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Identification of LncRNAs/circRNAs associated with testicular development and spermatogenesis in black goat

ABSTRACT: Establishment and maintenance of spermatogenesis need a complex process and vast regulatory network. There is growing evidence reveals that long noncoding RNAs (lncRNA) plays important role in regulating testicular development and spermatogenesis in a stage-specific way. We here report the identification of lncRNA LOC108635509 as key lncRNA regulator in black goat spermatogenesis. In the current study, we screened the transcriptomes (lncRNA and mRNA) of testicular from Guangxi black goats before puberty (3 days old, D3; 30 days old, D30), puberty (90 days old, D90) and postpuberty (180 days old, D180), and found there were 1211, 12180, 834 differential lncRNAs and 1196, 8838,269 differential mRNAs at the ages of D30 vs D3, D90 vs D30, and D180 vs D90. The expression pattern of differentially expressed (DE) lncRNAs indicated that D90 was a key node of lncRNAs participated in the regulation of testicular development and spermatogenesis in black goat. The of GO and KEGG analyses identified that DE lncRNAs and their target genes regulated spermatogenesis through MAPK, Ras, and PI3K-Akt signal pathways. Using cis- and trans-acting, 39 DE lncRNA-targeted genes were found to be enriched for male reproduction. Of these, LOC108635509, which specific expressed in testis and upregulated the expression levels at D90, was found participated in the regulation of testicular development through promoting the proliferation of SCs. Overall, this study provides new insight into the regulatory mechanisms that support spermatogenesis and testicular development in black goats.

ORGANISM(S): Capra hircus

PROVIDER: GSE276236 | GEO | 2024/10/01

REPOSITORIES: GEO

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Project description:Only a minuscule fraction of long non-coding RNAs (lncRNAs) are well characterized. The evolutionary history of lncRNAs can provide insights into their functionality, but comparative analyses have been precluded by our ignorance of lncRNAs in non-model organisms. Here, we use RNA sequencing to identify lncRNAs in eleven tetrapod species and we present the first large-scale evolutionary study of lncRNA repertoires and expression patterns. We identify ~11,000 primate- specific lncRNA families, which show evidence for selective constraint during recent evolution, and ~2,400 highly conserved lncRNAs (including ~400 genes that likely originated more than 300 million years ago). We find that lncRNAs, in particular ancient ones, are generally actively regulated and may predominantly function in embryonic development. lncRNA X-inactivation patterns reveal an extremely female-biased monotreme-specific lncRNA, which may partially compensate X-dosage in this lineage. Most lncRNAs evolve rapidly in terms of sequence and expression levels, but global patterns like tissue specificities are often conserved. We compared expression patterns of homologous lncRNA and protein-coding families across tetrapods to reconstruct an evolutionarily conserved co-expression network. This network, which surprisingly contains many lncRNA hubs, suggests potential functions for lncRNAs in fundamental processes like spermatogenesis or synaptic transmission, but also in more specific mechanisms such as placenta growth suppression through miRNA production. [Batch 1 and 2] To broaden our understanding of lncRNA evolution, we used an extensive RNA-seq dataset to establish lncRNA repertoires and homologous gene families in 11 tetrapod species. We analyzed the poly- adenylated transcriptomes of 8 organs (cortex/whole brain without cerebellum, cerebellum, heart, kidney, liver, placenta, ovary and testis) and 11 species (human, chimpanzee, bonobo, gorilla, orangutan, macaque, mouse, opossum, platypus, chicken and the frog Xenopus tropicalis), which shared a common ancestor ~370 millions of years (MY) ago. Our dataset included 47 strand-specific samples, which allowed us to confirm the orientation of gene predictions and to address the evolution of sense-antisense transcripts. See also GSE43721 (Soumillon et al, Cell Reports, 2013) for three strand-specific samples for mouse brain, liver and testis.

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Identification of LncRNAs/circRNAs associated with testicular development and spermatogenesis in black goat

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