HEN1 is the Arabidopsis SAM-dependent small RNA 3' terminal 2'-O-methyltransferase. It methylates the 2'-OH of the 3'-terminal ribose on miRNA/miRNA-star and siRNA/siRNA-star duplexes after Dicer-like processing, protecting small RNAs from uridylation, trimming, and degradation. HEN1 acts in the DCL1/HYL1-associated small-RNA maturation context and supports miRNA, siRNA, ta-siRNA, and antiviral silencing outputs; floral and leaf patterning phenotypes are downstream consequences of destabilized small RNAs.
Definition: A small-RNA metabolic process in which methylation of the 2-prime-OH of the 3-prime-terminal ribose protects mature small RNAs from uridylation, trimming, and exonucleolytic decay.
Justification: HEN1's direct molecular function is captured by small RNA 2-prime-O-ribose methyltransferase activity, but the current core-function summary also needs to distinguish the downstream protective effect of that modification. A process term for small-RNA 3-prime-end protection would avoid reusing the same catalytic molecular-function term for both methyl transfer and stabilization.
Parent term: RNA processing
| GO Term | Evidence | Action | Reason |
|---|---|---|---|
| GO:0034587 piRNA processing | IBA GO_REF:0000033 | REMOVE | Summary: HEN1-family proteins include animal piRNA methyltransferases, but Arabidopsis HEN1 methylates plant miRNA and siRNA duplexes. Reason: piRNA processing is an over-transfer from metazoan HEN1/HENMT1 family context and is not supported for Arabidopsis HEN1. Propagation Review Root cause: PROPAGATION BAD Failure modes: LINEAGE OR TAXON MISMATCH Sources checked: PANTHER:PTN000483941 Β· HEN1/HENMT1 family node SUPPORTS SOURCE BUT NOT TARGET The piRNA-processing IBD is seeded exclusively by metazoan HEN1/HENMT1 orthologs (fly, mouse, worm, zebrafish) but placed at a Eukaryota-wide node; the piRNA pathway does not exist in plants, so the term cannot apply to Arabidopsis HEN1. A taxon constraint or shallower IBD placement would fix this at source. MGI:MGI:1913965 Β· mouse Henmt1 SUPPORTS SOURCE BUT NOT TARGET Genuine piRNA 2-prime-O-methyltransferase seed; the piRNA context is metazoan-specific. |
| GO:0008171 O-methyltransferase activity | IBA GO_REF:0000033 | MODIFY | Summary: HEN1 is an RNA methyltransferase, but O-methyltransferase activity is less specific than the small-RNA 2-prime-O-ribose methyltransferase term. Reason: Use the small-RNA terminal 2-prime-O-methyltransferase term to capture HEN1 substrate and reaction specificity. Propagation Review Root cause: TERM SCOPING PROBLEM Failure modes: GRANULARITY MISMATCH Sources checked: PANTHER:PTN000483941 Β· HEN1/HENMT1 family node SUPPORTS TRANSFER All seeds are small-RNA terminal 2-prime-O-methyltransferases; the generic O-methyltransferase term under-specifies the shared activity, hence the refinement. Proposed replacements: small RNA 2'-O-ribose methyltransferase activity |
| GO:0003755 peptidyl-prolyl cis-trans isomerase activity | IEA GO_REF:0000002 | REMOVE | Summary: HEN1 includes a PPIase-like/FKBP-like domain, but its curated function is small-RNA methyltransferase activity. Reason: The PPIase-like/FKBP-like domain is present, but no evidence supports HEN1 peptidyl-prolyl isomerase catalytic activity; the supported biochemical function is small-RNA methyltransferase activity. |
| GO:0005634 nucleus | IEA GO_REF:0000044 | ACCEPT | Summary: HEN1 is associated with the nuclear DCL1/HYL1 small-RNA maturation context. Reason: The best-supported site for HEN1 action is nuclear small-RNA processing/methylation before or around AGO loading. Supporting Evidence: file:ARATH/HEN1/HEN1-deep-research-falcon.md Direct interaction mapping and mechanistic models place HEN1 in the nuclear miRNA-processing context. |
| GO:0008171 O-methyltransferase activity | IEA GO_REF:0000002 | MODIFY | Summary: HEN1 is an RNA methyltransferase, but O-methyltransferase activity is less specific than the small-RNA 2-prime-O-ribose methyltransferase term. Reason: Use the small-RNA terminal 2-prime-O-methyltransferase term to capture HEN1 substrate and reaction specificity. Proposed replacements: small RNA 2'-O-ribose methyltransferase activity |
