西藏牛和三江牛大脑组织中低氧适应相关circRNAs的比较分析

doi:10.11843/j.issn.0366-6964.2020.03.009

Abstract

Abstract: The aim of this study was to enhance the understanding of mammals' adaptability to high altitude hypoxia environment at the circRNA level and explore the differentially expressed circRNA and related regulatory networks in brain of Zang cattle and Sanjiang cattle, which would lay the theoretical foundation for further researching the molecular regulation mechanism of circRNA in hypoxia adaptation in Zang cattle. In this study, the brain tissues of three 4.5-year-old female healthy Zang cattles and Sanjiang cattles were sampled to construct the cDNA libraries for high-throughput sequencing. Bioinformatics methods were used to analyze host genes of circRNA by GO and KEGG, and predict the target genes of differentially expressed circRNA. At the same time, the circRNA-miRNA and circRNA-miRNA-mRNA visualization regulatory networks were constructed. Moreover, the reliability of sequence data was verified by RNaseR enzyme resistance assay and real-time quantitative PCR (qRT-PCR). The results showed that 858 significantly differentially expressed circRNAs were filtered in 6 samples of Zang cattle and Sanjiang cattle, included 394 up-regulated circRNAs and 464 down-regulated circRNAs. The host genes of these differentially expressed circRNAs were involved in 49 functional subclasses, involved in 31 significantly enriched signaling pathways (P<0.05), mainly included MAPK signaling pathway, glutamatergic synapse, Rap1 signaling pathway, phospholipase D signaling pathway, cGMP-PKG signaling pathway, etc.. The result of target gene prediction revealed that 350 up-regulated and 364 down-regulated differentially expressed circRNAs were able to target 492 and 508 miRNAs, respectively. Among them, the novel_circ_017825 (235) and novel_circ_046762 (231) had the most target points to miRNAs, indicated that novel_circ_017825 and novel_circ_046762 might play an important role in the function regulation of Zang cattle brain. The circRNA-bta-miR-2284z-mRNA regulatory network showed the targeting relationship between bta-miR-2284z and circRNA, mRNA. It was speculated that the above circRNAs might indirectly affect the related targeted mRNA expression levels in Zang cattle brain by acting as bta-miR-2284z sponge. In addition, the RNaseR enzyme resistance test and qRT-PCR were performed on the randomly selected 6 circRNAs. The expression trend was consistent with the sequence results, which indicated that these obtained circRNAs were the circular transcript.The expression profile and signaling pathways of circRNA in brain tissues of Zang cattle and Sanjiang cattle were obtained by high-throughput sequencing technology, and the interaction model of circRNA-miRNA-mRNA network was initially constructed, which provided reliable data for further researching the biological process and molecular function of circRNA in Zang cattle hypoxia adaptability, as well as the regulation mechanism of circRNA in hypoxia adaptability in large mammals.

Key words: Zang cattle, Sanjiang cattle, hypoxia adaptability, transcriptome, circRNA

CLC Number:

S823.2

DENG Lei, CHAI Zhixin, WANG Jiabo, WANG Hui, WANG Jikun, WU Zhijuan, XIN Jinwei, ZHONG Jincheng, JI Qiumei. Comparative Analysis of Hypoxia-Adapted circRNAs in Brain Tissues of Zang Cattle and Sanjiang Cattle[J]. Acta Veterinaria et Zootechnica Sinica, 2020, 51(3): 490-504.

