Identification and characterization of long noncoding RNAs and mRNAs expression profiles related to postnatal liver maturation of breeder roosters using Ribo-zero RNA Sequencing

The liver, which is mainly hematopoietic in the embryo but converts into a major metabolic tissue in the adult, is extensively remodeled after birth to adapt and perform adult functions. Long non-coding RNAs (lncRNAs) are involved in organ development and cell differentiation, which indicate that they have potential roles in regulating postnatal liver development. Overall design: In order to understand the roles of lncRNAs in postnatal liver maturation, we analyzed the lncRNAs and mRNAs expression profiles in immature and mature livers from one-day-old and adult (40 weeks of age) breeder roosters by Ribo-Zero RNA-Sequencing. Around 27,353 mRNAs and 9,063 predicted lncRNAs were expressed in breeder rooster livers, and the identified chicken lncRNAs shared fewer exons, shorter transcript length, and significantly lower expression levels compared to protein-coding genes. Notably, in comparison between the livers of newborn and adult breeder roosters, a total of 1480 mRNAs and 622 lncRNAs were differentially expressed with the criteria of log2fold change > 1 or < -1 and P values < 0.05, which were validated by qPCR using randomly selected five mRNAs and five lncRNAs. Further GO and KEGG analyses have revealed that the differentially expressed mRNAs were involved in the hepatic metabolic and immune change, as well as some biological processes and pathways including cell division, proliferation, apoptotic and cell cycle that are implicated in the development of liver. We also investigated the cis- and trans- regulatory effects of lncRNAs on its target genes. Further GO and KEGG analyses indicated that these differentially expressed lncRNAs have their neighbor protein coding genes and co-expressed genes associated with adapting of adult hepatic functions, as well as some pathways involved in liver development, such as cell cycle pathway, Notch signaling pathway, Hedgehog signaling pathway, adherens junction and Wnt signaling pathway.

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Wu S, Liu Y, Guo W, Cheng X, Ren X, Chen S, Li X, Duan Y, Sun Q, Yang X