| GO:0008173 RNA methyltransferase activity | IEA GO_REF:0000002 | MODIFY | Summary: HEN1 is an RNA methyltransferase, but RNA methyltransferase activity is less specific than the small-RNA 2-prime-O-ribose methyltransferase term. Reason: Use the small-RNA terminal 2-prime-O-methyltransferase term to capture HEN1 substrate and reaction specificity. Proposed replacements: small RNA 2'-O-ribose methyltransferase activity |
| GO:0016070 RNA metabolic process | IEA GO_REF:0000117 | MODIFY | Summary: HEN1 participates in small-RNA metabolism by methylating mature miRNA/siRNA duplexes. Reason: RNA metabolic process is too broad; small-RNA methylation and miRNA/siRNA processing-stabilization outputs are more informative. Proposed replacements: small RNA 2'-O-ribose methyltransferase activity miRNA processing |
| GO:0090486 small RNA 2'-O-ribose methyltransferase activity | IEA GO_REF:0000003 | ACCEPT | Summary: HEN1 catalyzes terminal 2-prime-O-ribose methylation of plant small RNAs. The HEN1 crystal structure (PDB 3HTX) shows the SAH cofactor product bound in the Rossmann MTase domain as in classical SAM-dependent methyltransferases, with a catalytic Mg ion coordinating the 3-prime-terminal 2-prime and 3-prime hydroxyls, consistent with 2-prime-O-ribose methyl transfer. Reason: This is the most specific molecular-function term for Arabidopsis HEN1. Supporting Evidence: file:ARATH/HEN1/HEN1-deep-research-falcon.md HEN1 is a small RNA 3-prime-terminal 2-prime-O-methyltransferase. file:ARATH/HEN1/HEN1-uniprot.txt Reaction=small RNA 3'-end nucleotide + S-adenosyl-L-methionine = small RNA 3'-end 2'-O-methylnucleotide + S-adenosyl-L-homocysteine + H(+); file:interpro/panther/PTHR21404/PTHR21404-entries.csv Q9C5Q8,Small RNA 2'-O-methyltransferase PMID:19812675 The MTase domain of HEN1 adopts a core Ξ±/Ξ² Rossmann structure, in which the cofactor product AdoHcy is bound as in classical S-adenosyl-l-methionine (AdoMet)-dependent MTases PMID:19812675 both the 2β² and 3β² hydroxyls of G22m and the side chains of four invariant residues (E796, E799, H800 and H860) are coordinated to a metal ion, Mg2+ |
| GO:0090486 small RNA 2'-O-ribose methyltransferase activity | IEA GO_REF:0000116 | ACCEPT | Summary: HEN1 catalyzes terminal 2-prime-O-ribose methylation of plant small RNAs. The 3.1 A crystal structure of full-length Arabidopsis HEN1 (PDB 3HTX) bound to a 22-nucleotide small RNA duplex with the cofactor product SAH (S-adenosyl-L-homocysteine) and Mg directly visualizes the substrate as a small-RNA duplex and confirms terminal 2-prime-O-methyltransferase chemistry. Reason: This is the most specific molecular-function term for Arabidopsis HEN1. Supporting Evidence: file:ARATH/HEN1/HEN1-deep-research-falcon.md HEN1 is a small RNA 3-prime-terminal 2-prime-O-methyltransferase. file:ARATH/HEN1/HEN1-uniprot.txt Reaction=small RNA 3'-end nucleotide + S-adenosyl-L-methionine = small RNA 3'-end 2'-O-methylnucleotide + S-adenosyl-L-homocysteine + H(+); file:interpro/panther/PTHR21404/PTHR21404-entries.csv Q9C5Q8,Small RNA 2'-O-methyltransferase PMID:19812675 report the 3.1 A crystal structure of full-length HEN1 from Arabidopsis in complex with a 22-nucleotide small RNA duplex and cofactor product S-adenosyl-l-homocysteine PMID:19812675 A subset of small RNAs, such as microRNAs and small interfering RNAs (siRNAs) in plants, Piwi-interacting RNAs in animals and siRNAs in Drosophila, requires an additional crucial step for their maturation; that is, 2'-O-methylation on the 3' terminal nucleotide. A conserved S-adenosyl-l-methionine-dependent RNA methyltransferase, HUA ENHANCER 1 (HEN1), and its homologues are responsible for this specific modification. |
| GO:0010267 ta-siRNA processing | IMP PMID:15469823 Endogenous trans-acting siRNAs regulate the accumulation of ... | KEEP AS NON CORE | Summary: HEN1 supports ta-siRNA processing by methylating and stabilizing the small-RNA duplexes that feed these pathways. Reason: HEN1 is required for stable miRNA/siRNA pathway outputs, but the direct catalytic step is small-RNA 2-prime-O-methylation rather than Dicer cleavage or AGO-mediated target repression. Supporting Evidence: file:ARATH/HEN1/HEN1-uniprot.txt Can methylate 3'-end of microRNAs (miRNAs), small interfering RNAs (siRNas) and trans-acting small interfering RNAs (ta-siRNAs). |
