Histological characterization and lncRNA-mRNA integrated profiling analysis of the scales in rainbow trout (Oncorhynchus mykiss) under salinity acclimation

Abstract

Long noncoding RNAs (lncRNAs) play a multifaceted role in transcriptional regulation and are important regulators of bone metabolism. Bone metabolism of rainbow trout (Oncorhynchus mykiss) has been previously shown to be affected by salinity change, and the regeneration process of scales would serve as an ideal model for studying the regulatory mechanism underlying this process. Here in this study, the effect of salinity acclimation on histological characteristics of scales during a 21-day regenerating process was determined using paraffin section and HE staining; in addition, the calcium (Ca), phosphorus (P) content and the molar mass ratio of calcium to phosphorus (Ca/P) in the regenerated scales were also detected by Inductively Coupled Plasma Mass Spectrometry (ICP-MS). The results showed that only the P content was significantly affected by salinity acclimation. In order to further clarify the regulatory mechanism of the regenerated scales in adaptation to the salinity change, the global lncRNA expression profiles of both the regenerated and ontogenic scales of rainbow trout under salinity acclimation were examined using Illumina sequencing platform. As a result, a total of 612 significantly differentially expressed (DE) lncRNAs were identified in the regenerated scales, and target gene prediction of these DE lncRNAs has obtained 2330 DE target genes (DETGs). GO and KEGG analysis showed that the aforementioned DETGs were significantly annotated to GO terms including S-adenosylmethionine-homocysteine S-methyltransferase activity, cobalamin binding, etc.; and enriched in bone metabolism related signaling pathways such as hypertrophic cardiomyopathy and dilated cardiomyopathy signaling. As for the ontogenic scales, the STEM analysis of 3432 DE lncRNAs showed that eight patterns (consisted of 1093 DE lncRNAs) were significantly clustered (P < 0.05) at different time points during the salinity acclimation (7, 14 and 21d), and a total of 201 DETGs were subsequently obtained. Furthermore, the DE lncRNAs respectively identified from the regenerated and ontogenic scales collected at 14d were compared using the Venn diagram, a total of 81 DE lncRNAs were identified in both scale types, while 531 and 653 DE lncRNAs were respectively found to be specially identified in the regenerated and ontogenic scales. GO and KEGG analysis of the DETGs respectively predicted from the aforementioned DE lncRNAs also revealed significantly different enriched functions and pathways. Co-expression network of these DE lncRNA and DETGs suggested that 66 DE lncRNA and 57 DETGs have generated a network of 77 pairs of relationships in the regenerated scales, while 12 DE lncRNAs and 12 DETGs produced 12 relationship pairs in the ontogenic scales. The results indicated that they might be related to the functions including metal ion binding, membrane and nucleotide binding, etc. The DE lncRNAs and DETGs identified in this study might provide reference information for further research on the regulation of bone metabolism in teleost species.