References 45

[1]	黄兴,柴志欣,信金伟,等.西藏牛亚科部分品种线粒体DNA遗传多样性研究[J].西南民族大学学报:自然科学版, 2019, 45(2):117-124.HUANG X,CHAI Z X,XIN J W,et al.Genetic diversity of mitochondrial DNA of some subfamilies of cattle in Tibet[J].Journal of Southwest Minzu University:Natural Science Edition,2019,45(2):117-124.(in Chinese)
[2]	王莉,旦增洛桑,马金英,等.娟姗牛杂交改良西藏本地黄牛的效果调查[J].中国奶牛,2015(2):13-15.WANG L,DANZENG L S,MA J Y,et al.Hybrid improvement of jersey cattle crossbreeding with Tibet local yellow cattle[J].China Dairy Cattle,2015(2):13-15.(in Chinese)
[3]	郭琳,柴志欣,钟金城,等.三江黄牛DKK1、DKK4和MyoG基因遗传多态性分析[J].家畜生态学报,2018,39(6):16-20.GUO L,CHAI Z X,ZHONG J C,et al.Genetic diversity of DKK1,DKK4 and MyoG in Sanjiang cattle[J].Acta Ecologae Animalis Domastici,2018,39(6):16-20.(in Chinese)
[4]	MA Q F,LI L Z,YU B X,et al.Circular RNA profiling of neutrophil transcriptome provides insights into asymptomatic Moyamoya disease[J].Brain Res,2019,1719:104-112.
[5]	YOU X T,VLATKOVIC I,BABIC A,et al.Neural circular RNAs are derived from synaptic genes and regulated by development and plasticity[J].Nat Neurosci,2015,18(4):603-610.
[6]	MAASS P G,GLAŽR P,MEMCZAK S,et al.A map of human circular RNAs in clinically relevant tissues[J].J Mol Med (Berl), 2017, 95(11):1179-1189.
[7]	XU K Y,CHEN D,WANG Z B,et al.Annotation and functional clustering of circRNA expression in rhesus macaque brain during aging[J].Cell Discov,2018,4:48.
[8]	THÖKEN C,THAMM M,ERBACHER C,et al.Sequence and structural properties of circular RNAs in the brain of nurse and forager honeybees (Apis mellifera)[J].BMC Genomics,2019,20(1):88.
[9]	LI X, YANG L, CHEN L L. The biogenesis, functions, and challenges of circular RNAs[J]. Mol Cell, 2018, 71(3):428-442.
[10]	张进威,龙科任,王讯,等.环状RNA研究进展[J].畜牧兽医学报,2016,47(11):2151-2158.ZHANG J W,LONG K R,WANG X,et al.The research advance of circular RNA[J].Acta Veterinaria et Zootechnica Sinica,2016,47(11):2151-2158.(in Chinese)
[11]	ENUKA Y,LAURIOLA M,FELDMAN M E,et al.Circular RNAs are long-lived and display only minimal early alterations in response to a growth factor[J].Nucleic Acids Res,2016,44(3):1370-1383.
[12]	LASDA E,PARKER R.Circular RNAs:diversity of form and function[J].RNA,2014,20(12):1829-1842.
[13]	吴艳,潘爱銮,杜金平,等.环状RNA及其在畜禽中的研究进展[J].西北农业学报,2018,27(3):301-305.WU Y,PAN A L,DU J P,et al.Research advance of circular RNA in livestock and poultry[J].Acta Agriculturae Boreali-occidentalis Sinica,2018,27(3):301-305.(in Chinese)
[14]	HANSEN T B,JENSEN T I,CLAUSEN B H,et al.Natural RNA circles function as efficient microRNA sponges[J].Nature, 2013,495(7441):384-388.
[15]	QU S B,YANG X S,LI X L,et al.Circular RNA:a new star of noncoding RNAs[J].Cancer Lett,2015,365(2):141-148.
[16]	HANSEN T B,WIKLUND E D,BRAMSEN J B,et al.miRNA-dependent gene silencing involving Ago2-mediated cleavage of a circular antisense RNA[J].EMBO J,2011,30(21):4414-4422.
[17]	MEMCZAK S,JENS M,ELEFSINIOTI A,et al.Circular RNAs are a large class of animal RNAs with regulatory potency[J].Nature,2013,495(7441):333-338.
[18]	XIE C,MAO X Z,HUANG J J,et al.KOBAS 2.0:a web server for annotation and identification of enriched pathways and diseases[J].Nucleic Acids Res,2011,39(S2):W316-W322.
[19]	LI J H,LIU S,ZHOU H,et al.StarBase v2.0:decoding miRNA-ceRNA,miRNA-ncRNA and protein-RNA interaction networks from large-scale CLIP-Seq data[J].Nucleic Acids Res,2014,42(D1):D92-D97.
[20]	SHANNON P,MARKIEL A,OZIER O,et al.Cytoscape:a software environment for integrated models of biomolecular interaction networks[J].Genome Res,2003,13(11):2498-2504.
[21]	PANDA A C,GOROSPE M.Detection and analysis of circular RNAs by RT-PCR[J].Bio Protoc,2018,8(6):e2775.
[22]	CHEN L L.The biogenesis and emerging roles of circular RNAs[J].Nat Rev Mol Cell Biol,2016,17(4):205-211.
[23]	HANSEN T B,VENØ M T,DAMGAARD C K,et al.Comparison of circular RNA prediction tools[J].Nucleic Acids Res,2016, 44(6):e58.
[24]	JECK W R,SHARPLESS N E.Detecting and characterizing circular RNAs[J].Nat Biotechnol,2014,32(5):453-461.