| GO:0005737 cytoplasm | ISM GO_REF:0000122 | UNDECIDED | Summary: The AtSubP-inferred cytoplasm row lacks positive experimental support for HEN1 cytoplasmic localization. Reason: HEN1's best-supported context is small-RNA methylation around nuclear miRNA/siRNA maturation; downstream cytoplasmic small-RNA turnover is not sufficient evidence for a cytoplasm localization annotation. |
| GO:0010305 leaf vascular tissue pattern formation | IMP PMID:22623415 The microRNA pathway genes AGO1, HEN1 and HYL1 participate i... | KEEP AS NON CORE | Summary: hen1 mutants affect leaf vascular tissue pattern formation. Reason: The developmental process is a downstream phenotype of altered miRNA/siRNA stability rather than a direct HEN1 function. |
| GO:0010589 leaf proximal/distal pattern formation | IMP PMID:22623415 The microRNA pathway genes AGO1, HEN1 and HYL1 participate i... | KEEP AS NON CORE | Summary: hen1 mutants affect leaf proximal/distal pattern formation. Reason: The developmental process is a downstream phenotype of altered miRNA/siRNA stability rather than a direct HEN1 function. |
| GO:0009616 RNAi-mediated antiviral immune response | IMP PMID:17090584 Four plant Dicers mediate viral small RNA biogenesis and DNA... | KEEP AS NON CORE | Summary: HEN1 contributes to virus-induced silencing and viral-small-RNA stability through terminal small-RNA methylation. Reason: The antiviral role is a pathway output of HEN1-mediated small-RNA stabilization; the direct catalytic function remains small-RNA 2-prime-O-methylation rather than Dicing or Argonaute effector activity. Supporting Evidence: PMID:17090584 DCL4 in conjunction with RDR6 and HEN1 specifically facilitates extensive virus-induced silencing in new growth. |
| GO:0005634 nucleus | IDA PMID:17442570 Identification of nuclear dicing bodies containing proteins ... | ACCEPT | Summary: The cited D-body paper places plant miRNA processing in the nucleus but directly images DCL1/HYL1/SE rather than HEN1. Reason: Although PMID:17442570 directly images other D-body proteins, HEN1 has independent support for the same nuclear miRNA-processing context, so the nucleus annotation is retained consistently. Supporting Evidence: file:ARATH/HEN1/HEN1-deep-research-falcon.md Direct interaction mapping and mechanistic models place HEN1 in the nuclear miRNA-processing context. |
| GO:0005737 cytoplasm | IDA PMID:17442570 Identification of nuclear dicing bodies containing proteins ... | UNDECIDED | Summary: The cited D-body paper contrasts animal cytoplasmic miRNA processing with plant nuclear processing and does not directly support HEN1 cytoplasmic localization. Reason: HEN1 may influence cytoplasmic small-RNA turnover indirectly, but PMID:17442570 does not provide direct HEN1 cytoplasm evidence. |
| GO:0008173 RNA methyltransferase activity | IDA PMID:15705854 Methylation as a crucial step in plant microRNA biogenesis. | MODIFY | Summary: Experimental Arabidopsis work supports HEN1-dependent methylation/protection of miRNAs and siRNAs. The HEN1 crystal structure (PDB 3HTX) confirms it is a SAM-dependent RNA methyltransferase, with the AdoHcy (SAH) product bound in a Rossmann MTase domain as in classical AdoMet-dependent MTases. Reason: Use the small-RNA terminal 2-prime-O-methyltransferase term to capture HEN1 substrate and reaction specificity. Proposed replacements: small RNA 2'-O-ribose methyltransferase activity Supporting Evidence: file:ARATH/HEN1/HEN1-deep-research-falcon.md HEN1 catalyzes transfer of a methyl group from AdoMet to the 2-prime-OH of the 3-prime-terminal nucleotide of small RNAs. file:ARATH/HEN1/HEN1-uniprot.txt Methyltransferase that adds a methyl group to the ribose of the last nucleotide of small RNAs (sRNAs). PMID:19812675 A conserved S-adenosyl-l-methionine-dependent RNA methyltransferase, HUA ENHANCER 1 (HEN1), and its homologues are responsible for this specific modification. PMID:19812675 The MTase domain of HEN1 adopts a core Ξ±/Ξ² Rossmann structure, in which the cofactor product AdoHcy is bound as in classical S-adenosyl-l-methionine (AdoMet)-dependent MTases |
