牛体内囊胚全转录组模式解析

doi:10.11843/j.issn.0366-6964.2020.011

Abstract

Abstract: The purpose of this study was to explore the whole transcription pattern of bovine in vivo blastocysts. Three lactating cows over 15-month-old and in good health were selected, superovulation technology was used to obtain in vivo blastocysts. Single-cell whole transcriptome sequencing technology was used to detect the transcription pattern of mRNA, lncRNA, and circRNA of bovine blastocyst, and bioinformatics tools were used to analyze the related informations. As a result of the experiment, bovine blastocysts had about 19 975 mRNAs, 12 715 novel lncRNAs, and 887 circRNAs. There were 12 alternative splicing methods for mRNAs, mainly the transcription start site (TSS). GO and KEGG were used to analyze mRNAs. It was found that biological functions were mainly enriched in metabolism, cell membrane and protein binding, cell communication, cellular component organization and developmental process in GO enrichment analysis; The pathways were enriched in cell cycle, membrane transport, and chromosome tissue regulation. There were 6 types of circRNAs, of which the CLASSIC type had the largest number. This type of splicing would form a circular exon circRNA (EcircRNA). The whole transcriptome pattern of bovine in vivo blastocyst was clarified in this study, which provided new ideas for a comprehensive understanding of bovine in vivo blastocysts.

Key words: in vivo bovine blastocyst, mRNA, lncRNA, circRNA

CLC Number:

S823.3

WANG Jingjing, ZHANG Peipei, HAO Haisheng, DU Weihua, PANG Yunwei, QUAN Guobo, ZHAO Shanjiang, ZOU Huiying, ZHU Huabin, ZHAO Xueming. Analysis of Whole Transcriptome Pattern of Bovine in vivo Blastocyst[J]. Acta Veterinaria et Zootechnica Sinica, 2020, 51(6): 1271-1280.

