id: MODULE:mirna_biogenesis_and_silencing title: Human canonical microRNA pathway — Microprocessor (DROSHA-DGCR8) pri-miRNA cleavage, XPO5-RAN-GTP pre-miRNA export, DICER1-TARBP2/PRKRA dicing, AGO1-4 RISC loading, and TNRC6-directed CCR4-NOT/PAN2-PAN3 deadenylation, DCP2 decapping and XRN1 decay description: >- MicroRNAs (miRNAs) are ~22-nucleotide RNAs that guide Argonaute proteins to partially complementary sites, mostly in the 3' untranslated regions of messenger RNAs, and so repress translation and promote decay of hundreds of transcripts. Most human miRNAs are transcribed by RNA polymerase II as long primary transcripts (pri-miRNAs) that fold into stem-loop hairpins. In the nucleus the Microprocessor, made of the RNase III enzyme DROSHA and its double-stranded RNA-binding partner DGCR8, cuts the hairpin out of the pri-miRNA to release a ~60-70-nucleotide precursor (pre-miRNA) with a two-nucleotide 3' overhang. Exportin-5 (XPO5) binds the pre-miRNA together with GTP-bound RAN and carries it through the nuclear pore; GTP hydrolysis in the cytoplasm releases the cargo. The cytoplasmic RNase III enzyme DICER1, partnered by the dsRNA-binding protein TARBP2 (TRBP) or PRKRA (PACT), removes the terminal loop and leaves a ~22-base-pair miRNA duplex. The duplex is loaded into one of the four human Argonautes (AGO1-AGO4); one strand, the guide, is kept and the other is discarded, forming the miRNA-induced silencing complex (miRISC). AGO2 is the only efficient slicer and can cut fully complementary targets, but most animal miRNA targets pair only through the seed (guide nucleotides 2-7) and are silenced without cleavage. For those, AGO binds a GW182-family protein (TNRC6A, TNRC6B or TNRC6C), whose tryptophan-containing motifs recruit the CCR4-NOT deadenylase complex (through CNOT1 and CNOT9) and the PAN2-PAN3 deadenylase (through PAN3, which also binds the poly(A)-binding protein PABPC1). Deadenylation is followed by removal of the 5' cap by the DCP2-DCP1 decapping complex with its activators DDX6, PATL1, EDC3 and EDC4, and by 5'-to-3' degradation by XRN1. The same CCR4-NOT-DDX6 axis represses translation of the target. A few miRNAs bypass parts of this route: mirtrons are excised by the spliceosome instead of DROSHA, and miR-451 is matured by AGO2 slicing instead of DICER1. status: DRAFT scope: CONCRETE evidence: - source_id: PW:0000808 title: microRNA pathway statement: >- The module boundary follows the RGD Pathway Ontology term and its interactive diagram. The diagram draws Dgcr8 associated with Drosha, Xpo5 associated with Ran (and Ran with GTP and GDP, GTP positively affecting GDP), Tarbp2 associated with and acting on Dicer1, AGO associated with Tnrc6, Tnrc6 acting on the CCR4-NOT complex and on the PAN2-PAN3 complex, Pabpc1 associated with PAN2-PAN3 and with Tnrc6, the RISC complex acting on the DCP1-DCP2 complex, DCP1-DCP2 associated with Xrn1, and the RISC complex negatively affecting the translation pathway, with the labels "target deadenylation", "target decapping", "target degradation" and "target translational repression". It also draws adenosine-to-inosine editing and uridylation as side reactions. Derived through projects/RGD_PATHWAY_ONTOLOGY (pathways/PW_0000808.yaml). - source_id: GO:0035196 title: miRNA processing statement: >- The GO process mapped to PW:0000808 (skos:relatedMatch from the PW definition xref, recorded in projects/RGD_PATHWAY_ONTOLOGY/data/module_seeds.yaml). It covers parts 1-3 of this module; the PW pathway also includes RISC assembly and silencing, so GO:0035195 miRNA-mediated post-transcriptional gene silencing is the second module concept. - source_id: PMID:14508493 title: The nuclear RNase III Drosha initiates microRNA processing. statement: >- Establishes the two-step, two-compartment processing route that the module's first three parts follow. supporting_text: >- the nuclear processing of the pri-miRNAs into stem-loop precursors of approximately 70 nucleotides (pre-miRNAs), and the cytoplasmic processing of pre-miRNAs into mature miRNAs - source_id: PMID:21981923 title: GW182 proteins directly recruit cytoplasmic deadenylase complexes to miRNA targets. statement: >- Establishes that deadenylation is a direct, GW182-mediated effect of miRISC, which is why the deadenylases are modelled as parts of this pathway and not as downstream context. supporting_text: >- human GW182 proteins recruit the PAN2-PAN3 and CCR4-CAF1-NOT deadenylase complexes through direct interactions with PAN3 and NOT1, respectively - source_id: PMID:17964270 title: Mammalian mirtron genes. statement: >- Mammals have mirtrons, which bypass DROSHA by using splicing; recorded as a non-canonical entry route (context), not as a part, because it adds no protein to the module boundary. supporting_text: >- These short hairpin introns use splicing to bypass Drosha cleavage, which is otherwise essential for the generation of canonical animal microRNAs. notes: >- Derived from the RGD Pathway Ontology diagram PW:0000808 (microRNA pathway) through the RGD_PATHWAY_ONTOLOGY project's diagram->module route. RGD curates 35 human genes to PW:0000808: ADAR ADARB1 AGO1 AGO2 AGO3 AGO4 CNOT1 CNOT10 CNOT2 CNOT3 CNOT6 CNOT6L CNOT7 CNOT8 CNOT9 DCP1B DCP2 DDX6 DGCR8 DICER1 DROSHA EDC3 EDC4 PABPC1 PAN2 PAN3 PATL1 RAN TARBP2 TNRC6A TNRC6B TNRC6C TUT4 TUT7 XPO5. Thirty-one are modelled as participants; ADAR, ADARB1, TUT4 and TUT7 are left as context (decision 4). Three genes not on the RGD list are added: PRKRA (the second DICER1 dsRBD partner, which the task brief and the DICER1 gene review both name), DCP1A (the better characterised DCP1 paralog; RGD lists only DCP1B) and XRN1 (drawn on the RGD diagram as associated with DCP1-DCP2, but absent from the human gene list). The mapped GO process GO:0035196 miRNA processing is the first module concept and an evidence entry; it is a relatedMatch, not an exact match, because the PW pathway also covers silencing, so GO:0035195 miRNA-mediated post-transcriptional gene silencing is the second concept. The diagram's sub-pathway links (PW:0000101 translation pathway, PW:0000127 RNA polymerase II transcription pathway, PW:0001073 spliceosome pathway) are neighbouring pathways and are not counted as covered by this module; transcription of pri-miRNAs by RNA polymerase II, and the translation that miRISC represses, are outside the boundary. Existing modules. No human mRNA deadenylation, CCR4-NOT or decapping module exists in modules/ (searched November 2026 for CCR4, CNOT, deadenylation, decapping, PAN2, DCP2, XRN1), so there was nothing to module_ref and parts 6-8 model these complexes directly. They are general mRNA-decay machinery recruited to miRNA targets by TNRC6, and are good candidates for a separate, reusable human "cytoplasmic mRNA deadenylation and decapping" module; when one is created, parts 6-8 should become module_ref links to it. modules/dmel_ccr4_not_complex.yaml (fly CCR4-NOT) and modules/dmel_risc_loading_complexes.yaml (fly Dicer-1/Loqs-PB loading into AGO1 and the AGO1-Gawky miRISC) model the Drosophila counterparts of parts 4-6, and modules/plant_mirna_biogenesis.yaml models the plant pathway, where a