Screening and identification of MicroRNAs expressed in perirenal adipose tissue during rabbit growth

Abstract

Background MicroRNAs (miRNAs) regulate adipose tissue development, which are closely related to subcutaneous and intramuscular fat deposition and adipocyte differentiation. As an important economic and agricultural animal, rabbits have low adipose tissue deposition and are an ideal model to study adipose regulation. However, the miRNAs related to fat deposition during the growth and development of rabbits are poorly defined. Methods In this study, miRNA-sequencing and bioinformatics analyses were used to profile the miRNAs in rabbit perirenal adipose tissue at 35, 85 and 120 days post-birth. Differentially expressed (DE) miRNAs between different stages were identified by DEseq in R. Target genes of DE miRNAs were predicted by TargetScan and miRanda. To explore the functions of identified miRNAs, Gene Ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed. Results Approximately 1.6 GB of data was obtained by miRNA-seq. A total of 987 miRNAs (780 known and 207 newly predicted) and 174 DE miRNAs were identified. The miRNAs ranged from 18 nt to 26 nt. GO enrichment and KEGG pathway analyses revealed that the target genes of the DE miRNAs were mainly involved in zinc ion binding, regulation of cell growth, MAPK signaling pathway, and other adipose hypertrophy-related pathways. Six DE miRNAs were randomly selected, and their expression profiles were validated by q-PCR. Conclusions This is the first report of the miRNA profiles of adipose tissue during different growth stages of rabbits. Our data provide a theoretical reference for subsequent studies on rabbit genetics, breeding and the regulatory mechanisms of adipose development.

Characterization of microRNA Profiles in Pasteurella multocida-Infected Rabbits and Identification of miR-29-5p as a Regulator of Antibacterial Immune Response

“…miRNA from 21 to 24 nt were responsible for 88%−92% of all reads in each library ( Figure 1 ), reflecting miRNA plurality. Moreover, predominant miRNAs in libraries were 22-nt long, consistent with earlier findings from other research with rabbit ( 39 ), pig ( 40 ) and cow ( 41 ). Thus, nine miRNA libraries developed from rabbit tissues were technically reliable and suitable for subsequent investigation.…”

Characterization of differentially expressed and lipid metabolism-related lncRNA-mRNA interaction networks during the growth of liver tissue through rabbit models

“…Through the functional enrichment analysis of DE mRNA, we found that these DE mRNA could be classified into six categories: Cellular Processes, Genetic Information Processing, Environmental Information Processing, Human Diseases, Metabolism and organic Systems. The functional attributes of genes and their expression level in organs or cells are important factors to determine their function realization ( 42 ). When we excluded some genes with low FPKM, we further obtained that 54 DE mRNAs may play the key roles in lipid metabolism during the growth and development of liver, including EPHX1, ACSS2 and CYP39A1 , which were continuously up-regulated in four growth stages, and LDHB, CA2, ELOVL2 , which were continuously down-regulated, and these DE mRNAs were regulated by 249 lncRNAs.…”

Dynamics of transcriptome and chromatin accessibility revealed sequential regulation of potential transcription factors during the brown adipose tissue whitening in rabbits

“…In this study, the Tianfu Black rabbits (native species in Sichuan province of China) were raised at the breeding center of Sichuan Agricultural University, Ya’an, China. These rabbits were breast-fed before 30 days and then fed with the same standard diet (a commercial pelleted food (16% protein, 10.8 MJ/kg)) as described in our previous study after weaning ( Wang G. et al, 2020 ) and water ad libitum . Interscapular adipose tissues were collected from 12 male rabbits at different growth stages of 0 days (D0), D15, D85, and 2 years (Y2) (three individuals per stage), which represent the infant stage, early whitening stage, puberty stage, and elder stage, respectively.…”