[25]	JIANG L,LI H J,FAN Z M,et al.Circular RNA expression profiles in neonatal rats following hypoxic-ischemic brain damage[J].Int J Mol Med,2019,43(4):1699-1708.
[26]	ZHANG M J,JIA L F,ZHENG Y F.circRNA expression profiles in human bone marrow stem cells undergoing osteoblast differentiation[J].Stem Cell Rev Rep,2019,15(1):126-138.
[27]	ABDELMOHSEN K, PANDA A C, DE S, et al. Circular RNAs in monkey muscle:age-dependent changes[J]. Aging (Albany NY), 2015, 7(11):903.
[28]	LI A,HUANG W,ZHANG X,et al.Identification and characterization of CircRNAs of two pig breeds as a new biomarker in metabolism-related diseases[J].Cell Physiol Biochem,2018,47(6):2458-2470.
[29]	CHEN X,SHI W,CHEN C.Differential circular RNAs expression in ovary during oviposition in honey bees[J].Genomics, 2019, 111(4):598-606.
[30]	HUANG J P,ZHAO J H,ZHENG Q Z,et al.Characterization of circular RNAs in Chinese buffalo (Bubalus bubalis) adipose tissue:a focus on circular RNAs involved in fat deposition[J].Animals (Basel),2019,9(7):403.
[31]	邹双霞,金澄艳,鲍建军,等.感染大肠杆菌F17湖羊羔羊脾脏中差异circRNA分析[J].中国农业科学,2019,52(6):1090-1101.ZOU S X,JIN C Y,BAO J J,et al.Differential circRNA analysis in the spleen of Hu-sheep lambs infected with F17Escherichia coli[J].Scientia Agricultura Sinica,2019,52(6):1090-1101.(in Chinese)
[32]	GAO Y,WU M L,FAN Y Z,et al.Identification and characterization of circular RNAs in Qinchuan cattle testis[J].R Soc Open Sci, 2018,5(7):180413.
[33]	LU C X,SUN X M,LI N,et al.CircRNAs in the tree shrew (Tupaia belangeri) brain during postnatal development and aging[J]. Aging (Albany NY),2018,10(4):833-852.
[34]	VAN ROSSUM D,VERHEIJEN B M,PASTERKAMP R J.Circular RNAs:novel regulators of neuronal development[J].Front Mol Neurosci,2016,9:74
[35]	CHEN J,AGUILERA G.Vasopressin protects hippocampal neurones in culture against nutrient deprivation or glutamate-induced apoptosis[J].J Neuroendocrinol,2010,22(10):1072-1081.
[36]	KIM S W,LIM C M,KIM J B,et al.Extracellular HMGB1 released by NMDA treatment confers neuronal apoptosis via RAGE-p38 MAPK/ERK signaling pathway[J].Neurotox Res,2011,20(2):159-169.
[37]	SARAAV I,SINGH S,SHARMA S.Outcome of Mycobacterium tuberculosis and Toll-like receptor interaction:immune response or immune evasion?[J].Immunol Cell Biol,2014,92(9):741-746.
[38]	TAO L,LI D,LIU H X,et al.Neuroprotective effects of metformin on traumatic brain injury in rats associated with NF-κB and MAPK signaling pathway[J].Brain Res Bull,2018,140:154-161.
[39]	李晶,杜永平,张月萍.缺氧对谷氨酸能和GABA能突触传递的影响[J].中国病理生理杂志,2013,29(2):371-375.LI J,DU Y P,ZHANG Y P.Effects of hypoxia on glutamatergic and GABAergic synaptic transmission[J].Chinese Journal of Pathophysiology,2013,29(2):371-375.(in Chinese)
[40]	SHAH S,BROCK E J,JI K,et al.Ras and Rap1:a tale of two GTPases[J].Semin Cancer Biol,2019,54:29-39.
[41]	LEI B X,HUANG Y T,ZHOU Z W,et al.Circular RNA hsa_circ_0076248 promotes oncogenesis of glioma by sponging miR-181a to modulate SIRT1 expression[J].J Cell Biochem,2019,120(4):6698-6708.
[42]	ZHANG X,WANG S,WANG H X,et al.Circular RNA circNRIP1 acts as a microRNA-149-5p sponge to promote gastric cancer progression via the AKT1/mTOR pathway[J].Mol Cancer,2019,18(1):20.
[43]	GRIFFITHS-JONES S,SAINI H K,VAN DONGEN S,et al.miRBase:tools for microRNA genomics[J].Nucleic Acids Res,2008, 36(S1):D154-D158.
[44]	JIN W W,IBEAGHA-AWEMU E M,LIANG G X,et al.Transcriptome microRNA profiling of bovine mammary epithelial cells challenged with Escherichia coli or Staphylococcus aureus bacteria reveals pathogen directed microRNA expression profiles[J].BMC Genomics,2014,15:181.
[45]	DAS K,GARNICA O,DHANDAYUTHAPANI S.Modulation of host miRNAs by intracellular bacterial pathogens[J].Front Cell Infect Microbiol,2016,6:79.

Comparative Analysis of Hypoxia-Adapted circRNAs in Brain Tissues of Zang Cattle and Sanjiang Cattle

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