single nuclear DCL1 makes both cuts and HEN1 methylates the duplex. They are referenced in prose only: a cross-species module_ref would assert an identity between fly or plant complexes and the human ones that this module does not need. Molecular functions were taken from each protein's experimental (and, where noted, IBA) GO annotations in QuickGO (checked 2026-11-05) and from completed gene reviews where they exist (AGO1, AGO2, AGO3, AGO4, CNOT1, CNOT3, DICER1). DROSHA and DICER1: GO:0004525 ribonuclease III activity (IBA in GOA; DICER1 core function; DROSHA by the cited biochemistry). DGCR8: GO:0140517 protein-RNA adaptor activity (IDA, PMID:15574589), the term the human TRUB1 GO-CAM uses. XPO5: GO:0005049 nuclear export signal receptor activity (IBA), because its experimental pre-miRNA binding row is contributes_to (with RAN). RAN: GO:0003925 G protein activity (IDA). TARBP2: GO:0003725 double-stranded RNA binding (IBA); its pre-miRNA binding row is contributes_to. PRKRA: GO:0070883 pre-miRNA binding (IDA). AGO1-4: GO:0035198 miRNA binding (core in all four reviews); AGO2 additionally GO:0090624 endoribonuclease activity, cleaving miRNA-paired mRNA (IDA/IMP; core in the AGO2 review). TNRC6A/B/C: GO:0030674 protein-macromolecule adaptor activity (see the GOA observation below). CNOT1: GO:0140378 protein complex scaffold activity (core in the CNOT1 review). CNOT6, CNOT6L, CNOT7, CNOT8 and PAN2: GO:0004535 poly(A)-specific ribonuclease activity (EXP/IDA). PABPC1: GO:0008143 poly(A) binding (IDA). DCP2: GO:0140933 m7G-cap hydrolase activity (EXP/IDA). XRN1: GO:0004534 5'-3' RNA exonuclease activity (IDA/IMP). CNOT9, PAN3, DCP1A/B, EDC3, EDC4, DDX6 and PATL1 have no experimental MF in GOA that describes their role here (only binding terms, contributes_to rows, or an adaptor row from a different complex), so they carry a role and evidence but no GO function id, rather than a plausible-looking term the evidence does not support. CNOT2, CNOT3 and CNOT10 are listed as structural CCR4-NOT subunits without a function; the CNOT3 review's core term is GO:0180014 protein-tRNA adaptor activity, a role unrelated to this pathway. Boundary decisions. (1) Canonical route only as parts. Mirtrons (short introns released by the spliceosome and debranched, bypassing DROSHA; PMID:17964270) and the DICER1-independent miR-451 route (pre-miR-451 cut by AGO2 slicer activity, PMID:20448148) are recorded in prose and on the AGO2 slicer annoton, not as parts. Neither adds a protein to the module (mirtrons use the spliceosome and lariat-debranching enzyme, outside this boundary; miR-451 uses AGO2, already a participant), and both converge on the same export, loading and silencing steps. (2) Argonautes are a ONE_OR_MORE variant set on the slicer axis: AGO2 has two annotons (miRNA binding and GO:0090624 slicing); AGO1 (NOT|enables RNA endonuclease activity, IDA), AGO3 (slicing only with particular guides and targets) and AGO4 carry miRNA binding only. AGO3's restricted slicing is recorded on its annoton but not asserted as its role here. (3) TARBP2 and PRKRA are a ONE_OR_MORE variant set of DICER1 partners; neither is required for the cleavage chemistry, so neither is given a ribonuclease activator activity. (4) RNA editing and uridylation are context, not parts. ADAR and ADARB1 deaminate adenosines in some pri- and pre-miRNAs, which can block DROSHA or DICER1 processing or retarget a miRNA, and TUT4 and TUT7 uridylate pre-miRNAs (monouridylation of group II pre-let-7 promotes dicing; LIN28-directed oligouridylation blocks it). These are substrate- specific regulatory layers acting on the pathway's RNA intermediates, not steps every miRNA passes through; they are what RGD draws as side reactions. Such roles fit GO's regulation-of-miRNA-processing terms rather than miRNA processing itself, and modelling them as parts would make the canonical route look conditional on editing or uridylation. Their gene symbols are recorded here for the triage, and they are the obvious first members of a future "regulation of miRNA biogenesis" module together with LIN28A/B. (5) The RAN cycle (RCC1, RANGAP1, RANBP1) is general nuclear-transport machinery and is left out; RAN itself is a part because the XPO5-pre-miRNA complex does not form without RAN-GTP. (6) Deadenylation, decapping and XRN1 decay are parts, not context, because miRISC recruits the deadenylases directly through TNRC6 (PMID:21981923, PMID:21984185) and RGD draws all three as outputs of the pathway. XRN1 is optional (decision in part 8). (7) Translational repression is recorded as a process term on the TNRC6 and DDX6/PATL1 annotons and not as a separate part, because its mechanism in human cells (CCR4-NOT-DDX6 and 4E-T/4EHP, eIF4A displacement) is not settled and RGD itself calls it poorly understood. (8) The "substrate is not a participant" rule was applied to PABPC1: it is included because it does part of the work (stimulating PAN2-PAN3 and binding the TNRC6 PAM2 motif), not because it sits on the poly(A) tail being removed. Target mRNAs and the miRNAs themselves are not participants. GO-CAM and GOA observations for upstream review. Few production GO-CAMs contain these proteins (gocams/index.tsv, checked November 2026). The seed's best GO-CAM lead, gomodel:653b0ce600001283 (KSHV-ORF57 inhibition of host P-body formation), is a viral-antagonism model whose AGO2 RNA endonuclease and TNRC6A adaptor activities are linked here only as partial matches. The DGCR8 activity is grounded in gomodel:62183af000000874 (miRNA maturation by TRUB1) and the CNOT7 deadenylase in gomodel:63894f2500001378 (FMR1-CAPRIN1 condensates). No GO-CAM models the canonical human pathway itself (no model contains DROSHA, DICER1, XPO5 with pre-miRNA, PAN2, DCP2 in a miRNA context, or AGO1/3/4); this is the largest curation gap the module reveals. RAN's only GO-CAM (protein export from nucleus, PKM2 model) is unrelated. TARBP2's and PRKRA's GO-CAMs are antiviral models (PKR, IRF7), not miRNA processing. TNRC6A's only GOA row for GO:0030674 is HDA from an mRNA-interactome screen (PMID:22681889), which can establish RNA binding but not adaptor activity; it may be worth an upstream look, and a literature-based IDA from PMID:21981923 or PMID:21984185 would be the better grounding. Gene reviews exist for AGO1, AGO2, AGO3, AGO4, CNOT1, CNOT3 and DICER1; DROSHA, DGCR8, XPO5, RAN, TARBP2, PRKRA, TNRC6A-C, the other CNOT subunits, PAN2, PAN3, PABPC1, DCP1A/B, DCP2, EDC3, EDC4, DDX6, PATL1 and XRN1 have none. PANTHER family ids and PTNs are deliberately not asserted. module: id: mirna_biogenesis_and_silencing label: Human canonical miRNA biogenesis and miRISC-mediated silencing module_type: BIOLOGICAL_PROCESS description: >- Eight ordered parts: nuclear pri-miRNA cleavage by the Microprocessor, XPO5-RAN-GTP export of the pre-miRNA, cytoplasmic DICER1 cleavage with a dsRBD cofactor, loading of the duplex into an Argonaute, TNRC6 (GW182) recruitment by the loaded Argonaute, deadenylation by CCR4-NOT and PAN2-PAN3, decapping by DCP2-DCP1 and its activators, and 5'-3' exonucleolytic decay by XRN1. concepts: - preferred_term: miRNA processing term: id: GO:0035196 label: