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Integrative analysis of microRNA-mRNA of muscle tissues in Qianhua Mutton Merino and Small Tail Han sheep

ABSTRACT: Integrative analysis of microRNA-mRNA of muscle tissues in Qianhua Mutton Merino and Small Tail Han sheep

PROVIDER: PRJNA450541 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR7013782.fastq.gz	Fastqsanger.gz
	SRR7013783.fastq.gz	Fastqsanger.gz
	SRR7013784.fastq.gz	Fastqsanger.gz
	SRR7013785.fastq.gz	Fastqsanger.gz
	SRR7013786.fastq.gz	Fastqsanger.gz

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Comparative transcriptome profiling of longissimus muscle tissues from Qianhua Mutton Merino and Small Tail Han sheep

Project description:We aimed to evaluate the transcriptome regulators associated with muscle growth and development between the Qianhua Mutton Merino (QHMM) and Small Tail Han (STH) sheep.We used RNA-Seq to obtain the transcriptome profiles of the longissimus muscle from the QHMM and STH.The genome-wide transcriptome analysis of QHMM and STH muscle in present study is reported first time.

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Integrative analysis of microRNA-mRNA of muscle tissues in Qianhua Mutton Merino and Small Tail Han sheep

Project description:We aimed to evaluated the key microRNA-mRNA network associated with sheep muscle growth and development. We used RNA-Seq to obtain the smallRNA profiles of the longissimus muscle from the QHMM and STH. The results showed that a total of 153 known sheep miRNAs were identified, and 4 known sheep miRNAs were differently expressed. Combining mRNA library data, 26 target genes of 4 known miRNAs were selected and the miRNA–mRNA network was successfully built. GO and KEGG analysis showed that 26 target genes were significantly enriched in 86 biological processes, including muscle organogenesis, myoblast migration, cell proliferation, and adipose tissue development, and nine metabolic pathways, including carbohydrate, nucleotide, and amino acid metabolic pathways. The oar-miR-655-3p and target gene ACSM3, and oar-miR-381-5p and target gene ABAT were selected for subsequent analysis based on GO and KEGG analyses. The results suggested that the DEmiRNAs, especially oar-miR-655-3p and oar-miR-381-5p play crucial roles in muscle growth and development processes. This Integrative analysis of microRNA-mRNA analysis of QHMM and STH muscle is reported for the first time.

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Project description:In this study, we selected differentially expressed miRNAs through construcing and analyzing the miRNA expression profile during 2-, 6-, and 12- month-old Small Tail Han Sheep ovaries, which provided a theoretical basis for the study of miRNAs regulating the reproduction of Small Tail Han Sheep. RNASeq techniques were used to perform profile analysis for these ovaries. The results showed that 11, 13 and 19 DE miRNAs were identified in 2- vs 6-, 6- vs 12-, and 2- vs 12-month-old ovaries, respectively. In total, 54, 37, and 198 predicted target genes of DE miRNAs were obtained from these three groups, respectively. GO and KEGG analyses showed that, in 2- vs 6-month-olds, the target genes of DE known sheep miRNAs were involved in 102 GO terms and 7 signaling pathways; in 6- vs 12-month-olds, the target genes of DE known sheep miRNAs were involved in 52 GO terms and 3 signaling pathways; and in 2- vs 12-month-olds, the target genes of DE known sheep miRNAs were involved in 88 GO terms and 6 signaling pathways. Three miR–target regulatory networks were constructed based on these DE miRNA–targets. 9 miRNAs were selected to validate the accuracy of miRNA sequencing data by qRT-PCR. The binding sites of oar-miR-432 with RPS6KA1 was validated by a dual luciferase reporter gene detection system. This is the first integrative analysis of miRNA and mRNA expression profiles in Small Tail Han Sheep ovarian development. These data help elucidate the molecular regulatory mechanisms in sheep ovarian development and identify the biomarkers that influence reproductive performance of Small Tail Han Sheep ewe.

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Comparative transcriptome profiling of longissimus muscle tissues from Qianhua Mutton Merino and Small Tail Han sheep.

Project description:The Qianhua Mutton Merino (QHMM) is a new sheep (Ovis aries) variety with better meat performance compared with the traditional local variety Small Tail Han (STH) sheep. We aimed to evaluate the transcriptome regulators associated with muscle growth and development between the QHMM and STH. We used RNA-Seq to obtain the transcriptome profiles of the longissimus muscle from the QHMM and STH. The results showed that 960 genes were differentially expressed (405 were up-regulated and 555 were down-regulated). Among these, 463 differently expressed genes (DEGs) were probably associated with muscle growth and development and were involved in biological processes such as skeletal muscle tissue development and muscle cell differentiation; molecular functions such as catalytic activity and oxidoreductase activity; cellular components such as mitochondrion and sarcoplasmic reticulum; and pathways such as metabolic pathways and citrate cycle. From the potential genes, a gene-act-network and co-expression-network closely related to muscle growth and development were identified and established. Finally, the expressions of nine genes were validated by real-time PCR. The results suggested that some DEGs, including MRFs, GXP1 and STAC3, play crucial roles in muscle growth and development processes. This genome-wide transcriptome analysis of QHMM and STH muscle is reported for the first time.

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Project description:Comparative transcriptome profiling of longissimus muscle tissues from Qianhua Mutton Merino and Small Tail Han sheep

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