| GO:0008173 RNA methyltransferase activity | IMP PMID:16111943 Methylation protects miRNAs and siRNAs from a 3'-end uridyla... | MODIFY | Summary: Experimental Arabidopsis work supports HEN1-dependent methylation/protection of miRNAs and siRNAs. The HEN1 crystal structure (PDB 3HTX) shows a catalytic Mg2+ ion coordinated by the 2-prime and 3-prime hydroxyls of the 3-prime-terminal nucleotide and four invariant active-site residues, defining a Mg2+-dependent 2-prime-O-methylation mechanism. Reason: Use the small-RNA terminal 2-prime-O-methyltransferase term to capture HEN1 substrate and reaction specificity. Proposed replacements: small RNA 2'-O-ribose methyltransferase activity Supporting Evidence: file:ARATH/HEN1/HEN1-deep-research-falcon.md HEN1 catalyzes transfer of a methyl group from AdoMet to the 2-prime-OH of the 3-prime-terminal nucleotide of small RNAs. file:ARATH/HEN1/HEN1-uniprot.txt Methyltransferase that adds a methyl group to the ribose of the last nucleotide of small RNAs (sRNAs). PMID:19812675 Metal ion coordination by both 2' and 3' hydroxyls on the 3'-terminal nucleotide and four invariant residues in the active site of the methyltransferase domain suggests a novel Mg(2+)-dependent 2'-O-methylation mechanism. PMID:19812675 both the 2β² and 3β² hydroxyls of G22m and the side chains of four invariant residues (E796, E799, H800 and H860) are coordinated to a metal ion, Mg2+ |
| GO:0035279 miRNA-mediated gene silencing by mRNA destabilization | IMP PMID:15851028 microRNA-directed phasing during trans-acting siRNA biogenes... | KEEP AS NON CORE | Summary: HEN1 supports miRNA-mediated gene silencing by mRNA destabilization by methylating and stabilizing the small-RNA duplexes that feed these pathways. Reason: HEN1 is required for stable miRNA/siRNA pathway outputs, but the direct catalytic step is small-RNA 2-prime-O-methylation rather than Dicer cleavage or AGO-mediated target repression. Supporting Evidence: file:ARATH/HEN1/HEN1-uniprot.txt Can methylate 3'-end of microRNAs (miRNAs), small interfering RNAs (siRNas) and trans-acting small interfering RNAs (ta-siRNAs). |
| GO:0035196 miRNA processing | IMP PMID:12747833 Arabidopsis HEN1: a genetic link between endogenous miRNA co... | ACCEPT | Summary: HEN1 supports miRNA processing by methylating and stabilizing the small-RNA duplexes that feed these pathways. Reason: HEN1 methylation is a required post-dicing maturation/protection step in plant miRNA biogenesis, so miRNA processing is supported even though the more specific catalytic role is small-RNA 2-prime-O-methylation. Supporting Evidence: file:ARATH/HEN1/HEN1-uniprot.txt Can methylate 3'-end of microRNAs (miRNAs), small interfering RNAs (siRNas) and trans-acting small interfering RNAs (ta-siRNAs). file:ARATH/HEN1/HEN1-deep-research-falcon.md HEN1 methylation is a defining post-dicing step in plants that stabilizes miRNAs and siRNAs. PMID:19812675 A subset of small RNAs, such as microRNAs and small interfering RNAs (siRNAs) in plants, Piwi-interacting RNAs in animals and siRNAs in Drosophila, requires an additional crucial step for their maturation; that is, 2'-O-methylation on the 3' terminal nucleotide. |
| GO:0009909 regulation of flower development | IMP PMID:11917084 Formation of corymb-like inflorescences due to delay in bolt... | KEEP AS NON CORE | Summary: hen1 mutants affect regulation of flower development. Reason: The developmental process is a downstream phenotype of altered miRNA/siRNA stability rather than a direct HEN1 function. |
| GO:0010093 specification of floral organ identity | IMP PMID:11874905 HEN1 functions pleiotropically in Arabidopsis development an... | KEEP AS NON CORE | Summary: hen1 mutants affect specification of floral organ identity. Reason: The developmental process is a downstream phenotype of altered miRNA/siRNA stability rather than a direct HEN1 function. |
Loading supporting contentβ¦
Download this section (compressed HTML)Q: Should piRNA-processing IBA transfer be excluded systematically for plant HEN1 proteins without piRNA pathway evidence?
Q: Should GO add a process term such as small RNA 3-prime-end protection by 2-prime-O-methylation for HEN1-dependent protection from uridylation, trimming, and decay?
Experiment: Quantify methylation efficiency of Arabidopsis HEN1 on defined miRNA, siRNA, and ta-siRNA duplex substrates with varying overhang geometry.
Experiment: Map the compartment and timing of HEN1 methylation relative to DCL1/HYL1 processing and AGO1 loading using endogenous tagged proteins.
Loading supporting contentβ¦
Download this section (compressed HTML)Loading supporting contentβ¦
Download this section (compressed HTML)