U bodies are cytoplasmic structures that contain uridine-rich small nuclear ribonucleoproteins and associate with P bodies

Abstract

Uridine-rich small nuclear ribonucleoproteins (U snRNPs) are involved in key steps of pre-mRNA processing in the nucleus of eukaryotic cells. U snRNPs are enriched in the nucleus in discrete organelles that include speckles, Cajal bodies, and histone locus bodies. However, most U snRNPs are assembled in the cytoplasm, not in the nucleus. Despite extensive biochemical information, little is known about the spatial organization of U snRNPs in the cytoplasm. Here we show that U snRNPs in Drosophila are concentrated in discrete cytoplasmic structures, which we call U bodies, because they contain the major U snRNPs. In addition to snRNPs, U bodies contain essential snRNP assembly factors, suggesting that U bodies are sites for assembly or storage of snRNPs before their import into the nucleus. U bodies invariably associate with P bodies, which are involved in RNA surveillance and decay. Genetic disruption of P body components affects the organization of U bodies, suggesting that the two cytoplasmic bodies may cooperate in regulating aspects of snRNP metabolism. The identification of U bodies provides an opportunity to correlate specific biochemical steps of snRNP biogenesis with structural features of the cytoplasm.

Fig. 1.

U bodies contain U snRNPs. Nurse cells from the ovary of transgenic (A) and wild-type flies (B–H). (Center) FISH for U2 snRNA (red), which defines the cytoplasmic U bodies. (Left) Second probe (green). (Right) Overlay stained with DNA-specific DAPI (blue). (A) Lsm11-YFP expressed from a transgene. (B) Antibody stain for Lsm 10. (C) FISH for U7 snRNA. (D) FISH for U85 scaRNA, specific for the Cajal body in the nucleus. The three bright dots in Upper Left are Cajal bodies in three follicle nuclei. (E–H) FISH for U1, U4, U5, and U6 snRNAs. (Scale bars: 10 μm.)

Fig. 2.

U bodies and the snRNP assembly machinery. (A–D) Colocalization of SMN protein with U body components in nurse cells of transgenic (A) and wild-type (B–D) flies. (Center) Antibody staining for SMN (red). (Left) U body component (green). (Right) Overlay plus DAPI stain for DNA (blue). SMN staining is present in the nuclear Cajal bodies but is not visible without overexposing the intensely stained cytoplasmic U bodies. (A) Lsm11-YFP expressed from a transgene. (B) Antibody stain for Lsm10. (C) mAb Y12 stain, specific for symmetrical dimethylarginine residues. (D) FISH for U2 snRNA. (Scale bars: 10 μm.) (E and F) Comparison of egg chambers from wild-type females and dart5 mutant females, which lack DART5, the major enzyme that methylates snRNP proteins. U bodies are detectable with an antibody against SMN or by FISH for U2 snRNA in wild-type flies (Left) but are missing from dart5 mutant flies (Right). (Scale bars: 50 μm.)

Fig. 3.

The U body–P body relationship. (A–C) U bodies invariably associate with P bodies. (Center) Nurse cells stained with antibodies for three P body markers: Dcp1, eIF4E, and Me31B. (Left) U body markers. (Right) Overlay with DAPI stain for DNA (blue). (A and B) Lsm11-YFP expressed from a transgene (green). (C) Antibody staining for SMN (red). (Scale bars: 10 μm.) (D and E) Giant U bodies form in nurse cells of flies that lack Trailer Hitch protein, a P body component. (D) Typical U bodies from a heterozygous tral¹/+ fly. (E) Giant U bodies in tral¹ flies, which lack Trailer Hitch protein. (Scale bars: 5 μm.)

Fig. 4.

Nuclear and cytoplasmic bodies involved in snRNP assembly. U snRNAs are transcribed in the nucleus and exported to the cytoplasm, where they form snRNP complexes with Sm and Lsm proteins. U bodies may be sites for assembly, modification, or storage of cytoplasmic snRNPs. On return to the nucleus, snRNPs target to Cajal bodies (splicing snRNPs) or the histone locus body (U7 snRNP). Cytoplasmic U bodies invariably associate with P bodies, which function in RNA surveillance and decay.