nuclear dicing body

GO:0010445 · Ribonucleoprotein · Other · Proposed

A small round nuclear body, measuring 0.2-0.8 microns in diameter that is diffusely distributed throughout the nucleoplasm. Several proteins known to be involved in miRNA processing have been localized to these structures. D-bodies are thought to be involved in primary-miRNA processing and/or storage/assembly of miRNA processing complexes. [GO:0010445]

Synonyms: D body; D-body

Part of: nuclear lumen (GO:0031981)

UniProt location names: UniProt Consortium, CC BY 4.0. Reference label and route sources.

Components

Component	Type	Part of / acts on	Grounding	Genes	Essential	Role
Dicer-like 1	Protein	part of	Reviewed label only (reviewed name; no accession asserted)	DCL1	UNKNOWN	RNase III enzyme concentrated in D-bodies and acting in plant primary miRNA processing with HYL1 and SERRATE. `DOI:10.1016/j.cub.2007.04.005` Fang and Spector 2007 localized Arabidopsis DCL1 with HYL1 to nuclear dicing bodies and showed that a DCL1 mutant impaired in miRNA processing failed to target to D-bodies. `DOI:10.1073/pnas.0701061104` Song et al. 2007 showed that HYL1 and DCL1 fusion proteins colocalize to small nuclear bodies that lack the Cajal-body marker Atcoilin.
HYPONASTIC LEAVES1	Protein	part of	Reviewed label only (reviewed name; no accession asserted)	HYL1	UNKNOWN	Double-stranded RNA-binding partner of DCL1 that localizes to D-bodies during plant primary miRNA processing. `DOI:10.1016/j.cub.2007.04.005` Fang and Spector 2007 colocalized HYL1 with DCL1 in nuclear dicing bodies in living Arabidopsis cells. `DOI:10.1073/pnas.0701061104` Song et al. 2007 found that HYL1 and DCL1 nuclear bodies are distinct from Arabidopsis Cajal bodies.
SERRATE	Protein	part of	Reviewed label only (reviewed name; no accession asserted)	SE	ESSENTIAL	D-body scaffold-like protein whose phase separation recruits DCL1, HYL1 and pri/pre-miRNAs into D-body condensates. `DOI:10.1016/j.cub.2007.04.005` Fang and Spector 2007 observed DCL1, HYL1 and SERRATE bimolecular-fluorescence-complementation interactions in nuclear dicing bodies. `DOI:10.1038/s41556-020-00606-5` Xie et al. 2021 showed that SERRATE can drive DCL1, HYL1 and pri/pre-miRNAs into phase-separated D-body droplets and that SERRATE mutation abrogates D-body formation in vivo.
pri/pre-miRNA substrate cohort	Rna	part of	Reviewed label only (reviewed name; no accession asserted)		UNKNOWN	Primary and precursor miRNA substrates recruited into D-bodies for DCL1/HYL1/SERRATE-dependent processing. `DOI:10.1016/j.cub.2007.04.005` Fang and Spector 2007 recruited an introduced primary miRNA transcript to Arabidopsis D-bodies. `DOI:10.1038/s41556-020-00606-5` Xie et al. 2021 reported that SERRATE brings pri/pre-miRNAs into D-body droplets and that pre-miRNAs can be processed inside those droplets.

Taxonomic distribution

NCBITaxon:3702 Arabidopsis thaliana — VARIABLE: Nuclear dicing bodies were defined in living Arabidopsis cells as DCL1- and HYL1-containing nuclear bodies involved in plant miRNA biogenesis. [DOI:10.1016/j.cub.2007.04.005]

Canonical examples

NCBITaxon:3702 Arabidopsis thaliana — Arabidopsis cells were used to identify D-bodies, distinguish them from Cajal bodies and connect DCL1, HYL1, SERRATE and pri-miRNA recruitment to primary miRNA processing. [DOI:10.1016/j.cub.2007.04.005]

Functions

primary miRNA processing GO:0031053 — Arabidopsis D-bodies concentrate DCL1, HYL1, SERRATE and pri-miRNA substrates in nuclear foci associated with primary miRNA processing.
- DOI:10.1016/j.cub.2007.04.005 Fang and Spector 2007 proposed that D-bodies orchestrate pri-miRNA processing and/or storage and assembly of miRNA-processing complexes.
- DOI:10.1038/s41556-020-00606-5 Xie et al. 2021 linked SERRATE-driven D-body formation to efficient pri-miRNA and pre-miRNA processing.

