Prediction of target genes and tissue expression analysis of miR-144 in cattle

doi:10.3969/j.issn.1004-1524.2022.03.07

Acta Agriculturae Zhejiangensis ›› 2022, Vol. 34 ›› Issue (3): 471-479.DOI: 10.3969/j.issn.1004-1524.2022.03.07

• Animal Science • Previous Articles Next Articles

Prediction of target genes and tissue expression analysis of miR-144 in cattle

DING Yanling(), WANG Pengfei, YANG Chaoyun, ZHOU Xiaonan, ZHAO Zhiyan, ZHANG Yanfeng, SHI Yuan- gang, KANG Xiaolong()

School of Agriculture,Ningxia University, Yinchuan 750021, China

Received:2021-06-08 Online:2022-03-25 Published:2022-03-30
Contact: KANG Xiaolong

Abstract

Abstract:

To study the target genes of miR-144 and their expression patterns in different tissues of cattle, and to predict the regulatory mechanism of miR-144 on muscle growth and development, the conservation, potential target genes and their enrichment pathways of miR-144 among different species were analyzed, and expression of miR-144 in different tissues of cattle was detected by qRT-PCR. The results showed that mature sequence of miR-144 was highly conserved among species; Enrichment analysis showed that target genes were significantly enriched in vascular smooth muscle contraction, cGMP-PKG, cAMP and other pathways related to muscle development. qRT-PCR results showed that miR-144 had the highest expression in liver and the lowest expression in subcutaneous fat; There was no significant difference(P>0.05) in the expression of miR-144 in leg muscle and heart, but the expression of miR-144 in liver was significantly (P<0.05) higher than that in leg muscle and heart; The expression of miR-144 in longissimus dorsi was significantly (P<0.05) higher than that in rumen and subcutaneous adipose, but there was no significant difference (P>0.05) between rumen and subcutaneous adipose.

Key words: miR-144, tissue expression, target gene prediction, qRT-PCR, enrichment pathway

CLC Number:

S823

DING Yanling, WANG Pengfei, YANG Chaoyun, ZHOU Xiaonan, ZHAO Zhiyan, ZHANG Yanfeng, SHI Yuan- gang, KANG Xiaolong. Prediction of target genes and tissue expression analysis of miR-144 in cattle[J]. Acta Agriculturae Zhejiangensis, 2022, 34(3): 471-479.

