Sponge Long Non-Coding RNAs Are Expressed in Specific Cell Types and Conserved Networks.

Area of Science:

• Developmental Biology
• Evolutionary Biology
• Genomics

Background:

• Long non-coding RNAs (lncRNAs) play crucial roles in animal development.
• The evolutionary origin and conservation of lncRNA-mediated developmental regulation are not well understood.
• Previous work showed sponges express developmental lncRNAs, similar to bilaterians.

Purpose of the Study:

• To investigate the cell-type-specific expression of lncRNAs during sponge development.
• To explore the evolutionary conservation of lncRNA function by comparing gene co-expression networks between different sponge species.
• To determine if sponge lncRNAs operate within conserved gene regulatory networks.

Main Methods:

• Single-cell RNA sequencing to analyze lncRNA expression in specific cell types across developmental stages (larvae, juveniles, adults).
• Comparative analysis of gene co-expression networks between *Amphimedon queenslandica* and *Sycon ciliatum* (a distantly related calcisponge).
• Identification of shared co-expression modules and network-embedded lncRNAs.

Main Results:

• Sponge lncRNAs are dynamically expressed in specific cell types throughout development, mirroring patterns in bilaterians.
• Comparative network analysis revealed conserved co-expression modules in distantly related sponges.
• Identified sponge lncRNAs within these conserved modules show no sequence similarity, suggesting functional conservation despite sequence divergence.

Conclusions:

• Sponge lncRNAs are developmentally regulated in a cell type- and context-specific manner.
• Conserved gene regulatory networks involving lncRNAs are present in sponges.
• These findings suggest that lncRNA-mediated developmental regulation is an ancient feature in animals, predating the emergence of bilaterians.