Mechanism graphs

SERRATE scaffolds plant D-body assembly (ASSEMBLY)

Arabidopsis nuclear dicing bodies concentrate the DCL1/HYL1/SERRATE miRNA-processing module with primary miRNA substrates in nuclear foci whose assembly is driven by SERRATE phase separation.

Subject	Predicate	Object	Evidence
SERRATE	drives assembly of	nuclear dicing body	`DOI:10.1038/s41556-020-00606-5` Xie et al. 2021 showed that SERRATE droplets recruit DCL1, HYL1 and pri/pre-miRNAs in vitro and that SERRATE mutation abrogates D-body formation in vivo.
Dicer-like 1	localizes to	nuclear dicing body	`DOI:10.1016/j.cub.2007.04.005` Fang and Spector 2007 observed DCL1 in discrete nuclear D-bodies in Arabidopsis.
HYPONASTIC LEAVES1	localizes to	nuclear dicing body	`DOI:10.1073/pnas.0701061104` Song et al. 2007 observed HYL1-mCherry and YFP-DCL1 colocalization in small nuclear bodies distinct from Atcoilin-marked Cajal bodies.
pri/pre-miRNA substrate cohort	localize to	nuclear dicing body	`DOI:10.1016/j.cub.2007.04.005` Fang and Spector 2007 localized DCL1, HYL1 and introduced pri-miRNA transcript to Arabidopsis nuclear dicing bodies. `DOI:10.1038/s41556-020-00606-5` Xie et al. 2021 connected SERRATE phase separation to D-body assembly and efficient pri/pre-miRNA processing.
nuclear dicing body	supports	primary miRNA processing	`DOI:10.1016/j.cub.2007.04.005` Fang and Spector 2007 localized DCL1, HYL1 and introduced pri-miRNA transcript to Arabidopsis nuclear dicing bodies. `DOI:10.1038/s41556-020-00606-5` Xie et al. 2021 connected SERRATE phase separation to D-body assembly and efficient pri/pre-miRNA processing.

Discussions

CURATION_TODO (OPEN): Resolve exact source-neutral component boundaries for nuclear dicing bodies. This first GO:0010445 record captures Arabidopsis DCL1, HYL1, SERRATE and pri/pre-miRNA substrate classes directly supported by D-body imaging and assembly evidence. Exact source-neutral protein-family and RNA-substrate groundings should be reviewed against InterPro, Pfam, NCBIfam and Sequence Ontology instead of guessed.

Evidence

GO:0010445 Gene Ontology cellular-component term for nuclear dicing body and its exact D body synonym.
GO:0016604 Gene Ontology cellular-component term for nuclear body.
GO:0031981 Gene Ontology cellular-component term for the nuclear lumen; GO:0010445 defines D-bodies as distributed throughout the nucleoplasm.
GO:0031053 Gene Ontology biological-process term for primary miRNA processing.
GO:1904258 Gene Ontology biological-process term for nuclear dicing body assembly.
DOI:10.1016/j.cub.2007.04.005 Fang and Spector 2007, Identification of nuclear dicing bodies containing proteins for microRNA biogenesis in living Arabidopsis plants, Current Biology.
DOI:10.1073/pnas.0701061104 Song, Han, Lesicka and Fedoroff 2007, Arabidopsis primary microRNA processing proteins HYL1 and DCL1 define a nuclear body distinct from the Cajal body, Proceedings of the National Academy of Sciences.
DOI:10.1038/s41556-020-00606-5 Xie et al. 2021, Phase separation of SERRATE drives dicing body assembly and promotes miRNA processing in Arabidopsis, Nature Cell Biology.

Curation history

2026-09-28T03:04:47Z codex · CREATED_RECORD — Scaffolded by scripts/new_record.py
2026-09-28T03:05:49Z codex · EXPANDED_RECORD — Added nuclear dicing-body GO synonymy, nuclear-body parentage, nuclear-lumen parthood, Arabidopsis DCL1/HYL1/SERRATE and pri-miRNA components, Arabidopsis scope, primary-miRNA-processing function evidence, DOI/GO evidence, a nonmechanistic SERRATE-driven D-body assembly graph and a component-boundary TODO.
2026-09-28T03:19:50Z codex · RESOLVED_REVIEW — Resolved #1699 by renaming the D-body RNA component and graph node from a primary-miRNA-only cohort to a pri/pre-miRNA substrate cohort matching the cited SERRATE recruitment evidence.

Source: data/structures/ribonucleoprotein/nuclear_dicing_body.yaml