Identification and characterization of circular RNA in lactating mammary glands from two breeds of sheep with different milk production profiles using RNA-Seq

Hao, Zhiyun; Zhou, Huitong; Hickford, Jonathan G. H.; Gong, Hua; Wang, Jiqing; Hu, Jiang; Liu, Xiu; Li, Shaobin; Zhao, Mengli; Luo, Yuzhu

doi:10.1016/j.ygeno.2019.12.014

Cited by 47 publications

(49 citation statements)

References 39 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…CircRNAs are produced via different mechanisms and have multiple origins, thus resulting in different forms (Dong et al, 2017;. The results of our analysis suggest that circRNAs are generated from diverse genomic locations (intergenic, exon, intron, and antisense) but derived primarily from exon circularization, findings consistent with those of previous studies involving a variety of different species, including human, mice, cattle, sheep, and pigs (Rybak-Wolf et al, 2015;Zheng et al, 2016;Legnini et al, 2017;Liang et al, 2017;Wei et al, 2017;Hao et al, 2019). As such, mammalian circRNAs may primarily be formed by precursor mRNA back-splicing of the exons.…”

Section: Discussionsupporting

confidence: 90%

Profiling and Functional Analysis of Circular RNAs in Porcine Fast and Slow Muscles

Yin

et al. 2020

Front. Cell Dev. Biol.

View full text Add to dashboard Cite

The different skeletal muscle fiber types exhibit distinctively different physiological and metabolic properties, and have been linked to both human metabolic diseases and meat quality traits in livestock. Circular RNAs (circRNAs) are a new class of endogenous RNA regulating gene expression, but regulatory mechanisms of skeletal muscle fibers involved in circRNAs remain poorly understood. Here, we constructed circRNA expression profiles of three fast-twitch biceps femoris (Bf) and three slowtwitch soleus (Sol) muscles in pigs using RNA-seq and identified 16,342 distinct circRNA candidates. Notably, 242 differentially expressed (DE) circRNAs between Bf and Sol muscles were identified, including 105 upregulated and 137 downregulated circRNAs, and are thus potential candidates for the regulation of skeletal muscle fiber conversion. Moreover, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of host genes of DE circRNAs revealed that host genes were mainly involved in skeletal muscle fiber-related GO terms (e.g., muscle contraction, contractile fiber part, and Z disk) and skeletal muscle fiber-related signaling pathways (e.g., AMPK and cGMP-PKG). We also constructed co-expression networks of DE circRNA-miRNA-mRNA using previously acquired high-throughput sequencing mRNA and miRNA data, from which 112 circRNA-miRNA and 95 miRNA-mRNA interactions were identified. Multiple circRNAs essentially serve as a sponge for miR-499-5p, which is preferentially expressed in slow-twitch muscle and reduces the severity of Duchenne muscular dystrophy (DMD). Taken together, a series of novel candidate circRNAs involved in the growth and development of porcine skeletal muscle was identified. Furthermore, they provide a comprehensive circRNA resource for further in-depth research on the regulatory mechanisms of circRNA in the formation of skeletal muscle fiber, and may provide insights into human skeletal muscle diseases.

show abstract

Section: Discussionsupporting

confidence: 90%

Profiling and Functional Analysis of Circular RNAs in Porcine Fast and Slow Muscles

Yin

et al. 2020

Front. Cell Dev. Biol.

View full text Add to dashboard Cite

show abstract

“…Another study showed that a total of 38,722 circRNAs were identified from porcine ovaries with smaller or larger litter size (LLS), of which 56 circRNAs significantly downregulated and 54 circRNAs upregulated in ovaries with variant litter sizes (Xu et al, 2019). (Hao et al, 2020). A total of 4,906 circRNAs were found, and of which 33 exhibited differentially expressed between two sheep breeds.…”