miRNA processing description: >- Conversion of a pri-miRNA into a mature miRNA duplex (parts 1-3); the GO process mapped to PW:0000808. - preferred_term: miRNA-mediated post-transcriptional gene silencing term: id: GO:0035195 label: miRNA-mediated post-transcriptional gene silencing description: >- Silencing of target mRNAs by the miRNA-loaded Argonaute and its TNRC6-recruited effectors (parts 4-8). context: taxa: - preferred_term: Homo sapiens term: id: NCBITaxon:9606 label: Homo sapiens cellular_components: - preferred_term: nucleus term: id: GO:0005634 label: nucleus description: Where the Microprocessor cleaves the pri-miRNA (part 1). - preferred_term: cytoplasm term: id: GO:0005737 label: cytoplasm description: >- Where dicing, RISC loading and target silencing take place (parts 3-8). Both compartments are listed because the pathway is spatially split, with XPO5 moving the intermediate from one to the other. parts: - order: 1 role: nuclear cleavage of the pri-miRNA hairpin by the Microprocessor node: id: microprocessor_cleavage label: Microprocessor (DROSHA-DGCR8) cleavage of pri-miRNA to pre-miRNA module_type: PROTEIN_COMPLEX description: >- DROSHA is a class II RNase III enzyme whose two RNase III domains form an intramolecular dimer that cuts the 3' and 5' strands of the pri-miRNA stem about one helical turn from the basal single-stranded junction. DGCR8 binds the hairpin through its two dsRNA-binding domains and binds DROSHA, positioning the cut; DROSHA without DGCR8 does not process pri-miRNA. The product is a pre-miRNA with a two-nucleotide 3' overhang. concepts: - preferred_term: primary miRNA processing term: id: GO:0031053 label: primary miRNA processing - preferred_term: microprocessor complex term: id: GO:0070877 label: microprocessor complex description: The DROSHA-DGCR8 complex that performs this step. annotons: - id: drosha_rnase3 label: "DROSHA: RNase III cleavage of the pri-miRNA stem" participant: selector_type: GENE_PRODUCT gene_product: preferred_term: DROSHA term: id: UniProtKB:Q9NRR4 label: Ribonuclease 3 function: preferred_term: ribonuclease III activity term: id: GO:0004525 label: ribonuclease III activity evidence: - source_id: PMID:14508493 statement: Immunopurified DROSHA cleaves pri-miRNA to release pre-miRNA; knockdown traps pri-miRNA. supporting_text: >- Immunopurified Drosha cleaved pri-miRNA to release pre-miRNA in vitro. - source_id: PMID:15574589 statement: The two RNase III domains of DROSHA cut the two strands of the stem. supporting_text: >- the RNase III domains A and B form an intramolecular dimer and cleave the 3' and 5' strands of the stem, respectively processes: - preferred_term: primary miRNA processing term: id: GO:0031053 label: primary miRNA processing locations: - preferred_term: nucleus term: id: GO:0005634 label: nucleus - id: dgcr8_rna_adaptor label: "DGCR8: pri-miRNA-binding partner that links the substrate to DROSHA" participant: selector_type: GENE_PRODUCT gene_product: preferred_term: DGCR8 term: id: UniProtKB:Q8WYQ5 label: Microprocessor complex subunit DGCR8 function: preferred_term: protein-RNA adaptor activity term: id: GO:0140517 label: protein-RNA adaptor activity targets: - preferred_term: DROSHA term: id: UniProtKB:Q9NRR4 label: Ribonuclease 3 evidence: - source_id: PMID:15574589 statement: >- DGCR8 has two dsRNA-binding domains, binds DROSHA, and is an essential component of the pri-miRNA processing complex; the source of the GOA IDA row for GO:0140517. supporting_text: >- we show that DGCR8 may be an essential component of the pri-miRNA processing complex, along with Drosha processes: - preferred_term: primary miRNA processing term: id: GO:0031053 label: primary miRNA processing locations: - preferred_term: nucleus term: id: GO:0005634 label: nucleus gocam_associations: - model: gomodel:62183af000000874 activity: gomodel:62183af000000874/62183af000000889 title: DGCR8 protein-RNA adaptor activity (GO:0140517) in miRNA maturation by TRUB1 (Human) description: >- Same molecular function as this annoton. The model places it in GO:2000633 positive regulation of pre-miRNA processing, with TRUB1 and LIN28A as regulators of pri-let-7 processing; it grounds the DGCR8 activity, not the regulation. - order: 2 role: RAN-GTP-dependent nuclear export of the pre-miRNA by exportin-5 node: id: pre_mirna_export label: XPO5-RAN-GTP export of pre-miRNA to the cytoplasm module_type: TRANSPORT_STEP description: >- Exportin-5 is a karyopherin that binds the pre-miRNA stem and its 3' overhang only when it also binds RAN-GTP. The ternary complex crosses the nuclear pore; in the cytoplasm RAN-GAP stimulated GTP hydrolysis on RAN dissociates the complex and frees the pre-miRNA for DICER1. The RAN GTPase cycle factors (RCC1 in the nucleus, RANGAP1 and RANBP1 in the cytoplasm) are general nuclear-transport machinery and are not parts of this module. concepts: - preferred_term: pre-miRNA export from nucleus term: id: GO:0035281 label: pre-miRNA export from nucleus evidence: - source_id: PMID:14681208 statement: Human pre-miRNA export depends on XPO5, which binds pre-miRNA only with RAN-GTP. supporting_text: >- Exportin-5 can bind pre-miRNAs specifically in vitro, but only in the presence of the Ran-GTP cofactor. annotons: - id: xpo5_export_receptor label: "XPO5: nuclear export receptor for pre-miRNA" participant: selector_type: GENE_PRODUCT gene_product: preferred_term: XPO5 (exportin-5) term: id: UniProtKB:Q9HAV4 label: Exportin-5 function: preferred_term: nuclear export signal receptor activity term: id: GO:0005049 label: nuclear export signal receptor activity cargo: - preferred_term: pre-miRNA source_location: preferred_term: nucleus term: id: GO:0005634 label: nucleus destination_location: preferred_term: cytoplasm term: id: GO:0005737 label: cytoplasm evidence: - source_id: PMID:14681208 statement: XPO5 is required for pre-miRNA and shRNA nuclear export. supporting_text: >- we demonstrate that Exp5 is indeed required for the nuclear export and, hence biological activity, of pre-miRNAs and shRNAs but not for synthetic siRNA function processes: - preferred_term: pre-miRNA export from nucleus term: id: GO:0035281 label: pre-miRNA export from nucleus role_description: >- The GO term is the IBA-supported karyopherin activity. XPO5's experimental pre-miRNA binding row (GO:0070883, IDA) is contributes_to, shared with RAN, which is why the exporter activity rather than pre-miRNA binding is used here. - id: ran_gtp_cofactor label: "RAN: GTP-bound cofactor of the XPO5 export complex" participant: selector_type: GENE_PRODUCT gene_product: preferred_term: RAN term: id: UniProtKB:P62826 label: GTP-binding nuclear protein Ran function: preferred_term: G protein activity term: id: GO:0003925 label: G protein activity evidence: - source_id: PMID:14681208 statement: >- Cargo binding by export karyopherins requires RAN-GTP, and cytoplasmic GTP hydrolysis releases the cargo. supporting_text: >- A defining characteristic of karyopherins that function in nuclear export is that nuclear cargo binding requires the GTP-bound form of the Ran GTPase, whereas cytoplasmic hydrolysis of Ran-GTP to Ran-GDP induces cargo