Activation of transcription enforces the formation of distinct nuclear bodies in zebrafish embryos

Abstract

Nuclear bodies are cellular compartments that lack lipid bilayers and harbor specific RNAs and proteins. Recent proposals that nuclear bodies form through liquid-liquid phase separation leave the question of how different nuclear bodies maintain their distinct identities unanswered. Here we investigate Cajal bodies (CBs), histone locus bodies (HLBs) and nucleoli -involved in assembly of the splicing machinery, histone mRNA 3 0 end processing, and rRNA processing, respectively -in the embryos of the zebrafish, Danio rerio. We take advantage of the transcriptional silence of the 1-cell embryo and follow nuclear body appearance as zygotic transcription becomes activated. CBs are present from fertilization onwards, while HLB and nucleolar components formed foci several hours later when histone genes and rDNA became active. HLB formation was blocked by transcription inhibition, suggesting nascent histone transcripts recruit HLB components like U7 snRNP. Surprisingly, we found that U7 base-pairing with nascent histone transcripts was not required for localization to HLBs. Rather, the type of Sm ring assembled on U7 determined its targeting to HLBs or CBs; the spliceosomal Sm ring targeted snRNAs to CBs while the specialized U7 Sm-ring localized to HLBs, demonstrating the contribution of protein constituents to the distinction among nuclear bodies. Thus, nucleolar, HLB, and CB components can mix in early embryogenesis when transcription is naturally or artificially silenced. These data support a model in which transcription of specific gene loci nucleates nuclear body components with high specificity and fidelity to perform distinct regulatory functions.

Transcription organizes euchromatin similar to an active microemulsion

“…This simplifies our analysis by limiting it to euchromatin. Late blastula cells also do not have distinguishable nucleoli (Heyn et al, 2016). The absence of nucleoli, which are sites of ribosome biogenesis, removes another complication from the analysis.…”

Membraneless nuclear organelles and the search for phases within phases

“…Indeed, how the physical surface interaction dynamics between two distinct nuclear bodies varies under different physiological conditions is an outstanding question. Cajal bodies associate more frequently with HLBs in transcriptionally arrested zebrafish, potentially by HLB‐localized U7 snRNP enrichment in the Cajal body, suggesting this system is responsive to cellular context (Heyn et al, ). We propose that the nuclear body RNA–protein network is more complex than previously thought, and that a comprehensive assessment of inter‐ and intranuclear body component demixing by SRM is an important step for a clear characterization of nuclear function.…”

The translational regulation of maternal mRNAs in time and space

“…To date, very few studies were performed on cytoplasmic granules in zebrafish embryogenesis or for that matter during the embryogenesis of vertebrates. However, it is known that the activation of zygotic transcription results in the formation of distinct types of nuclear granules including those involved in the processing of histone mRNAs and assembly of splicing machinery . Given the nature of cytoplasmic bodies in other systems known to be dependent on the presence of mRNA itself, it is plausible that the activation of zygotic transcription represents a trigger for the formation of such granules.…”