References 40

[1]	侯银仙.牛体外胚胎生产技术研究进展[J].畜牧兽医科技信息,2013(9):8-10.HOU Y X.Research progress of bovine in vitro embryo production technology[J].Chinese Journal of Animal Husbandry and Veterinary Medicine,2013(9):8-10.(in Chinese)
[2]	MANDAWALA A A,HARVEY S C,ROY T K,et al.Cryopreservation of animal oocytes and embryos:current progress and future prospects[J].Theriogenology,2016,86(7):1637-1644.
[3]	BEACKETT B G, BOUSQUET D, BOICE M L, et al. Normal development following in vitro fertilization in the cow[J]. Biol Reprod, 1982,27:147-158.
[4]	EALY A D,WOOLDRIDGE L K,MCCOSKI S R.BOARD INVITED REVIEW:Post-transfer consequences of in vitro-produced embryos in cattle[J].J Anim Sci,2019,97(6):2555-2568.
[5]	WRENZYCKI C,HERRMANN D,CARNWATH J W,et al.Expression of the gap junction gene connexin43(Cx43) in preimplantation bovine embryos derived in vitro or in vivo[J].Reproduction,1996,108(1):17-24.
[6]	DRIVER A M,PEÑAGARICANO F,HUANG W,et al.RNA-Seq analysis uncovers transcriptomic variations between morphologically similar in vivo- and in vitro-derived bovine blastocysts[J].BMC Genomics,2012,13:118.
[7]	TANG F C,BARBACIORU C,WANG Y Z,et al.mRNA-Seq whole-transcriptome analysis of a single cell[J].Nat Methods, 2009,6(5):377-382.
[8]	SOOD T J,LAGAH S V,MUKESH M,et al.RNA sequencing and transcriptome analysis of buffalo (Bubalus bubalis) blastocysts produced by somatic cell nuclear transfer and in vitro fertilization[J].Mol Reprod Dev,2019,86(9):1149-1167.
[9]	MARQUES A C,PONTING C P.Intergenic lncRNAs and the evolution of gene expression[J].Curr Opin Genet Dev,2014,27:48-53.
[10]	XU Y Y,QI X L,HU M Y,et al.Transcriptome analysis of adipose tissue indicates that the cAMP signaling pathway affects the feed efficiency of pigs[J].Genes,2018,9(7):336.
[11]	宋尚桥,马围围,张超龙,等.基于转录组测序生物信息学分析的研究进展[J].中国畜牧兽医,2020,47(2):392-398.SONG S Q,MA W W,ZHANG C L,et al.Advances in bioinformatics analysis based on transcriptome sequencing[J].China Animal Husbandry & Veterinary Medicine,2020,47(2):392-398.(in Chinese)
[12]	NG S Y,STANTON L W.Long non-coding RNAs in stem cell pluripotency[J].Wiley Interdiscip Rev RNA,2013,4(1):121-128.
[13]	JECK W R,SHARPLESS N E.Detecting and characterizing circular RNAs[J].Nat Biotechnol, 2014, 32(5):453-461.
[14]	FAN X Y,ZHANG X N,WU X L,et al.Single-cell RNA-seq transcriptome analysis of linear and circular RNAs in mouse preimplantation embryos[J].Genome Biol,2015,16(1):148.
[15]	SONG Y X,ZHANG L,LIU X R,et al.Analyses of circRNA profiling during the development from pre-receptive to receptive phases in the goat endometrium[J].J Anim Sci Biotechnol,2019,10:34.
[16]	SALIBA A E,WESTERMANN A J,GORSKI S A,et al.Single-cell RNA-seq:advances and future challenges[J].Nucl Acids Res,2014,42(14):8845-8860.
[17]	DJEBALI S,DAVIS C A,MERKEL A,et al.Landscape of transcription in human cells[J]. Nature,2012,489(7414):101-108.
[18]	郝海生,程小强,穆秋玲.图说奶牛繁殖技术与繁殖管理[M].北京:化学工业出版社,2016.HAO H S,CHENG X Q,MU Q L.Cow breeding technology and breeding management[M].Beijing:Chemical Industry Press,2016.(in Chinese)
[19]	CHITWOOD J L,RINCON G,KAISER G G,et al.RNA-seq analysis of single bovine blastocysts[J].BMC Genomics,2013,14:350.
[20]	滕春波,徐立滨,李世杰,等.环氧合酶-1和环氧合酶-2在兔早期妊娠子宫内膜及早期胚胎中的表达[J].中国兽医学报, 2003,23(5):499-502.TENG C B,XU L B,LI S J,et al.Expression of cyclooxygenase-1 and cyclooxygenase-2 in rabbit endometrium during early pregnancy and in early stage embryos[J].Chinese Journal of Veterinary Science,2003,23(5):499-502.(in Chinese)
[21]	ZHAO X M,MIN J T,DU W H,et al. Melatonin enhances the in vitro maturation and developmental potential of bovine oocytes denuded of the cumulus oophorus[J].Zygote,2015,23(4):525-536.
[22]	BROADY A J,LOICHINGER M H,AHN H J,et al.Protective proteins and telomere length in placentas from patients with pre-eclampsia in the last trimester of gestation[J].Placenta, 2017,50:44-52.
[23]	TIAN G G,LI J,WU J.Alternative splicing signatures in preimplantation embryo development[J].Cell Biol,2020,10:33.
[24]	SULTAN M,SCHULZ M H,RICHARD H,et al.A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome[J].Science, 2008,321(5891):956-960.
[25]	JIN S L,SU H R,TRAN N T,et al.Splicing factor SF3B1K700E mutant dysregulates erythroid differentiation via aberrant alternative splicing of transcription factor TAL1[J].PLoS One, 2017,12(5):e0175523.
[26]	CHACKO E, RANGANATHAN S.Genome-wide analysis of alternative splicing in cow:implications in bovine as a model for human diseases[J].BMC Genomics,2009,10(S3):S11.
[27]	NODERER W L,FLOCKHART R J,BHADUR A,et al. Quantitative analysis of mammalian translation initiation sites by FACS-seq[J].Mol Syst Biol, 2014,10(8):748.
[28]	NEININGER K,MARSCHALL T,HELMS V.SNP and indel frequencies at transcription start sites and at canonical and alternative translation initiation sites in the human genome[J].PLoS One,2019,14(4):e0214816.
[29]	DERRIEN T,JOHNSON R,BUSSOTTI G,et al.The GENCODE v7 catalog of human long noncoding RNAs:analysis of their gene structure,evolution,and expression[J].Genome Res,2012,22(9):1775-1789.
[30]	LAPIDOT M,PILPEL Y. Genome-wide natural antisense transcription:coupling its regulation to its different regulatory mechanisms[J].EMBO Rep,2006,7(12):1216-1222.
[31]	HUANG W,KHATIB H.Comparison of transcriptomic landscapes of bovine embryos using RNA-Seq[J].BMC Genomics,2010, 11:711.
[32]	EIßMANN M,GUTSCHNER T,HÄMMERLE M,et al.Loss of the abundant nuclear non-coding RNA MALAT1 is compatible with life and development[J].RNA Biol,2012,9(8):1076-1087.
[33]	SARANGDHAR M A,CHAUBEY D,SRIKAKULAM N,et al.Parentally inherited long non-coding RNA Cyrano is involved in zebrafish neurodevelopment[J].Nucleic Acids Res,2018,46(18):9726-9735.
[34]	SANGER H L,KLOTZ G,RIESNER D,et al.Viroids are single-stranded covalently closed circular RNA molecules existing as highly base-paired rod-like structures[J].Proc Natl Acad Sci U S A, 1976,73(11):3852-3856.
[35]	ZHANG Y,ZHANG X O,CHEN T,et al.Circular intronic long noncoding RNAs[J].Mol Cell, 2013,51(6):792-806.
[36]	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.
[37]	MA Z,ZHAO H S,ZHANG Y,et al.Novel circular RNA expression in the cumulus cells of patients with polycystic ovary syndrome[J].Arch Gynecol Obstet,2019,299(6):1715-1725.
[38]	LI Y,ZHENG Q P,BAO C Y,et al.Circular RNA is enriched and stable in exosomes:a promising biomarker for cancer diagnosis[J]. Cell Res,2015,25(8):981-984.
[39]	QUAN G B,LI J L.Circular RNAs:biogenesis,expression and their potential roles in reproduction[J].J Ovarian Res,2018,11(1):9.
[40]	LI Z Y,HUANG C,BAO C,et al.Exon-intron circular RNAs regulate transcription in the nucleus[J].Nat Struct Mol Biol,2015,22(3):256-264.