release. processes: - preferred_term: pre-miRNA export from nucleus term: id: GO:0035281 label: pre-miRNA export from nucleus role_description: >- RAN serves every RAN-dependent exportin; it is a part here because the XPO5-pre-miRNA complex does not form without it (PMID:14681208). The G protein activity term is RAN's IDA row in GOA. - order: 3 role: cytoplasmic cleavage of the pre-miRNA loop by DICER1 with a dsRBD cofactor node: id: dicer_cleavage label: DICER1 cleavage of pre-miRNA to the miRNA duplex, with TARBP2 or PRKRA module_type: PROTEIN_COMPLEX description: >- DICER1 measures from the 2-nt 3' overhang left by DROSHA (PAZ domain) and its two RNase III domains cut both strands near the terminal loop, releasing a ~22-bp miRNA duplex. DICER1 works with one of two paralogous dsRBD proteins, TARBP2 (TRBP) or PRKRA (PACT), which bind its helicase domain. Neither is needed for the cleavage itself; they tune substrate choice and cleavage site (and so isomiR length) and bridge DICER1 to AGO2 in the RISC-loading complex. concepts: - preferred_term: pre-miRNA processing term: id: GO:0031054 label: pre-miRNA processing annotons: - id: dicer1_rnase3 label: "DICER1: RNase III cleavage of the pre-miRNA" participant: selector_type: GENE_PRODUCT gene_product: preferred_term: DICER1 term: id: UniProtKB:Q9UPY3 label: Endoribonuclease Dicer function: preferred_term: ribonuclease III activity term: id: GO:0004525 label: ribonuclease III activity evidence: - source_id: PMID:12411504 statement: Recombinant human Dicer cuts dsRNA to ~21-23-nt products and processes pre-let-7. supporting_text: >- Processing of the microRNA let-7 precursor by Dicer produced an apparently mature let-7 RNA. - source_id: file:genes/human/DICER1/DICER1-ai-review.yaml statement: >- GO:0004525 ribonuclease III activity in GO:0031054 pre-miRNA processing is the core function in the DICER1 gene review. processes: - preferred_term: pre-miRNA processing term: id: GO:0031054 label: pre-miRNA processing locations: - preferred_term: cytoplasm term: id: GO:0005737 label: cytoplasm variant_sets: - id: dicer_dsrbd_cofactor label: DICER1 dsRBD cofactor axis: paralogous dsRNA-binding partner of DICER1 (TARBP2 or PRKRA), with distinct substrate and isomiR preferences selection: ONE_OR_MORE variants: - id: tarbp2_variant label: TARBP2 (TRBP) module_type: REGULATORY_STEP annotons: - id: tarbp2_dicer_cofactor label: "TARBP2: dsRNA-binding DICER1 cofactor" participant: selector_type: GENE_PRODUCT gene_product: preferred_term: TARBP2 (TRBP) term: id: UniProtKB:Q15633 label: RISC-loading complex subunit TARBP2 function: preferred_term: double-stranded RNA binding term: id: GO:0003725 label: double-stranded RNA binding evidence: - source_id: PMID:15973356 statement: TRBP has three dsRBDs and is an integral component of the DICER1 complex. supporting_text: >- TRBP (the human immunodeficiency virus transactivating response RNA-binding protein), which contains three double-stranded, RNA-binding domains, is an integral component of a Dicer-containing complex. processes: - preferred_term: pre-miRNA processing term: id: GO:0031054 label: pre-miRNA processing - preferred_term: RISC complex assembly term: id: GO:0070922 label: RISC complex assembly locations: - preferred_term: cytoplasm term: id: GO:0005737 label: cytoplasm role_description: >- The RGD-curated cofactor (drawn as acting on Dicer1). dsRNA binding is TARBP2's IBA row; its experimental pre-miRNA binding row (GO:0070883, IDA, PMID:18178619) is contributes_to, with DICER1, so it is not asserted as TARBP2's own activity here. - id: prkra_variant label: PRKRA (PACT) module_type: REGULATORY_STEP annotons: - id: prkra_dicer_cofactor label: "PRKRA: pre-miRNA-binding DICER1 cofactor" participant: selector_type: GENE_PRODUCT gene_product: preferred_term: PRKRA (PACT) term: id: UniProtKB:O75569 label: Interferon-inducible double-stranded RNA-dependent protein kinase activator A function: preferred_term: pre-miRNA binding term: id: GO:0070883 label: pre-miRNA binding evidence: - source_id: PMID:23661684 statement: >- In a reconstituted system PACT and TRBP have distinct effects on DICER1 processing, including the length of miRNA products; source of the PRKRA GO:0070883 IDA row. supporting_text: >- PACT and TRBP show non-redundant effects on the production of different-sized miRNAs (isomiRs), which in turn alter target-binding specificities processes: - preferred_term: pre-miRNA processing term: id: GO:0031054 label: pre-miRNA processing locations: - preferred_term: cytoplasm term: id: GO:0005737 label: cytoplasm role_description: >- Not on the RGD list for PW:0000808; added as the second DICER1 partner because it binds the same DICER1 helicase region and is needed for normal mature miRNA accumulation (PMID:16424907). Like TARBP2 it is not needed for the cleavage reaction itself. evidence: - source_id: PMID:16424907 statement: PACT is not required for cleavage but its depletion lowers mature miRNA levels. supporting_text: >- Like TRBP, PACT is not required for the pre-microRNA (miRNA) cleavage reaction step. However, the depletion of PACT strongly affects the accumulation of mature miRNA in vivo - order: 4 role: loading of the miRNA duplex into an Argonaute and guide-strand selection (miRISC assembly) node: id: ago_loading label: Argonaute (AGO1-AGO4) loading and miRISC formation module_type: PROTEIN_COMPLEX description: >- DICER1-TARBP2 hands the duplex to an Argonaute in the RISC-loading complex. The Argonaute keeps the strand whose 5' end is less stably paired (the guide), anchoring its 5' phosphate in the MID domain and its 3' end in the PAZ domain, and discards the passenger strand. The four human Argonautes bind miRNAs without sequence preference and are largely redundant for seed-mediated repression; they differ in slicing. AGO2 cleaves perfectly paired targets and also cuts the passenger strand of perfectly paired duplexes; AGO1 and AGO4 lack efficient slicer activity, and AGO3 slices only with particular guides and targets. The loaded Argonaute is the core of miRISC and the hand-off point to the TNRC6 effectors. concepts: - preferred_term: RISC complex assembly term: id: GO:0070922 label: RISC complex assembly - preferred_term: RISC complex term: id: GO:0016442 label: RISC complex description: The product of this part, and the complex that parts 5-8 act through. evidence: - source_id: PMID:18178619 statement: >- The human RISC-loading complex (AGO2, DICER1, TARBP2) assembles from purified proteins and carries out dicing, guide-strand selection and AGO2 loading. supporting_text: >- The reconstituted RLC, containing one copy of each protein, has the dicing, slicing, guide-strand selection, and Ago2-loading activities observed for the endogenous RLC. - source_id: PMID:15260970 statement: miRNAs are loaded into AGO1-AGO4 without sequence preference. supporting_text: >- Our results suggest that miRNAs are incorporated indiscriminately of their sequence into Ago1 through Ago4 containing microRNPs (miRNPs). variant_sets: - id: argonaute_paralog label: Human Argonaute paralog axis: Argonaute paralog (AGO2 slicer versus AGO1, AGO3 and AGO4, which silence