Figures/Tables 8

References 36

[1]	MANSOORI B, SHOTORBANI S S, BARADARAN B. RNA interference and its role in cancer therapy[J]. Advanced Pharmaceutical Bulletin, 2014, 4(4): 313-321.
[2]	WIGMORE P M, STICKLAND N C. Muscle development in large and small pig fetuses[J]. Journal of Anatomy, 1983, 137(Pt 2): 235-245.
[3]	CAO X N, TANG S Y, DU F, et al. miR-99a-5p regulates the proliferation and differentiation of skeletal muscle satellite cells by targeting MTMR3 in chicken[J]. Genes, 2020, 11(4): 369. DOI URL
[4]	ELSAEID E I, DONG D, WANG X G, et al. Bta-miR-885 promotes proliferation and inhibits differentiation of myoblasts by targeting MyoD1[J]. Journal of Cellular Physiology, 2020, 235(10): 6625-6636. DOI URL
[5]	WINBANKS C E, WANG B, BEYER C, et al. TGF-beta regulates miR-206 and miR-29 to control myogenic differentiation through regulation of HDAC4[J]. The Journal of Biological Chemistry, 2011, 286(16): 13805-13814. DOI URL
[6]	WU N Z, GU T T, LU L, et al. Roles of miRNA-1 and miRNA-133 in the proliferation and differentiation of myoblasts in duck skeletal muscle[J]. Journal of Cellular Physiology, 2019, 234(4): 3490-3499. DOI URL
[7]	张伟, 王世银, 邓双义, 等. oar-miR-133的表达对巴什拜羊骨骼肌细胞增殖和分化的影响[J]. 西北农业学报, 2019, 28(3): 315-322.
	ZHANG W, WANG S Y, DENG S Y, et al. Effect of oar-miR-133 expression on proliferation and differentiation of skeletal muscle satellite cell of bashbay sheep(Ovis aries)[J]. Acta Agriculturae Boreali-Occidentalis Sinica, 2019, 28(3): 315-322. (in Chinese with English abstract)
[8]	TONG H L, JIANG R Y, LIU T T, et al. Bta-miR-378 promote the differentiation of bovine skeletal muscle-derived satellite cells[J]. Gene, 2018, 668: 246-251. DOI URL
[9]	ZHANG W R, ZHANG H N, WANG Y M, et al. miR-143 regulates proliferation and differentiation of bovine skeletal muscle satellite cells by targeting IGFBP5[J]. In Vitro Cellular & Developmental BiologyAnimal, 2017, 53(3): 265-271.
[10]	王伟, 滚双宝, 王鹏飞, 等. 猪miR-204组织表达与重要靶基因筛选[J]. 浙江农业学报, 2020, 32(9): 1564-1573.
	WANG W, GUN S B, WANG P F, et al. Tissue expression and significant target genes analysis of swine miR-204[J]. Acta Agriculturae Zhejiangensis, 2020, 32(9): 1564-1573. (in Chinese with English abstract)
[11]	ZHOU J X, TIAN Z G, ZHU L F, et al. MicroRNA-615-3p promotes the osteoarthritis progression by inhibiting chondrogenic differentiation of bone marrow mesenchymal stem cells[J]. European Review for Medical and Pharmacological Sciences, 2018, 22(19): 6212-6220.
[12]	陈雯, 张伟伟, 邵淑丽, 等. miR-423-5p在牛肌肉组织中表达及其靶基因预测[J]. 浙江农业学报, 2021, 33(5): 785-793.
	CHEN W, ZHANG W W, SHAO S L, et al. Expression of miR-423-5p in bovine muscle and predicted target genes[J]. Acta AgriculturaeZhejiangensis, 2021, 33(5): 785-793. (in Chinese with English abstract)
[13]	樊赟, 樊纪民, 卞华. miR-144t通过对肝细胞生长因子的调控抑制肝癌细胞MHCC97H的增殖、迁移及延缓肝癌进展[J]. 中国老年学杂志, 2021, 41(10): 2161-2165.
	FAN Y, FAN J M, BIAN H. miR-144t inhibits the proliferation and migration of hepatocellular carcinoma cell MHCC97H and delays the progression of hepatocellular carcinoma by regulating hepatocyte growth factor[J]. Chinese Journal of Gerontology, 2021, 41(10): 2161-2165. (in Chinese)
[14]	XU Q H, LIAO B L, HU S, et al. Circular RNA 0081146 facilitates the progression of gastric cancer by sponging miR-144 and up-regulating HMGB1[J]. Biotechnology Letters, 2021, 43(4): 767-779. DOI URL
[15]	JONES N C, FEDOROV Y V, ROSENTHAL R S, et al. ERK1/2 is required for myoblast proliferation but is dispensable for muscle gene expression and cell fusion[J]. Journal of Cellular Physiology, 2001, 186(1): 104-115. DOI URL
[16]	WEBER C, HAMETNER C, TUCHSCHERER A, et al. Variation in fat mobilization during early lactation differently affects feed intake, body condition, and lipid and glucose metabolism in high-yielding dairy cows[J]. Journal of Dairy Science, 2013, 96(1): 165-180. DOI URL
[17]	AMOS L A, MA F Y, TESCH G H, et al. ASK 1 inhibitor treatment suppresses p38/JNK signalling with reduced kidney inflammation and fibrosis in rat crescentic glomerulonephritis[J]. Journal of Cellular and Molecular Medicine, 2018, 22(9): 4522-4533. DOI URL
