Journal of Integrative Agriculture ›› 2021, Vol. 20 ›› Issue (5): 1346-1358.DOI: 10.1016/S2095-3119(20)63464-5

所属专题：动物科学合辑Animal Science

• 论文 • 上一篇下一篇

收稿日期:2020-03-29 出版日期:2021-05-01 发布日期:2021-04-12

circRNA landscape of non-pregnant endometrium during the estrus cycle in dairy goats

LIU Xiao-rui^{1, 2*}, ZHANG Lei^{1, 2*}, CUI Jiu-zeng¹, YANG Li-chun¹, HaAN Jin-cheng¹, CHE Si-cheng¹, CAO Bin-yun^{1, 2}, LI Guang^{1, 2}, SONG Yu-xuan^{1, 2}

¹ College of Animal Science and Technology, Northwest A&F University, Yangling 712100, P.R.China
² Shaanxi Provincial Key Laboratory of Animal Genetics, Breeding and Reproduction, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, P.R.China

Received:2020-03-29 Online:2021-05-01 Published:2021-04-12
Contact: Correspondence ZHANG Lei, Tel: +86-29-87092527, Fax: +86-29-87092164, E-mail: zhanglei07dongke@163.com
About author:* These authors contributed equally to this study.
Supported by:
This work was supported by the China Postdoctoral Science Foundation (2019M653776, 2020M673516), the National Key Research and Development Program of China (2016YFD0500508), the Natural Science Foundation of Shaanxi Province, China (2020JQ-265), and the PhD research startup foundation of Northwest A&F University, China (00400/Z109021811).

摘要/Abstract

摘要：

哺乳动物子宫内膜的发育是一个涉及众多的调节因素的复杂过程。环状RNA （circRNAs）是一种自然存在的内源性非编码RNA家族的重要成员之一，有研究报道circRNAs在多种生理过程中发挥着重要的调控作用。目的：本研究旨在分析奶山羊发情周期非妊娠子宫内膜组织中circRNA的表达谱。方法：采用链特异性去核糖体转录组测序技术对发情第5天和发情第15天奶山羊的非妊娠子宫内膜组织样进行circRNAs表达谱分析，筛选两个时期差异表达的circRNAs并利用RT-qPCR进行验证；然后利用生物信息学分析两个时期差异表达circRNAs的宿主基因，进而进行GO 和KEGG分析；最后利用Targetscan 7.0和miRanda网站分析circRNAs和miRNAs的靶向结合关系。结果：奶山羊发情第5天和发情第15天的非妊娠子宫内膜组织中共有2331个差异表达的circRNAs（P<0.05），RT-qPCR检测的10个circRNAs变化趋势与测序结果一致；其中circRNA1460的宿主基因Nipped-B 样蛋白（Nipped-B-like，NIPBL）和circRNA8694的宿主基因钙反应性转录因子（calcium responsive transcription factor，CARF）降低其circRNAs的转录形式的水平（P<0.05）参与子宫内膜的发育；差异表达circRNAs的宿主基因GO和KEGG分析结果显示注释到紧密连接（Tight junctions）条目上和鸟苷三磷酸酶（GTPases）通路上的circRNAs参与了奶山羊子发情周期中非妊娠子宫内膜的发育过程；另外，本研究中得到的circRNAs与公共数据库中的436个山羊miRNAs有靶向结合位点。结论：奶山羊发情第5天和发情第15天的非妊娠子宫内膜组织中存在差异的circRNAs，生物信息学分析表明一些circRNAs参与奶山羊发情周期非妊娠子宫内膜的发育过程；本研究构建了奶山羊发情周期非妊娠子宫内膜circRNAs文库，丰富了奶山羊的转录组信息，有助于我们研究奶山羊子宫内膜发育过程中的分子调控机制，为进一步提高奶山羊的胚胎着床的成功率和繁殖率提供理论依据。创新点：本研究选择发情第5天和发情第15天奶山羊的非妊娠子宫内膜组织进行circRNAs表达谱分析；采用核糖体去除和链特异性文库构建方案进行RNA-seq测序，保留了完整的circRNAs序列，对样本中几乎全部的circRNAs序列进行鉴定和分析。

Abstract:

Endometrial development is a complicated process involving numerous regulatory factors. Circular RNAs (circRNAs) have been known as a member of the naturally occurring non-coding RNA family, and are reportedly crucial for a variety of physiological processes. This study investigated the circRNA landscape of non-pregnant endometrium of dairy goats during estrus. Non-pregnant endometrial samples of goats at estrus day 5 (Ed5) and estrus day 15 (Ed15) were used to methodically analyze the circRNA landscape using strand-specific Ribo-Zero RNA-Seq. A total of 2 331 differentially expressed (P<0.05) circRNAs (DEciRs) between Ed5 and Ed15 were discovered in the goat endometrium. It was found that Nipped-B-like (NIPBL) and calcium responsive transcription factor (CARF) may participate in the development of the endometrium by decreasing (P<0.05) the levels of their circRNA-transcript forms. Furthermore, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses of DEciR host genes (hgDEciRs) revealed that tight junctions and GTPases may be involved in endometrial development during the estrus cycle. A total of 2 331 DEciRs were discovered in the endometrium at Ed5 and Ed15. Based on GO and KEGG enrichment analyses, it could be inferred that tight junctions and GTPases are likely to play an important role in the development of goat endometrium during the estrus cycle. This circRNA study greatly enhances our knowledge of global trends in the development of non-pregnant endometrium during the estrus cycle in goats; these results help us to better understand the molecular regulation of endometrial development in dairy goats.