mainly without cleavage) selection: ONE_OR_MORE variants: - id: ago2_variant label: AGO2 — miRNA-binding Argonaute with slicer activity module_type: PROTEIN_COMPLEX annotons: - id: ago2_mirna_binding label: "AGO2: miRNA guide binding in miRISC" participant: selector_type: GENE_PRODUCT gene_product: preferred_term: AGO2 term: id: UniProtKB:Q9UKV8 label: Protein argonaute-2 function: preferred_term: miRNA binding term: id: GO:0035198 label: miRNA binding evidence: - source_id: file:genes/human/AGO2/AGO2-ai-review.yaml statement: >- GO:0035198 miRNA binding is a core function in the AGO2 gene review, supported by multiple IDA and IPI rows. processes: - preferred_term: RISC complex assembly term: id: GO:0070922 label: RISC complex assembly - preferred_term: miRNA-mediated post-transcriptional gene silencing term: id: GO:0035195 label: miRNA-mediated post-transcriptional gene silencing locations: - preferred_term: cytoplasm term: id: GO:0005737 label: cytoplasm - id: ago2_slicer label: "AGO2: guide-directed cleavage of fully paired target RNA (slicer)" participant: selector_type: GENE_PRODUCT gene_product: preferred_term: AGO2 term: id: UniProtKB:Q9UKV8 label: Protein argonaute-2 function: preferred_term: endoribonuclease activity, cleaving miRNA-paired mRNA term: id: GO:0090624 label: endoribonuclease activity, cleaving miRNA-paired mRNA evidence: - source_id: PMID:15284456 statement: AGO2 is the only mammalian Argonaute with mRNA cleavage activity. supporting_text: >- a single mammalian family member, Argonaute2, being responsible for messenger RNA cleavage activity - source_id: PMID:15260970 statement: Endonuclease activity of purified human Argonaute complexes is confined to AGO2. supporting_text: >- revealed that endonuclease activity is exclusively associated with Ago2 processes: - preferred_term: miRNA-mediated gene silencing by mRNA destabilization term: id: GO:0035279 label: miRNA-mediated gene silencing by mRNA destabilization locations: - preferred_term: cytoplasm term: id: GO:0005737 label: cytoplasm role_description: >- Slicing is needed only for the minority of miRNA targets with extensive complementarity, and for the DICER1-independent maturation of miR-451, whose short pre-miRNA is cut by AGO2 instead of DICER1 and then trimmed. Both uses are recorded here rather than as separate parts because the enzyme and the activity are the same. evidence: - source_id: PMID:20448148 statement: miR-451 is matured independently of DICER1 by AGO2 catalysis. supporting_text: >- We identified a Dicer-independent miRNA biogenesis pathway that uses Argonaute2 (Ago2) slicer catalytic activity. gocam_associations: - model: gomodel:653b0ce600001283 activity: gomodel:653b0ce600001283/653b0ce600001398 title: AGO2 RNA endonuclease activity (GO:0004521) in KSHV-ORF57 inhibition of host P-body formation (Human-HHV8) description: >- The seed's best GO-CAM lead. It grounds AGO2 as an RNA endonuclease (the parent of GO:0090624) but places it in GO:0033962 P-body assembly in a viral-antagonism model, so it is a partial match, not a model of the miRNA pathway. - id: ago1_variant label: AGO1 — miRNA-binding Argonaute without efficient slicer activity module_type: PROTEIN_COMPLEX annotons: - id: ago1_mirna_binding label: "AGO1: miRNA guide binding in miRISC" participant: selector_type: GENE_PRODUCT gene_product: preferred_term: AGO1 term: id: UniProtKB:Q9UL18 label: Protein argonaute-1 function: preferred_term: miRNA binding term: id: GO:0035198 label: miRNA binding evidence: - source_id: file:genes/human/AGO1/AGO1-ai-review.yaml statement: GO:0035198 miRNA binding is the core function in the AGO1 gene review. processes: - preferred_term: RISC complex assembly term: id: GO:0070922 label: RISC complex assembly - preferred_term: miRNA-mediated post-transcriptional gene silencing term: id: GO:0035195 label: miRNA-mediated post-transcriptional gene silencing locations: - preferred_term: cytoplasm term: id: GO:0005737 label: cytoplasm role_description: >- AGO1 carries a NOT|enables RNA endonuclease activity row (IDA, PMID:23809764): its crystal structure shows a mutated catalytic tetrad and a cS7 loop that blocks a fully paired guide-target duplex. evidence: - source_id: PMID:23809764 statement: Restoring the AGO1 catalytic tetrad gives only low-level cleavage activity. supporting_text: >- reconstitution of the catalytic tetrad with R805H led to low-level hAGO1 cleavage activity - id: ago3_variant label: AGO3 — miRNA-binding Argonaute with context-restricted slicing module_type: PROTEIN_COMPLEX annotons: - id: ago3_mirna_binding label: "AGO3: miRNA guide binding in miRISC" participant: selector_type: GENE_PRODUCT gene_product: preferred_term: AGO3 term: id: UniProtKB:Q9H9G7 label: Protein argonaute-3 function: preferred_term: miRNA binding term: id: GO:0035198 label: miRNA binding evidence: - source_id: file:genes/human/AGO3/AGO3-ai-review.yaml statement: >- GO:0035198 miRNA binding is a core function in the AGO3 gene review, which also records guide- and target-dependent slicing (GO:0090624, IMP). processes: - preferred_term: miRNA-mediated post-transcriptional gene silencing term: id: GO:0035195 label: miRNA-mediated post-transcriptional gene silencing locations: - preferred_term: cytoplasm term: id: GO:0005737 label: cytoplasm role_description: >- AGO3 slicing is restricted to particular guides and targets and is not the basis of its role in seed-mediated silencing, so only miRNA binding is asserted here; AGO3 is grouped with the non-slicing paralogs on this axis. - id: ago4_variant label: AGO4 — miRNA-binding Argonaute without slicer activity module_type: PROTEIN_COMPLEX annotons: - id: ago4_mirna_binding label: "AGO4: miRNA guide binding in miRISC" participant: selector_type: GENE_PRODUCT gene_product: preferred_term: AGO4 term: id: UniProtKB:Q9HCK5 label: Protein argonaute-4 function: preferred_term: miRNA binding term: id: GO:0035198 label: miRNA binding evidence: - source_id: file:genes/human/AGO4/AGO4-ai-review.yaml statement: GO:0035198 miRNA binding is the core function in the AGO4 gene review. processes: - preferred_term: miRNA-mediated post-transcriptional gene silencing term: id: GO:0035195 label: miRNA-mediated post-transcriptional gene silencing locations: - preferred_term: cytoplasm term: id: GO:0005737 label: cytoplasm - order: 5 role: recruitment of a GW182-family scaffold (TNRC6A/B/C) by the miRNA-loaded Argonaute node: id: tnrc6_recruitment label: TNRC6 (GW182) binding to AGO and recruitment of deadenylases module_type: REGULATORY_STEP description: >- The N-terminal GW-repeat region of TNRC6 proteins contains several tryptophan-containing "AGO hooks" that dock into pockets on the Argonaute PIWI domain. The C-terminal silencing domain carries a PAM2 motif that binds PABPC1 and tryptophan motifs (CIM-1 and CIM-2) that bind CNOT1 and the W-binding pockets of CNOT9, and it binds PAN3. TNRC6 is thus the adaptor that converts target recognition by AGO into deadenylation, translational repression and decay. The three paralogs are largely redundant. concepts: - preferred_term: miRNA-mediated gene silencing by mRNA destabilization term: id: GO:0035279 