Section: F I G U R Ementioning

confidence: 99%

Biological functions of circRNAs and their progress in livestock and poultry

Huang

Wang

Zhang

et al. 2020

Reprod Domestic Animals

View full text Add to dashboard Cite

CircRNAs are a class of newly discovered RNAs extensively expressed in eukaryotic cells (Jeck et al., 2013). Compared with conventional linear RNAs (containing 5′ and 3′ ends), circRNAs are covalently closed RNA molecules. It was recognized as a class of functional RNA that differs from miRNA, piRNA and lncRNA due to its character of circularity (Xu, Wu, Han, Zhao, & Song, 2017). CircRNAs were first found in RNA viruses as a viroid as early as in 1976 (Sanger, Klotz, Riesner, Gross, & Kleinschmidt, 1976). And then in 1986, it was also founded that the HDV, an animal virus, has a circRNA genome, which were considered to be a characteristic of viroids (Kos, Dijkema, Arnberg, van der Meide, & Schellekens, 1986). Due to limitation of technology at that time, circRNAs were less reported and were once considered as by-products of mis-splicing or regarded as a meaningless abnormally cut RNA, which never got any attention by some researchers because traditional molecular techniques employed in RNA analysis were not able to detect circRNAs because they did not have cap of 5′ end and tail of 3′ end (Jeck & Sharpless, 2014). It was not until 1991 that endogenous circRNAs were demonstrated in human cells, which originated from exons (Nigro et al., 1991). Since then, with advancement of bioinformatics analysis and RNA sequencing technologies, circRNA has attracted more and more attention of many scientists because it has been reported to be ubiquitously present in eukaryotic organisms and have longer half-lives than linear RNAs (Memczak et al., 2013;

show abstract

“…In order to reduce the effect of variation within individual ewes, the nine RNA samples isolated from each breed were randomly pooled to produce three samples in equal volume and concentration, as suggested by Hao et al [23,24] and Paten et al [25,26]. Briefly, the RNA isolated from three ewes in each breed was randomly pooled into a single sample.…”

Section: Library Construction and Rna Sequencingmentioning

confidence: 99%

“…This brought about three separate sets of RNA from STH ewes and three sets of RNA from GAM ewes (i.e., six groups in total). The synthesis of cDNA and library construction was performed according to our previous study [24]. These six cDNA libraries (three from STH samples and three from GAM samples) were used for cluster generation with Illumina s Cluster Station and then subjected to paired-end sequenced by Personal Corporation (Shanghai, China) [23,24].…”

Section: Library Construction and Rna Sequencingmentioning

confidence: 99%

See 1 more Smart Citation

RNA-Seq Reveals the Expression Profiles of Long Non-Coding RNAs in Lactating Mammary Gland from Two Sheep Breeds with Divergent Milk Phenotype

Hao

Luo

Wang

et al. 2020

Animals

Self Cite

View full text Add to dashboard Cite

Long non-coding RNAs (lncRNAs) are a kind of non-coding RNA with >200 nucleotides in length. Some lncRNAs have been proven to have clear regulatory functions in many biological processes of mammals. However, there have been no reports on the roles of lncRNAs in ovine mammary gland tissues. In the study, the expression profiles of lncRNAs were studied using RNA-Seq in mammary gland tissues from lactating Small-Tailed Han (STH) ewes and Gansu Alpine Merino (GAM) ewes with different milk yield and ingredients. A total of 1894 lncRNAs were found to be expressed. Compared with the GAM ewes, the expression levels of 31 lncRNAs were significantly up-regulated in the mammary gland tissues of STH ewes, while 37 lncRNAs were remarkably down-regulated. Gene Ontogeny (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis found that the target genes of differentially expressed lncRNAs were enriched in the development and proliferation of mammary epithelial cells, morphogenesis of mammary gland, ErbB signaling pathway, and Wnt signaling pathway. Some miRNA sponges of differentially expressed lncRNAs, reported to be associated with lactation and mammary gland morphogenesis, were found in a lncRNA-miRNA network. This study reveals comprehensive lncRNAs expression profiles in ovine mammary gland tissues, thereby providing a further understanding of the functions of lncRNAs in the lactation and mammary gland development of sheep.

show abstract

Identification and characterization of circular RNA in lactating mammary glands from two breeds of sheep with different milk production profiles using RNA-Seq

Cited by 47 publications

References 39 publications

Profiling and Functional Analysis of Circular RNAs in Porcine Fast and Slow Muscles

Profiling and Functional Analysis of Circular RNAs in Porcine Fast and Slow Muscles

Biological functions of circRNAs and their progress in livestock and poultry

RNA-Seq Reveals the Expression Profiles of Long Non-Coding RNAs in Lactating Mammary Gland from Two Sheep Breeds with Divergent Milk Phenotype

Contact Info

Product

Resources

About