Analysis of Whole Transcriptome Pattern of Bovine in vivo Blastocyst

PDF (PC)

Knowledge

Abstract

Cite this article

share this article

References 40

Related Articles 15

Recommended Articles

Metrics

Comments

[1]	ZHANG De'an, YANG Ruozhu, LIU Jie, LIU Dewu, DENG Ming, LIU Guangbin, SUN Baoli, GUO Yongqing, LI Yaokun. Expression Analysis of Transcriptome in the Liver of Chuanzhong Black Goats Fed with Silage Neolamarckia Cadamba Substitute for Silage Corn [J]. Acta Veterinaria et Zootechnica Sinica, 2024, 55(1): 232-244.
[2]	WANG Zhengrong, MA Xun, ZHANG Yanyan, SUN Yan, MENG Jimeng, BO Xinwen. Differential Expression Profile of CircRNA in Protoscolex, Hydatid Cyst Wall and Adult of Echinococcus granulosus [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(8): 3474-3489.
[3]	CHEN Xin, QIN Tong. mRNA Vaccine and Its Research Prospect in Zoonotic Diseases [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(7): 2732-2742.
[4]	AN Zongqi, ZHAN Siyuan, LI Li, ZHANG Hongping. ceRNA-mediated Function of CircRNA on Critical Economic Traits in Animals [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(6): 2215-2222.
[5]	YANG Chuang, WU Longfei, LIU Guangbin, LI Yaokun, LIU Dewu, SUN Baoli. Expression Profile and Bioinformatics Analysis of lncRNA and Its Associated ceRNA Networks in Longissimus Dorsi from Lufeng Cattle and Leiqiong Cattle [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(5): 1951-1963.
[6]	QIN Xue, SHA Yiwen, YANG Menghao, CAI Rui, PANG Weijun. Advances in Regulation of Non-coding RNA on Mammalian Endometrial Receptivity and Decidualization [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(4): 1347-1358.
[7]	JIA Hongru, YANG Chaoqun, WANG Meng, WU Zhangqing, ZAN Linsen, YANG Wucai. LRTN4RL1-AS Mediates Milk Fat Synthesis in Bovine Mammary Epithelial Cells through miR-27a-3p Targeting PPARγ [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(4): 1465-1477.
[8]	JIN Meilin, LI Taotao, SUN Dongxiao, WEI Caihong. Research Progress of Epigenetic Regulation in Fat Deposition Mechanism of Livestock and Poultry [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(3): 855-867.
[9]	YE Junning, DENG Ming, XUE Huiwen, LIU Guangbin, ZOU Xian, SUN Baoli, GUO Yongqing, LIU Dewu, LI Yaokun. Identification and Analysis of mRNA and lncRNA Affecting Goat Fetal Muscle Development [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(3): 989-1002.
[10]	YANG Guang, XU Jing, LI Xin, HU Debao, GUO Yiwen, DING Xiangbin, GUO Hong, ZHANG Linlin. Effect of Interfering lncbMD on Proliferation and Differentiation of Bovine Skeletal Muscle Satellite Cells [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(3): 1015-1025.
[11]	MENG Zhaoyi, WANG Yunlu, XU Yefen, NIU Jiaqiang, SUOLANG Sizhu, GUO Min, XI Guangyin. Construction of Yak lncRNA ENSBGRT00000000387.1 Lentivirus Vector and Its Effect on Apoptosis of Yak Follicular Granulosa Cells [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(3): 1058-1070.
[12]	LUO Ju, MAO Jiani, XIA Yinzhao, YANG Zhenguo. Regulation of circRNAs on Mammalian Intestinal Barrier Function [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(11): 4439-4448.
[13]	JIANG Shengqiang, HU Jing, CHEN Hongying. Expression Analysis of CircRNAs in A549 Cells Infected with H1N1 Influenza A Virus [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(11): 4724-4734.
[14]	YANG Zhimei, LIANG Chengcheng, ZHANG Dianqi, LI Xuefeng, ZAN Linsen. Research Progress on the Regulation of circRNA by m⁶A Modification [J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(10): 4016-4027.
[15]	YU Zhirui, ZHANG Xu, NIU Shasha, DENG Guangcun, WU Xiaoling. LncRNA NR_003508 Regulates BCG-infected Mouse Macrophages Necrosis by the Sponge Adsorption of miR-483-3p and Targeting MLKL [J]. Acta Veterinaria et Zootechnica Sinica, 2022, 53(9): 3149-3159.