label: miRNA-mediated gene silencing by mRNA destabilization annotons: - id: tnrc6_adaptor label: "TNRC6A/B/C: adaptor linking AGO to CCR4-NOT and PAN2-PAN3" participant: selector_type: FAMILY family: preferred_term: GW182/TNRC6 family (TNRC6A, TNRC6B, TNRC6C) representative_members: - preferred_term: TNRC6A term: id: UniProtKB:Q8NDV7 label: Trinucleotide repeat-containing gene 6A protein - preferred_term: TNRC6B term: id: UniProtKB:Q9UPQ9 label: Trinucleotide repeat-containing gene 6B protein - preferred_term: TNRC6C term: id: UniProtKB:Q9HCJ0 label: Trinucleotide repeat-containing gene 6C protein description: >- The three human GW182 paralogs. No PANTHER family id is asserted. function: preferred_term: protein-macromolecule adaptor activity term: id: GO:0030674 label: protein-macromolecule adaptor activity evidence: - source_id: PMID:21984185 statement: >- Human GW182 binds PAN2-PAN3 and CCR4-NOT independently and acts as a platform and coactivator for deadenylation. supporting_text: >- GW182 serves as both a platform that recruits deadenylases and as a deadenylase coactivator that facilitates the removal of the poly(A) tail by CCR4-NOT. - source_id: PMID:21981923 statement: The TNRC6-deadenylase interactions are required for silencing. supporting_text: >- These interactions are critical for silencing and are conserved in D. melanogaster. - source_id: PMID:16289642 statement: TNRC6B co-purifies with AGO1 and AGO2 and is required for miRNA-guided silencing. supporting_text: >- the RNA recognition motif (RRM)-containing protein TNRC6B/KIAA1093 processes: - preferred_term: miRNA-mediated gene silencing by mRNA destabilization term: id: GO:0035279 label: miRNA-mediated gene silencing by mRNA destabilization - preferred_term: miRNA-mediated gene silencing by inhibition of translation term: id: GO:0035278 label: miRNA-mediated gene silencing by inhibition of translation locations: - preferred_term: P-body term: id: GO:0000932 label: P-body role_description: >- GO:0030674 is the activity the human P-body GO-CAM uses for TNRC6A. Its only GOA row for TNRC6A is HDA from an mRNA-interactome screen (PMID:22681889), an assay that cannot show adaptor activity, so the support used here is the direct recruitment studies cited above rather than that row. TNRC6B and TNRC6C have no experimental MF row beyond RNA or protein binding; the adaptor activity is asserted for them as members of the same family, on the basis of the shared GW, PAM2 and CIM motifs and the recruitment data obtained with the human GW182 paralogs. gocam_associations: - model: gomodel:653b0ce600001283 activity: gomodel:653b0ce600001283/653b0ce600001405 title: TNRC6A protein-macromolecule adaptor activity (GO:0030674) in KSHV-ORF57 inhibition of host P-body formation (Human-HHV8) description: >- Same MF as this annoton, placed in GO:0033962 P-body assembly in a viral-antagonism model; it grounds TNRC6A's adaptor activity, not its role in deadenylation. - order: 6 role: deadenylation of the target mRNA by the TNRC6-recruited CCR4-NOT and PAN2-PAN3 complexes node: id: target_deadenylation label: Deadenylation of miRNA targets by CCR4-NOT and PAN2-PAN3 module_type: PROTEIN_COMPLEX description: >- The two cytoplasmic deadenylases are the general mRNA-decay enzymes, recruited here by TNRC6. PAN2-PAN3 trims long poly(A) tails while PABPC1 is bound, and CCR4-NOT then removes the rest. In CCR4-NOT the large scaffold CNOT1 carries two catalytic modules (the DEDD-type CNOT7 or CNOT8, and the EEP-type CNOT6 or CNOT6L), the CNOT9 subunit whose tryptophan-binding pockets dock TNRC6, a NOT module (CNOT2, CNOT3) and CNOT10-CNOT11. CNOT1 also binds DDX6, which links deadenylation to translational repression and decapping (part 7). concepts: - preferred_term: nuclear-transcribed mRNA poly(A) tail shortening term: id: GO:0000289 label: nuclear-transcribed mRNA poly(A) tail shortening description: >- The GO process for the deadenylation step. Its "nuclear-transcribed" qualifier refers to the mRNA's origin; the step itself is cytoplasmic. evidence: - source_id: PMID:16284618 statement: >- In mammalian cells PAN2 starts deadenylation and CCR4 completes it, and decapping follows. supporting_text: >- PAN2 and CCR4 are the major poly(A) nucleases active in cytoplasmic deadenylation that have biphasic kinetics, with PAN2 initiating deadenylation followed by CCR4-mediated poly(A) shortening. parts: - order: 1 role: CCR4-NOT deadenylation (CNOT1 scaffold with CNOT7/8 and CNOT6/6L nucleases) node: id: ccr4_not_deadenylation label: CCR4-NOT complex module_type: PROTEIN_COMPLEX concepts: - preferred_term: CCR4-NOT core complex term: id: GO:0030015 label: CCR4-NOT core complex annotons: - id: ccr4_not_deadenylase label: "CCR4-NOT: poly(A)-specific 3'-5' exonuclease on miRNA targets" participant: selector_type: PROTEIN_COMPLEX protein_complex: preferred_term: human CCR4-NOT complex term: id: GO:0030015 label: CCR4-NOT core complex active_units: - id: cnot1_scaffold label: CNOT1 role: >- Scaffold that holds the nuclease and NOT modules and binds TNRC6 (with CNOT9) and DDX6. participant: selector_type: GENE_PRODUCT gene_product: preferred_term: CNOT1 term: id: UniProtKB:A5YKK6 label: CCR4-NOT transcription complex subunit 1 function: preferred_term: protein complex scaffold activity term: id: GO:0140378 label: protein complex scaffold activity evidence: - source_id: file:genes/human/CNOT1/CNOT1-ai-review.yaml statement: GO:0140378 protein complex scaffold activity is the core function in the CNOT1 gene review. - id: cnot7_nuclease label: CNOT7 (CAF1) role: DEDD-family deadenylase bound to CNOT1; paralog of CNOT8, either one occupies the site. participant: selector_type: GENE_PRODUCT gene_product: preferred_term: CNOT7 term: id: UniProtKB:Q9UIV1 label: CCR4-NOT transcription complex subunit 7 function: preferred_term: poly(A)-specific ribonuclease activity term: id: GO:0004535 label: poly(A)-specific ribonuclease activity - id: cnot8_nuclease label: CNOT8 (CAF1B) role: DEDD-family deadenylase, alternative to CNOT7. participant: selector_type: GENE_PRODUCT gene_product: preferred_term: CNOT8 term: id: UniProtKB:Q9UFF9 label: CCR4-NOT transcription complex subunit 8 function: preferred_term: poly(A)-specific ribonuclease activity term: id: GO:0004535 label: poly(A)-specific ribonuclease activity - id: cnot6_nuclease label: CNOT6 (CCR4A) role: EEP-family deadenylase bound through CNOT7/8; paralog of CNOT6L. participant: selector_type: GENE_PRODUCT gene_product: preferred_term: CNOT6 term: id: UniProtKB:Q9ULM6 label: CCR4-NOT transcription complex subunit 6 function: preferred_term: poly(A)-specific ribonuclease activity term: id: GO:0004535 label: poly(A)-specific ribonuclease activity - id: cnot6l_nuclease label: CNOT6L (CCR4B) role: EEP-family deadenylase, alternative to CNOT6. participant: selector_type: GENE_PRODUCT gene_product: preferred_term: CNOT6L term: id: UniProtKB:Q96LI5 label: CCR4-NOT transcription complex subunit 6-like function: preferred_term: poly(A)-specific ribonuclease activity term: id: GO:0004535 label: poly(A)-specific ribonuclease activity - id: cnot9_w_binding label: CNOT9 role: >- Binds the CNOT1 