Abstract
BackgroundThe transcriptional profiles of mammals during brain development and ageing have been characterized. However the global expression patterns of transcriptome in the chicken brain have not been explored. Here, we systematically investigated the temporal expression profiles of lncRNAs and mRNAs across 8 stages (including 3 embryonic stages, 2 growth stages and 3 adult stages) in the female chicken cerebrum.ResultsWe identified 39,907 putative lncRNAs and 14,558 mRNAs, investigated the temporal expression patterns by tracking a set of age-dependent genes and predicted potential biological functions of lncRNAs based on co-expression network. The results showed that genes with functions in development, synapses and axons exhibited a progressive decay; genes related to immune response were up-regulated with age.ConclusionsThese results may reflect changes in the regulation of transcriptional networks and provide non-coding RNA gene candidates for further studies and would contribute to a comprehensive understanding of the molecular mechanisms of chicken development and may provide insights or deeper understanding regarding the regulatory mechanisms of age-dependent protein coding and non-protein coding genes in chicken. In addition, as the chicken is an important model organism bridging the evolutionary gap between mammals and other vertebrates, these high resolution data may provide a novel evidence to improve our comprehensive understanding of the brain transcriptome during vertebrate evolution.
Highlights
The transcriptional profiles of mammals during brain development and ageing have been characterized
The present study provided an initial Long non-coding RNAs (lncRNAs) catalogue of the chicken cerebrum, which improves our understanding of the temporal expression profile during development and ageing, and may provide insights or deeper understanding regarding the regulatory mechanisms of age-dependent genes in chicken
Genomic characterization and classification of lncRNAs To compare the genomic characteristics of lncRNAs and mRNAs, we identified a total of 39,907 putative lncRNAs and 14,558 mRNAs that were expressed in more than one biological replicate (FPKM > 0)
Summary
The transcriptional profiles of mammals during brain development and ageing have been characterized. Large-scale genomic studies have revealed that the majority of cellular RNAs are transcribed as non-protein coding RNAs (ncRNAs) [1,2,3,4]. Xu et al BMC Genomics (2018) 19:917 programs, which means the regulatory factors scale quadratically with genome size, the untranslated regions (UTRs) in mRNAs increase with the developmental complexity of organisms, and the non-protein coding intronic and intergenic transcripts contain an expanded regulatory framework to control gene expression during differentiation and development [20]. Remarkable achievements have been made in characterizing the transcriptional underpinnings of brain development and ageing in vertebrates, the precise mechanisms of lncRNAs in defining the complexity of brain functions remain unclear, in birds. The chicken is one of the most versatile experimental systems available, as an established model organism for the study of vertebrate development, the chicken is under evaluated in the study of developmental transcriptomics [27]
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