Key words: circRNAs , Ribo-Zero RNA-Seq , non-pregnant endometrium , dairy goats

. [J]. Journal of Integrative Agriculture, 2021, 20(5): 1346-1358.

LIU Xiao-rui, ZHANG Lei, CUI Jiu-zeng, YANG Li-chun, HAN Jin-cheng, CHE Si-cheng, CAO Bin-yun, LI Guang, SONG Yu-xuan. circRNA landscape of non-pregnant endometrium during the estrus cycle in dairy goats[J]. Journal of Integrative Agriculture, 2021, 20(5): 1346-1358.

参考文献

Ashburner M, Ball C A, Blake J A, Botstein D, Butler H, Cherry J M, Davis A P, Dolinski K, Dwight S S, Eppig J T. 2000. Gene ontology: Tool for the unification of biology. Nature Genetics, 25, 25–29.
Bot C, Pfeiffer A, Giordano F, Manjeera D E, Dantuma N P, Strom L. 2017. Independent mechanisms recruit the cohesin loader protein NIPBL to sites of DNA damage. Journal of Cell Science, 130, 1134–1146.
Burns P D, Hayes S H, Silvia W J. 1998. Cellular mechanisms by which oxytocin mediates uterine prostaglandin F2 alpha synthesis in bovine endometrium: role of calcium. Domestic Animal Endocrinology, 15, 477–487.
Consortium G O. 2004. The Gene Ontology (GO) database and informatics resource. Nucleic Acids Research, 32, D258–D261.
Dang Y, Yan L, Hu B, Fan X, Ren Y, Rong L, Ying L, Jie Y, Li Q, Yan Z. 2016. Tracing the expression of circular RNAs in human pre-implantation embryos. Genome Biology, 17, 1–15.
Ebert M S, Neilson J R, Sharp P A. 2007. MicroRNA sponges, competitive inhibitors of small RNAs in mammalian cells. Nature Methods, 4, 721–726.
Fan X, Zhang X, Wu X, Guo H, Hu Y, Tang F, Huang Y. 2015. Single-cell RNA-seq transcriptome analysis of linear and circular RNAs in mouse preimplantation embryos. Genome Biology, 16, 1–17.
Franco-Zorrilla J M, Valli A, Todesco M, Mateos I, Puga M I, Rubio-Somoza I, Leyva A, Weigel D, García J A, Paz-Ares J. 2007. Target mimicry provides a new mechanism for regulation of microRNA activity. Nature Genetics, 39, 1033–1037.
Gong X, Chen Z, Liu Y, Lu Q, Jin Z. 2014. Gene expression profiling of the paracrine effects of uterine natural killer cells on human endometrial epithelial cells. International Journal of Endocrinology, 2014, 393707.
Grewal S, Carver J, Ridley A J, Mardon H J. 2010. Human endometrial stromal cell rho gtpases have opposing roles in regulating focal adhesion turnover and embryo invasion in vitro. Biology of Reproduction, 83, 75–82.
Guo Q, Ma X, Wei S, Qiu D, Wilson I W, Wu P, Tang Q, Liu L, Dong S, Zu W. 2014. De novo transcriptome sequencing and digital gene expression analysis predict biosynthetic pathway of rhynchophylline and isorhynchophylline from Uncaria rhynchophylla, a non-model plant with potent anti-alzheimer’s properties. BMC Genomics, 15, 676.
Hansen T B, Jensen T I, Clausen B H, Bramsen J B, Finsen B, Damgaard C K, Kjems J. 2013. Natural RNA circles function as efficient microRNA sponges. Nature, 495, 384–388.
He H, Liu X. 2013. Characterization of transcriptional complexity during longissimus muscle development in bovines using high-throughput sequencing. PLoS ONE, 8, e64356.
Hu S, Yao G, Wang Y, Xu H, Ji X, He Y, Zhu Q, Chen Z, Sun Y. 2014. Transcriptomic changes during the pre-receptive to receptive transition in human endometrium detected by RNA-Seq. Journal of Clinical Endocrinology & Metabolism, 99, 2744–2753.
Huisman S A, Redeker E J, Maas S M, Mannens M M, Hennekam R C. 2013. High rate of mosaicism in individuals with cornelia de lange syndrome. Journal of Medical Genetics, 50, 339–344.
Igwebuike U. 2009. A review of uterine structural modifications that influence conceptus implantation and development in sheep and goats. Animal Reproduction Science, 112, 1–7.
Jeck W R, Sharpless N E. 2014. Detecting and characterizing circular RNAs. Nature Biotechnology, 32, 453–461.
Jens M. 2013. Circular RNAs are a large class of animal rnas with regulatory potency. Nature, 495, 1439–1449.