DUF3819 domain and provides tandem tryptophan-binding pockets for TNRC6. No GO molecular function term describes this; CNOT9's experimental MF rows are binding terms. participant: selector_type: GENE_PRODUCT gene_product: preferred_term: CNOT9 term: id: UniProtKB:Q92600 label: CCR4-NOT transcription complex subunit 9 evidence: - source_id: PMID:24768540 statement: CNOT9 docks on CNOT1 and its W-binding pockets bind TNRC6. supporting_text: >- The resulting complex provides binding sites for TNRC6/GW182, and its crystal structure reveals tandem W-binding pockets located in CNOT9. - id: cnot_not_module label: CNOT2, CNOT3 and CNOT10 role: >- Structural NOT-module (CNOT2-CNOT3) and CNOT10-CNOT11 subunits on the CNOT1 scaffold; required for complex integrity but not catalytic. CNOT11 is not on the RGD list and is named here only for completeness. participant: selector_type: FAMILY family: preferred_term: CCR4-NOT non-catalytic subunits representative_members: - preferred_term: CNOT2 term: id: UniProtKB:Q9NZN8 label: CCR4-NOT transcription complex subunit 2 - preferred_term: CNOT3 term: id: UniProtKB:O75175 label: CCR4-NOT transcription complex subunit 3 - preferred_term: CNOT10 term: id: UniProtKB:Q9H9A5 label: CCR4-NOT transcription complex subunit 10 function: preferred_term: poly(A)-specific ribonuclease activity term: id: GO:0004535 label: poly(A)-specific ribonuclease activity evidence: - source_id: PMID:24768540 statement: CCR4-NOT is a major effector of miRNA silencing, recruited through TNRC6. supporting_text: >- CCR4-NOT is a major effector complex in miRNA-mediated gene silencing. processes: - preferred_term: nuclear-transcribed mRNA poly(A) tail shortening term: id: GO:0000289 label: nuclear-transcribed mRNA poly(A) tail shortening - preferred_term: miRNA-mediated gene silencing by mRNA destabilization term: id: GO:0035279 label: miRNA-mediated gene silencing by mRNA destabilization locations: - preferred_term: cytoplasm term: id: GO:0005737 label: cytoplasm gocam_associations: - model: gomodel:63894f2500001378 activity: gomodel:63894f2500001378/63894f2500001455 title: CNOT7 poly(A)-specific ribonuclease activity (GO:0004535) in an FMR1-CAPRIN1 condensate model (Human) description: >- Grounds the CNOT7 deadenylase activity, there placed in GO:0000290 deadenylation-dependent decapping; the model is about FMR1/CAPRIN1 condensates, not miRNA silencing. - order: 2 role: PAN2-PAN3 deadenylation stimulated by PABPC1 node: id: pan2_pan3_deadenylation label: PAN2-PAN3 complex with PABPC1 module_type: PROTEIN_COMPLEX concepts: - preferred_term: PAN complex term: id: GO:0031251 label: PAN complex annotons: - id: pan2_pan3_deadenylase label: "PAN2-PAN3: PABPC1-stimulated poly(A) nuclease" participant: selector_type: PROTEIN_COMPLEX protein_complex: preferred_term: human PAN2-PAN3 complex term: id: GO:0031251 label: PAN complex active_units: - id: pan2_nuclease label: PAN2 role: Catalytic 3'-5' poly(A) exonuclease subunit. participant: selector_type: GENE_PRODUCT gene_product: preferred_term: PAN2 term: id: UniProtKB:Q504Q3 label: PAN2-PAN3 deadenylation complex catalytic subunit PAN2 function: preferred_term: poly(A)-specific ribonuclease activity term: id: GO:0004535 label: poly(A)-specific ribonuclease activity evidence: - source_id: PMID:14583602 statement: PAN2 has intrinsic Mg2+-dependent 3'-5' exoribonuclease activity (GOA IDA). supporting_text: >- hPan2 has intrinsically a 3' to 5' exoribonuclease activity and requires Mg2+ for the enzyme activity - id: pan3_regulatory label: PAN3 role: >- Regulatory subunit that binds PABPC1 through its PAM2 motif and binds TNRC6; its GOA deadenylase row is contributes_to. participant: selector_type: GENE_PRODUCT gene_product: preferred_term: PAN3 term: id: UniProtKB:Q58A45 label: PAN2-PAN3 deadenylation complex subunit PAN3 evidence: - source_id: PMID:14583602 statement: PAN3 binds PABP to stimulate PAN2. supporting_text: >- hPan3 interacts with PABP to simulate hPan2 nuclease activity function: preferred_term: poly(A)-specific ribonuclease activity term: id: GO:0004535 label: poly(A)-specific ribonuclease activity processes: - preferred_term: nuclear-transcribed mRNA poly(A) tail shortening term: id: GO:0000289 label: nuclear-transcribed mRNA poly(A) tail shortening locations: - preferred_term: cytoplasm term: id: GO:0005737 label: cytoplasm - id: pabpc1_poly_a_binding label: "PABPC1: poly(A)-tail protein that binds PAN3 and TNRC6" participant: selector_type: GENE_PRODUCT gene_product: preferred_term: PABPC1 term: id: UniProtKB:P11940 label: Polyadenylate-binding protein 1 function: preferred_term: poly(A) binding term: id: GO:0008143 label: poly(A) binding processes: - preferred_term: nuclear-transcribed mRNA poly(A) tail shortening term: id: GO:0000289 label: nuclear-transcribed mRNA poly(A) tail shortening locations: - preferred_term: cytoplasm term: id: GO:0005737 label: cytoplasm role_description: >- PABPC1 coats the poly(A) tail that is being removed. It is included as a participant rather than as substrate because it does part of the work: its binding to PAN3 stimulates PAN2 and raises its poly(A) specificity, and its binding to the TNRC6 PAM2 motif helps recruit the deadenylases. RGD draws it associated with both PAN2-PAN3 and Tnrc6. GO:0008143 is its IDA row in GOA. evidence: - source_id: PMID:14583602 statement: PABP raises the poly(A) specificity of the PAN complex. supporting_text: >- the hPAN nuclease complex has a higher substrate specificity to poly(A) RNA upon its association with PABP - order: 7 role: removal of the 5' cap from the deadenylated target by DCP2 and its activators node: id: target_decapping label: Decapping of miRNA targets by DCP2-DCP1 with DDX6, PATL1, EDC3 and EDC4 module_type: PROTEIN_COMPLEX description: >- DCP2 is the Nudix hydrolase that removes the m7G cap, releasing m7GDP and a 5'-monophosphate mRNA. DCP1 (DCP1A or DCP1B) binds and stimulates DCP2; EDC4 is the scaffold that holds DCP1 and DCP2 together in human cells, and EDC3 binds DCP1 and DDX6. DDX6 (bound to CNOT1) and PATL1 link the deadenylated mRNA to the decapping complex and also repress translation. The step is general mRNA decay machinery recruited to miRNA targets after deadenylation. concepts: - preferred_term: deadenylation-dependent decapping of nuclear-transcribed mRNA term: id: GO:0000290 label: deadenylation-dependent decapping of nuclear-transcribed mRNA evidence: - source_id: PMID:16284618 statement: In mammalian cells DCP2 decapping follows deadenylation. supporting_text: >- DCP2-mediated decapping takes place after deadenylation - source_id: PMID:24768540 statement: >- CNOT1 binds DDX6, a translational repressor and decapping activator, linking miRNA target recognition to deadenylation and decapping. supporting_text: >- We further show that the CNOT1 MIF4G domain interacts with the C-terminal RecA domain of DDX6, a translational repressor and decapping activator. annotons: - id: dcp2_decapping label: "DCP2-DCP1 decapping complex: m7G cap hydrolysis" participant: selector_type: PROTEIN_COMPLEX protein_complex: preferred_term: human DCP1-DCP2 decapping complex term: id: GO:0098745 label: