Genome-Wide Integrated Analysis Revealed Functions of lncRNA–miRNA–mRNA Interaction in Growth of Intermuscular Bones in Megalobrama amblycephala

Abstract

Intermuscular bone (IB) occurs in the myosepta of teleosts. Its existence has an adverse influence on the edible and economic value of fish, especially for aquaculture species belonging to Cypriniformes. The growth mechanism of IBs is quite lacking. In this study, we firstly used single molecular real-time sequencing (SMRT) technology to improve the draft genome annotation and full characterization of the transcriptome for one typical aquaculture species, blunt snout bream (Megalobrama amblycephala). The long non-coding RNA (lncRNA), microRNA (miRNA), and messenger RNA (mRNA) expression profiles in two IB growth stages (1 and 3 years old) were compared through transcriptome and degradome analyses. A total of 126 miRNAs, 403 mRNAs, and 353 lncRNAs were found to be differentially expressed between the two stages. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that the significantly upregulated map2k6 and cytc in the MAPK/p53 signaling pathway and the significantly downregulated lama3 and thbs4b in the extracellular matrix (ECM)–receptor pathway may play a key regulatory role in IB growth. Bioinformatics analysis subsequently revealed 14 competing endogenous RNA (ceRNA) pairs related to the growth of IBs, consisting of 10 lncRNAs, 7 miRNAs, and 10 mRNAs. Of these, dre-miR-24b-3p and dre-miR-193b-3p are core regulatory factors interacting with four lncRNAs and three mRNAs, the interaction mechanism of which was also revealed by subsequent experiments at the cellular level. In conclusion, our data showed that IBs had higher activity of cell apoptosis and lower mineralization activity in IB_III compared to IB_I via interaction of MAPK/p53 and ECM–receptor signaling pathways. The downregulated zip1 interacted with miR-24a-3p and lnc017705, decreased osteoblast differentiation and Ca2+ deposition in the IB_III stage. Our identified functional mRNAs, lncRNAs, and miRNAs provide a data basis for in-depth elucidation of the growth mechanism of teleost IB.

The Emerging Role of Long Non-Coding RNAs in Development and Function of Gilthead Sea Bream (Sparus aurata) Fast Skeletal Muscle

“…LncRNAs can also interact with microRNAs (miRNAs), another type of ncRNAs involved in posttranscriptional regulation of protein-coding genes by mRNA cleavage, translational repression, or mRNA destabilization [21]. LncRNAs can act as miRNAs precursors or as miRNAs sponges, thus altering their regulatory effect on mRNAs and introducing an additional layer of complexity in the miRNA-target interaction network [21][22][23]. All the specific interactions of lncRNAs are sometimes based on sequence complementarity, but it is suggested that, in many cases, the lncRNAs' function is defined by their three-dimensional structure [24].…”

Genome assembly and isoform analysis of a highly heterozygous New Zealand fisheries species, the tarakihi (Nemadactylus macropterus)

“…These results were compared with reported AS values for other animal species from studies that also used SUPPA on Iso-Seq reads. Results reported were compiled for the zebrafish ( Danio rerio ) (Nudelman et al, 2018), the goldfish ( Carassius auratus auratus ) (Gan et al, 2021), the Wuchang bream ( Megalobrama amblycephala ) (Chen et al, 2021), the whiteleg shrimp ( Litopenaeus vannamei ) (X. Zhang et al, 2019), and the cave nectar bat ( Eonycteris spelaea ) (Wen et al, 2018).…”

Genome assembly and isoform analysis of a highly heterozygous New Zealand fisheries species, the tarakihi (Nemadactylus macropterus)

“…These results were compared with reported AS values for other animal species from studies that also used SUPPA on Iso-Seq reads. Results reported were compiled for the zebrafish ( Danio rerio ) ( Nudelman et al ., 2018 ), the goldfish ( Carassius auratus auratus ) ( Gan et al ., 2021 ), the Wuchang bream ( Megalobrama amblycephala ) ( Chen et al ., 2021 ), the whiteleg shrimp ( Litopenaeus vannamei ) ( Zhang et al ., 2019 ), and the cave nectar bat ( Eonycteris spelaea ) ( Wen et al ., 2018 ).…”