and editing optimization through knowledge learned from domain feature spaces

  2019cites this paper
• Regulation of Aldosterone Signaling by MicroRNAs.

  2019cites this paper
• Dissecting the Factors Involved in mRNA Trafficking to Germ Granules

  2019cites this paper
• miRNA as viral transcription tuners in HPV-mediated cervical carcinogenesis.

  2018cites this paper
• Rapid enhancement of α-tocopherol content in Nicotiana benthamiana by transient expression of Arabidopsis thaliana Tocopherol cyclase and Homogentisate phytyl transferase genes

  2018cites this paper
• biomarkers in pharmaceutical preclinical safety testing an update

  2018cites this paper
• Alshehhi, Suaad and McCallum, Nicola A. and Haddrill, Penelope R. (2017) Quantification of RNA degradation of blood-specific markers to indicate the age of bloodstains. Forensic Science International: Genetics

  2018cites this paper
• Bidirectional regulation of osteogenic differentiation by the FOXO subfamily of Forkhead transcription factors in mammalian MSCs

  2018cites this paper
• The role of miR-106p-5p in cervical cancer: from expression to molecular mechanism

  2018cites this paper
• Defining a microRNA‐mRNA interaction map for calcineurin inhibitor induced nephrotoxicity

  2018cites this paper
• Structure of the 30 kDa HIV-1 RNA Dimerization Signal by a Hybrid Cryo-EM, NMR, and Molecular Dynamics Approach.

  2018cites this paper
• Reverse Engineering Glaucoma

  2018cites this paper
• In silico analysis of endogenous siRNAs associated transposable elements and NATs in Schistosoma japonicum reveals their putative roles during reproductive development

  2018cites this paper
• MicroRNA-30d/JAG1 axis modulates pulmonary fibrosis through Notch signaling pathway.

  2018cites this paper
• Zerumbone inhibits epithelial‐mesenchymal transition and cancer stem cells properties by inhibiting the β‐catenin pathway through miR‐200c

  2018cites this paper
• In silico analysis of endogenous siRNAs associated transposable elements and NATs in Schistosoma japonicum reveals their putative roles during reproductive development

  2018cites this paper
• Structural basis of siRNA recognition by TRBP double‐stranded RNA binding domains

  2018cites this paper
• LncRNAs in Secondary Hair Follicle of Cashmere Goat: Identification, Expression, and Their Regulatory Network in Wnt Signaling Pathway

  2018cites this paper
• Molecular alterations during larval development of Haemonchus contortus in vitro are under tight post-transcriptional control.

  2018cites this paper
• The combinational effect of E6/E7 siRNA and anti-miR-182 on apoptosis induction in HPV16-positive cervical cells

  2018cites this paper
• miR-505 functions as a tumor suppressor in glioma by targeting insulin like growth factor 1 receptor expression.

  2018cites this paper
• Isolation and detection of small RNA molecules

  2018cites this paper
• A lncRNA-H19 transcript from secondary hair follicle of Liaoning cashmere goat: Identification, regulatory network and expression regulated potentially by its promoter methylation.

  2018cites this paper
• Stress‐responsive microRNAs are involved in re‐programming of metabolic functions in hibernators

  2018cites this paper
• miR‐129 targets CDK1 and iASPP to modulate Burkitt lymphoma cell proliferation in a TAp63‐dependent manner

  2018cites this paper
• Mammalian target of rapamycin as a therapeutic target in osteoporosis

  2018cites this paper