RNA decapping complex active_units: - id: dcp2_catalytic label: DCP2 role: Catalytic Nudix-domain cap hydrolase. participant: selector_type: GENE_PRODUCT gene_product: preferred_term: DCP2 term: id: UniProtKB:Q8IU60 label: m7GpppN-mRNA hydrolase function: preferred_term: 5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA] hydrolase activity term: id: GO:0140933 label: 5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA] hydrolase activity evidence: - source_id: PMID:12486012 statement: Recombinant human DCP2 is an active decapping enzyme (GOA EXP). supporting_text: >- we show that recombinant human Dcp2 (hDcp2) is enzymatically active - id: dcp1_activator label: DCP1A or DCP1B role: >- Paralogous DCP2 activators. RGD lists DCP1B; DCP1A is the better studied paralog and co-purifies with DCP2 and decapping activity. participant: selector_type: FAMILY family: preferred_term: DCP1 paralogs representative_members: - preferred_term: DCP1A term: id: UniProtKB:Q9NPI6 label: mRNA-decapping enzyme 1A - preferred_term: DCP1B term: id: UniProtKB:Q8IZD4 label: mRNA-decapping enzyme 1B evidence: - source_id: PMID:12417715 statement: DCP1A and DCP2 form a complex that co-purifies with decapping activity. supporting_text: >- hDcp1a and hDcp2 copurify with decapping activity - id: edc3_edc4 label: EDC3 and EDC4 role: >- Enhancers of decapping. EDC4 scaffolds DCP1-DCP2; EDC3 binds DCP1 and DDX6. Neither has a GO molecular function term for this role. participant: selector_type: FAMILY family: preferred_term: enhancers of decapping (not a sequence family) representative_members: - preferred_term: EDC3 term: id: UniProtKB:Q96F86 label: Enhancer of mRNA-decapping protein 3 - preferred_term: EDC4 term: id: UniProtKB:Q6P2E9 label: Enhancer of mRNA-decapping protein 4 function: preferred_term: 5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA] hydrolase activity term: id: GO:0140933 label: 5'-(N(7)-methylguanosine 5'-triphospho)-[mRNA] hydrolase activity processes: - preferred_term: deadenylation-dependent decapping of nuclear-transcribed mRNA term: id: GO:0000290 label: deadenylation-dependent decapping of nuclear-transcribed mRNA locations: - preferred_term: P-body term: id: GO:0000932 label: P-body - id: ddx6_patl1_activators label: "DDX6 and PATL1: decapping activators and translational repressors bridging CCR4-NOT to decapping" participant: selector_type: FAMILY family: preferred_term: decapping activators DDX6 and PATL1 (not a sequence family) representative_members: - preferred_term: DDX6 term: id: UniProtKB:P26196 label: Probable ATP-dependent RNA helicase DDX6 - preferred_term: PATL1 term: id: UniProtKB:Q86TB9 label: Protein PAT1 homolog 1 processes: - preferred_term: deadenylation-dependent decapping of nuclear-transcribed mRNA term: id: GO:0000290 label: deadenylation-dependent decapping of nuclear-transcribed mRNA - preferred_term: miRNA-mediated gene silencing by inhibition of translation term: id: GO:0035278 label: miRNA-mediated gene silencing by inhibition of translation locations: - preferred_term: P-body term: id: GO:0000932 label: P-body role_description: >- No molecular function term is asserted. DDX6's experimental adaptor row (GO:0030674, IDA, PMID:31439631) comes from the 4EHP-GIGYF translational-repression complex, not from miRNA targets, and PATL1's experimental MF rows are RNA-binding terms. Both are kept as participants because RGD lists them and because DDX6 is the physical link from CNOT1 to the decapping machinery on miRNA targets (PMID:24768540). - order: 8 role: 5'-3' exonucleolytic degradation of the decapped target by XRN1 optional: true node: id: xrn1_decay label: XRN1 5'-3' degradation of the decapped mRNA body module_type: REACTION description: >- Decapping leaves a 5'-monophosphate mRNA, the substrate of the processive 5'-3' exoribonuclease XRN1, which is recruited by the decapping machinery. Marked optional because miRNA silencing is complete once the target is deadenylated, decapped and translationally repressed, and because XRN1 is drawn on the RGD diagram but is not in the RGD-curated human gene list for PW:0000808. concepts: - preferred_term: nuclear-transcribed mRNA catabolic process term: id: GO:0000956 label: nuclear-transcribed mRNA catabolic process annotons: - id: xrn1_exonuclease label: "XRN1: 5'-3' exoribonuclease" participant: selector_type: GENE_PRODUCT gene_product: preferred_term: XRN1 term: id: UniProtKB:Q8IZH2 label: 5'-3' exoribonuclease 1 function: preferred_term: 5'-3' RNA exonuclease activity term: id: GO:0004534 label: 5'-3' RNA exonuclease activity evidence: - source_id: PMID:12486012 statement: DCP2 products are substrates for 5'-3' exonucleolytic decay. supporting_text: >- hDcp2 generates m7GDP and 5'-phosphorylated mRNAs that are 5'-3' exonuclease substrates - source_id: PMID:26950371 statement: >- In human cells XRN1 degrades RNA after DCP2 decapping (source of the XRN1 GO:0004534 IMP row); shown for telomerase RNA rather than a miRNA target. supporting_text: >- hTR can be degraded by DCP2-mediated decapping leading to 5’ to 3’ degradation by XRN1 processes: - preferred_term: nuclear-transcribed mRNA catabolic process term: id: GO:0000956 label: nuclear-transcribed mRNA catabolic process locations: - preferred_term: P-body term: id: GO:0000932 label: P-body connections: - source: microprocessor_cleavage target: pre_mirna_export connection_type: PROVIDES_INPUT_FOR description: The pre-miRNA with its 2-nt 3' overhang made by DROSHA is the cargo XPO5 recognises. chaining_status: NOT_APPLICABLE chaining_note: RNA intermediates, not CoA carriers. - source: pre_mirna_export target: dicer_cleavage connection_type: PROVIDES_INPUT_FOR description: Exported pre-miRNA released by RAN-GTP hydrolysis is the DICER1 substrate. chaining_status: NOT_APPLICABLE chaining_note: RNA intermediates, not CoA carriers. - source: dicer_cleavage target: ago_loading connection_type: PROVIDES_INPUT_FOR description: >- The miRNA duplex is handed from DICER1-TARBP2 to the Argonaute in the RISC-loading complex. chaining_status: NOT_APPLICABLE chaining_note: RNA intermediates, not CoA carriers. - source: ago_loading target: tnrc6_recruitment connection_type: PRECEDES description: The miRNA-loaded Argonaute binds the target and recruits TNRC6 through its AGO hooks. chaining_status: NOT_APPLICABLE chaining_note: Protein recruitment, not a metabolite chain. - source: tnrc6_recruitment target: target_deadenylation connection_type: POSITIVELY_REGULATES description: >- TNRC6 recruits CCR4-NOT (through CNOT1 and CNOT9) and PAN2-PAN3 (through PAN3) to the target and stimulates processive deadenylation by CCR4-NOT. - source: target_deadenylation target: target_decapping connection_type: PRECEDES description: >- Decapping follows deadenylation; CNOT1-bound DDX6 links the two steps. chaining_status: NOT_APPLICABLE chaining_note: Sequential mRNA-decay steps on the same RNA, not a CoA chain. - source: target_decapping target: xrn1_decay connection_type: PROVIDES_INPUT_FOR description: The 5'-monophosphate mRNA left by DCP2 is the XRN1 substrate. chaining_status: NOT_APPLICABLE chaining_note: RNA intermediates, not CoA carriers.