[18]	SACLIER M, LAPI M, BONFANTI C, et al. The transcription factor Nfix requires RhoA-ROCK1 dependent phagocytosis to mediate macrophage skewing during skeletal muscle regeneration[J]. Cells, 2020, 9(3):708. DOI URL
[19]	SHIMOKAWA H, KIKUCHI N, SATOH K. Shrinking basic cardiovascular research in Japan: the tip of the iceberg[J]. Circulation Research, 2017, 121(4): 331-334. DOI URL
[20]	CAI S D, CHEN J S, XI Z W, et al. microRNA 144 inhibits migration and proliferation in rectal cancer by downregulating ROCK1[J]. Molecular Medicine Reports, 2015, 12(5): 7396-7402. DOI URL
[21]	SHU L L, HOUGHTON P J. The mTORC2 complex regulates terminal differentiation of C2C12 myoblasts[J]. Molecular and Cellular Biology, 2009, 29(17): 4691-4700. DOI URL
[22]	ZHOU W, YE S D, WANG W. miR-217 alleviates high-glucose-induced vascular smooth muscle cell dysfunction via regulating ROCK1[J]. Journal of Biochemical and Molecular Toxicology, 2021, 35(3): e22668.
[23]	TAKIMOTO E. Cyclic GMP-dependent signaling in cardiac myocytes[J]. Circulation Journal:Official Journal of the Japanese Circulation Society, 2012, 76(8): 1819-1825. DOI URL
[24]	HAMMOND J, BALLIGAND J L. Nitric oxide synthase and cyclic GMP signaling in cardiac myocytes: from contractility to remodeling[J]. Journal of Molecular and Cellular Cardiology, 2012, 52(2): 330-340. DOI URL
[25]	LEITNER L M, WILSON R J, YAN Z, et al. Reactive oxygen species/nitric oxide mediated inter-organ communication in skeletal muscle wasting diseases[J]. Antioxidants & Redox Signaling, 2017, 26(13): 700-717.
[26]	BERDEAUX R, STEWART R. cAMP signaling in skeletal muscle adaptation: hypertrophy, metabolism, and regeneration[J]. American Journal of Physiology Endocrinology and Metabolism, 2012, 303(1): E1-E17.
[27]	PLANCHON P, VEBER N, MAGNIEN V, et al. Alteration of prostaglandin E receptors in advanced breast tumour cell lines[J]. Molecular and Cellular Endocrinology, 1995, 111(2): 219-223. DOI URL
[28]	MIGUELANGEL MD, JOHANA M G, KALENIA M F, et al. Morphological changes of physeal cartilage and secondary ossification centres in the developing femur of the house mouse (Mus musculus):amicro-CT based study[J]. Anatomia HistologiaEmbryologia, 2019, 48(2): 117-124.
[29]	MIWA M, SAURA R, HIRATA S, et al. Induction of apoptosis in bovine articular chondrocyte by prostaglandin E(2)through cAMP-dependent pathway[J]. Osteoarthritis and Cartilage, 2000, 8(1): 17-24. DOI URL
[30]	RAVNSKJAER K, MADIRAJU A, MONTMINY M. Role of the cAMP pathway in glucose and lipid metabolism[J]. Handbook of Experimental Pharmacology, 2016, 233: 29-49.
[31]	CELIK O, CELIK N, UGUR K, et al. NppcNpr2cGMP signaling cascade maintains oocyte developmental capacity[J]. Cellular and Molecular Biology (Noisy-le-grand, France), 2019, 65(4): 83-89. DOI URL
[32]	YASUDA M, KAWABATA J, AKIEDA-ASAI S, et al. Guanylyl cyclase C and guanylin reduce fat droplet accumulation in cattle mesenteric adipose tissue[J]. Journal of Veterinary Science, 2017, 18(3): 341-348. DOI URL
[33]	LEE K T, BYUN M J, KANG K S, et al. Neuronal genes for subcutaneous fat thickness in human and pig are identified by local genomic sequencing and combined SNP association study[J]. PLoS One, 2011, 6(2): e16356. DOI URL
[34]	LIU H, PALMER D, JIMMO S L, et al. Expression of phosphodiesterase 4D (PDE4D) is regulated by both the cyclic AMP-dependent protein kinase and mitogen-activated protein kinase signaling pathways:apotential mechanism allowing for the coordinated regulation of PDE4D activity and expression in cells[J]. Journal of Biological Chemistry, 2000, 275(34): 26615-26624. DOI URL
[35]	KANAME T, KI C S, NIIKAWA N, et al. Heterozygous mutations in cyclic AMP phosphodiesterase-4D (PDE4D) and protein kinase A (PKA) provide new insights into the molecular pathology of acrodysostosis[J]. Cellular Signalling, 2014, 26(11): 2446-2459. DOI URL
[36]	SILVA D, FONSECA L, PINHEIRO D G, et al. Prediction of hub genes associated with intramuscular fat content in Nelore cattle[J]. BMC Genomics, 2019, 20(1): 520. DOI URL

