High throughput circRNA sequencing for adipose tissue of Qinchuan cattle
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA552355 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR9636724_1.fastq.gz | Fastqsanger.gz | |||
| SRR9636724_2.fastq.gz | Fastqsanger.gz | |||
| SRR9636725_1.fastq.gz | Fastqsanger.gz | |||
| SRR9636725_2.fastq.gz | Fastqsanger.gz | |||
| SRR9636726_1.fastq.gz | Fastqsanger.gz |
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Project description:Adipose development is regulated by a series of complicate processes, and non-coding RNAs (ncRNAs) such as circRNA have been reported to play important roles in regulating adipocytes proliferation and differentiation. In this study we profifile the expression of circRNA in cattle fat tissue from calf and adult developmental stages and detect 14,274 circRNA candidates. Some of these circRNAs are differentially expressed between two developmental stages.
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Project description:Sex condition has been demonstrated to alter meat quality and sex is a major factor that affects the fatty acid composition of lipids of carcass dissectible or intramuscular depot fats. But the possible genetic molecular mechanism of gender causing meat quality differences is not well defined. Qinchuan cattle, Qinghai yak and Guangxi buffalo are three typical indigenous species of cattle in China. Obivious differences of meat quality exist among the three species of cattle. Few studies have been conducted to elucidate the muscle tissue expression of genes involved in pathways and mechanisms leading to meat quality differences beyond the phenotype properties of beef. Bovine Genome Arrays were used to construct muscle expression profiles of the longuissimus dorsi from Qinchuan cattle at 36 months and screen differentially expressed genes in the longuissimus dorsi muscle tissues among different genders of Qinchuan cattle, between Qinchuan cattle and Qinghai yak, and between Qinchuan cattle and Guangxi buffalo.
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Project description:Circular RNAs (circRNAs) have been identified in various tissues and cell types from human, monkey, porcine and mouse. However, expression profile of circRNAs across cattle muscle development has never been investigated. Here, we examine the expression of circRNA in cattle skeletal muscle at embryonic stage and adult stage, exhibiting the first report of circRNA in the cattle muscle development of a large animal. 12,981 circRNAs are identified and annotated in Qinchuan cattle muscle tissues, including 530 circular intronic RNAs (ciRNAs). We discovered that one parental gene could generate multiple circRNA isoforms with only one or two circRNA isoforms being expressed at higher levels, and several host genes produced different alternative circularization numbers between different muscle development stages. The most circRNA candidates contained two to seven exons, and the genomic distance of the back-splicing site was generally no more than 50 kb. The flanking intron length of most circRNAs was not more than 105 nt and the mean length of upstream or downstream flanking intron was about 11,000 nt. Real-time quantitative PCR (qPCR) analysis confirmed the expression profile of these circRNAs, including several highly abundant circRNAs, and a subset of differently expressed circRNAs according to the high-throughput RNA sequencing (RNA-seq) data. These results display that an abundant circRNAs are dynamically expressed in a spatio-temporal manner in cattle muscle, indicating important and diverse functions during mammalian muscle development.
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Project description:We constructed a transcriptional profiling of adipose tissue by RNA sequencing. Samples were collected from Chinese Qinchuan fetal bovine, heifers, bulls, and steers. We unambiguously detected a substantial number of differently expressed genes (DEGs), novel transcript units (NTUs), and splicing variants.The expressional profile of adipose tissue changed considerably from fetuses to adults, whereas smaller differences were detected between the adipose tissues of adult cows (ATACs). As an endocrine organ, DEGs related to inflammatory and immune process were significantly enriched in the ATACs. These genes may play some roles in different regulation mechanisms of adipose tissue in different genders. In addition, adipose tissue abundantly expressed genes concerning the functions of the mitochondria and the ribosomes. These support the adipose tissue as an extremely active tissue for energy and protein metabolism besides the storage of surplus fuel. In this study, about two-thirds of the NTUs did not have coding ability. Both the NTUs with and without coding ability were enriched from 300bp to 1,500bp. The main difference in the number of the two types of NTUs was also concentrated in this range. In total, about 18.2% of the genes in adipose tissues were alternatively spliced, and half of them were specially expressed in different patterns. Combined with previous studies, we concluded that alternatively splicing events occur variously in different tissues or different patterns of adipose tissue. Taken together, our study provided complete datasets involving the spatial and temporal transcriptome of adipose tissue which suggested the complexity of adipose tissue and our study will provide essential information for further research.
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Project description:Adipose gene expression profiles in different cattle breeds.
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Project description:Cattle-yak is the hybrid offspring of yak and cattle. It has obvious heterosis in production performance, but the male sterility of cattle-yak has always been the focus of attention. Studies have shown that non-coding RNA is involved in the regulation of spermatogenesis. We comprehensively compared the testicular transcription profiles of cattle, yak and cattle-yak. More DEGs, DECs and DEMs were found in the intersection of the two comparison groups of cattle and cattle-yak, yak and cattle-yak, with 4,968, 360 and 59, respectively. The DEGs of cattle-yak, cattle and yak were mainly enriched in biological processes such as spermatogenesis, male gamete generation and sexual reproduction. At the same time, GO and KEGG analysis suggested that DECs host genes and DEMs source genes were also involved in the regulation of spermatogenesis. The construction of potential ceRNA networks found that some differentially expressed ncRNAs may be involved in the regulation of genes related to testicular spermatogenesis, including miR-423-5p, miR-449b, miR-34b/c, miR-15b, etc., as well as unreported miR-6123, miR-1306 and some miRNA and circRNA interaction pairs. This study provides a reference for further study on the mechanism of male sterility in cattle-yak.
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