Sequence Characterization and Tissue Expression Analysis of Bovine Bta-miR-494

doi:10.7668/hbnxb.20194709

Abstract

Abstract:

In order to investigate the sequence characteristics of bovine Bta-miR-494 and its tissue expression,bioinformatics methods were used to analyze the characteristics of CpG islands,promoters and transcription factors of its upstream sequence and their conservatism among different species;then predicted and functionally enriched the target genes of bovine Bta-miR-494;and finally detected its spatial and temporal expression characteristics among different tissues and the same tissue at different periods of time of the bovine Bta-miR-494 by qRT-PCR method.The results showed that Bta-miR-494 was highly conserved among different species and had the closest affinity to goat,with no CpG island upstream and two transcriptional start sites;the target gene enrichment analysis showed that the target genes of Bta-miR-494 were significantly enriched in the signaling pathways related to muscle growth and metabolism,such as PI3K-Akt,p53 and MAPK; the predictive target gene enrichment analysis showed that the target genes of Bta-miR-494 were significantly enriched in the signaling pathways related to muscle growth and metabolism.qRT-PCR results showed that the expression of Bta-miR-494 was highest in the liver and lowest in the testis of adult cows;and the expression of Bta-miR-494 was significantly higher in the biceps femoris of adult cows than that of newborn calves,whereas the expression of Bta-miR-494 in the cardiac muscle and longitudinal muscle of dorsal cows was significantly lower than that of newborn calves,while the expression of Bta-miR-494 in the cardiac muscle and the longissimus dorsi muscle was significantly lower than that of newborn calves.This inter-tissue differential expression suggests that Bta-miR-494 may dominate different myogenic expression patterns during the development of muscle tissues at different growth stages in cattle.

Key words: Bovine, Bta-miR-494, Functional enrichment, Tissue expression, Skeletal muscle

XU Junjie, DING Yanling, LI Chenglong, ZHOU Xiaonan, SU Zonghua, QU Chang, SHI Yuangang, KANG Xiaolong. Sequence Characterization and Tissue Expression Analysis of Bovine Bta-miR-494[J]. Acta Agriculturae Boreali-Sinica, 2024, 39(3): 215-223. doi: 10.7668/hbnxb.20194709.

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http://www.hbnxb.net/EN/Y2024/V39/I3/215

Figures/Tables 9

Tab.1 Bovine Bta-miR-494 and housekeeping gene primer information

基因 Gene	引物序列(5'—3') Primer sequence(5'—3')	引物长度/bp Primer length
Bta-miR-494	RT primer:GTCGTATCCAGTGCAGGGTCCG	50
	AGGTATTCGCACTGGATACGACGAGGTT
	F:CCACCATGTGAAACATACACGGG	23
	R:ATCCAGTGCAGGGTCCGAGG	20
18S RNA	F:GTGGTGTTGAGGAAAGCAGACA	22
	R:TGATCACACGTTCCACCTCATC	22

Fig.1 Bovine Bta-miR-494 genomic location and inter-species conservation analysis A.Location of Bta-miR-494 in the bovine genome;B.Conserved features of miR-494 among species;C.Phylogenetic tree of miR-494 among species.

Fig.2 Characterization of the CpG island and promoter of the upstream sequence of bovine Bta-miR-494 A.Software EMBOSS CpGplot analysis results;B.Software MethPrimer analysis results.

Tab.2 Promoter-2.0 predicted promoter results

位点 Position	得分 Score	可能性 Likelihood
700	0.593	中
1 600	0.566	中

Tab.3 Promoter prediction results by BDGP:Neural Network Promoter Prediction

开始位点 Start	结束位点 End	得分 Score	启动子序列 Promoter Sequence
390	440	0.84	CTTGGTCAGCTCTAAAGCCGGGACACAGAGGTAGGTTGTCTGCATGGTGT
1 053	1 103	0.94	TCCTCTGCTCTAAAGGCCAGCTACAGAGAGAGGGGAGGGCACCATTATAC

Fig.3 Bta-miR-494 target gene prediction and GO and KEGG analysis results A.GO annotation of Bta-miR-494 target gene;B.Bta-miR-494 target gene prediction results based on three databases;C.KEGG pathway analysis of Bta-miR-494 target gene.

Fig.4 Interaction network of proteins encoded by Bta-miR-494 candidate target genes

Fig.5 Analysis of bovine Bta-miR-494 core target genes

Fig.6 Relative expression of Bta-miR-494 in major tissues of adult cattle and newborn calves Different lowercase letters indicate significant differences(P<0.05).

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