数据库名称 Databasename	功能 Function	网址 Website
miRBase	miRNA序列数据库miRNA sequence database	http://www.mirbase.org/index.shtml/
TargetScan	miRNA靶基因预测Prediction of miRNA target genes	http://www.targetscan.org/
miRWalk	miRNA靶基因预测Prediction of miRNA target genes	http://mirwalk.umm.uni-heidelberg.de/
miRDB	miRNA靶基因预测Prediction of miRNA target genes	http://www.mirdb.org/
Veney	维恩图绘制Drawing of wenn diagram	http//bioinfogp.cnb.csic.es/tools/Venny/index.html
miRTarbase	miRNA实验验证靶基因数据库	http://mirtar-base.mbc.nctu.edu.tw/
	Validation of target genes database by miRNA experiment
DAVID	功能注释Function notes	https://david.ncifcrf.gov/

数据库名称 Databasename	功能 Function	网址 Website
miRBase	miRNA序列数据库miRNA sequence database	http://www.mirbase.org/index.shtml/
TargetScan	miRNA靶基因预测Prediction of miRNA target genes	http://www.targetscan.org/
miRWalk	miRNA靶基因预测Prediction of miRNA target genes	http://mirwalk.umm.uni-heidelberg.de/
miRDB	miRNA靶基因预测Prediction of miRNA target genes	http://www.mirdb.org/
Veney	维恩图绘制Drawing of wenn diagram	http//bioinfogp.cnb.csic.es/tools/Venny/index.html
miRTarbase	miRNA实验验证靶基因数据库	http://mirtar-base.mbc.nctu.edu.tw/
	Validation of target genes database by miRNA experiment
DAVID	功能注释Function notes	https://david.ncifcrf.gov/

基因 Gene	引物序列(5'→3') Primer sequence(5'→3')	引物长度 Primer length/bp
miR-144	RTprimer:GTCGTATCCAGTGCAGGGTCCGAGGTATTCGCACTGGATACGACCTAGTA	50
	F:CGCGCGTACAGTATAGATGATG	23
	R:AGTGCAGGGTCCGAGGTATT	20
18S RNA	F:GTGGTGTTGAGGAAAGCAGACA	22
	R:TGATCACACGTTCCACCTCATC	22

基因 Gene	引物序列(5'→3') Primer sequence(5'→3')	引物长度 Primer length/bp
miR-144	RTprimer:GTCGTATCCAGTGCAGGGTCCGAGGTATTCGCACTGGATACGACCTAGTA	50
	F:CGCGCGTACAGTATAGATGATG	23
	R:AGTGCAGGGTCCGAGGTATT	20
18S RNA	F:GTGGTGTTGAGGAAAGCAGACA	22
	R:TGATCACACGTTCCACCTCATC	22

物种Species	登录号Accession No.	序列Sequence(5'~3')
牛Bos taurus	MIMAT0009234	UACAGUAUAGAUGAUGUACUAG
马Equus caballus	MIMAT0013024	UACAGUAUAGAUGAUGUACU
猪Sus scrofa	MIMAT0025364	UACAGUAUAGAUGAUGUAC
狗Canis lupus familiaris	MIMAT0006734	UACAGUAUAGAUGAUGUACUAG
鸡Gallus	MIMAT0003776	CUACAGUAUAGAUGAUGUACUC
小鼠Mus musculus	MIMAT0000156	UACAGUAUAGAUGAUGUACU
家鼠Rattus norvegicus	MIMAT0000850	UACAGUAUAGAUGAUGUACU
人Homo sapiens	MIMAT0000436	UACAGUAUAGAUGAUGUACU
黑猩猩Pan troglodytes	MIMAT0002262	UACAGUAUAGAUGAUGUACUAG
斑马鱼Brachydaniorerio var	MIMAT0001841	UACAGUAUAGAUGAUGUACU

Prediction of target genes and tissue expression analysis of miR-144 in cattle

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