Kanehisa M, Araki M, Goto S, Hattori M, Hirakawa M, Itoh M, Katayama T, Kawashima S, Okuda S, Tokimatsu T. 2008. KEGG for linking genomes to life and the environment. Nucleic Acids Research, 36, D480–D484.
Karakotchian M, Fraser I S. 2007. An ultrastructural study of microvascular inter-endothelial tight junctions in normal endometrium. Micron, 38, 632.
Kiatprasert P, Deachapunya C, Benjanirat C, Poonyachoti S. 2015. Soy isoflavones improves endometrial barrier through tight junction gene expression. Reproduction, 149, 269–280.
Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg S L. 2013. TopHat2: Accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biology, 14, 295–311.
Krantz I D, Mccallum J, Descipio C, Kaur M, Gillis L A, Yaeger D, Jukofsky L, Wasserman N, Bottani A, Morris C A. 2004. Cornelia de Lange syndrome is caused by mutations in NIPBL, the human homolog of Drosophila melanogaster Nipped-B. Nature Genetics, 36, 631–635.
Langmead B, Salzberg S L. 2012. Fast gapped-read alignment with Bowtie 2. Nature Methods, 9, 357–359.
Lasda E, Parker R. 2014. Circular RNAs: Diversity of form and function. RNA, 20, 1829–1842.
Ling Y H, Zheng Q, Zhu L, Xu L N, Sui M H, Zhang Y H, Liu Y, Fang F G, Ma Y H, Zhang X R. 2020. Trend analysis of the role of circular RNA in goat skeletal muscle development. BMC Genomics, 21, 12.
Lira-Albarrán S, Vega C C, Durand M, Rangel C, Larrea F. 2019. Functional genomic analysis of the human receptive endometrium transcriptome upon administration of mifepristone at the time of follicle rupture. Molecular and Cellular Endocrinology, 584, 88–96.
Liu X, Zhang L, Cui J, Che S, Song Y. 2019 The mRNA and lncRNA landscape of the non-pregnant endometrium during the oestrus cycle in dairy goat. Animal Production Science, 59, 1803–1813.
Liu X, Zhang L, Liu Y, Cui J, Che S, An X, Song Y, Cao B. 2018. Circ-8073 regulates CEP55 by sponging miR-449a to promote caprine endometrial epithelial cells proliferation via the PI3K/AKT/mTOR pathway. Biochimica et Biophysica Acta (BBA, Molecular Cell Research), 1865, 1130–1147.
Liu X, Zhang L, Yang L, Cui J, Song Y. 2020. miR-34a/c induce caprine endometrial epithelial cell apoptosis by regulating circ-8073/CEP55 via the RAS/RAF/MEK/ERK and PI3K/AKT/mTOR pathways. Journal of Cellular Physiology, 235, 10051–10067.
Lyons M R, Chen L F, Deng J V, Finn C, Pfenning A R, Sabhlok A, Wilson K M, West A E. 2016. The transcription factor calcium-response factor limits NMDA receptor-dependent transcription in the developing brain. Journal of Neurochemistry, 137, 164–176.
Lyons M R, Schwarz C M, West A E. 2012. Members of the myocyte enhancer factor 2 transcription factor family differentially regulate Bdnf transcription in response to neuronal depolarization. Journal of Neuroscience the Official Journal of the Society for Neuroscience, 32, 12780.
Ma D, Zhao Y, Yu S, Zhang H, Cheng M, Cao H, Li Q, Min L. 2019. CircRNA as CeRNA mediated by microRNA may be involved in goat lactation. Small Ruminant Research, 171, 63–72.
Ma S, Zhang H W. 2006. EL-004 Study of expression and function of Rho GTPases in mouse uterus endometrium during the process of implantation. Reproductive Biomedicine Online, 12, 40–40.
Ma X, Li P, Zhang Q, He L, Huang R. 2019. Transcriptome analysis of the endometrium from Chinese Erhualian sows that differ in calcium ion concentration and litter size. Animal Genetics, 50, 326–333.
Mazzoni G, Pedersen H S, Rabaglino M B, Hyttel P, Callesen H, Kadarmideen H N. 2020. Characterization of the endometrial transcriptome in early diestrus influencing pregnancy status in dairy cattle after transfer of in vitro-produced embryos. Physiological Genomics, 52, 269–279.
Morad A, Gemma P, Quentin F, Kathleen W, Roland A, Meynert A M, Hemant B, Chan C Y, Hülya K, ?ahin A. 2014. Genetic heterogeneity in Cornelia de Lange syndrome (CdLS) and CdLS-like phenotypes with observed and predicted levels of mosaicism. Journal of Medical Genetics, 51, 659–668.
Mortazavi A, Williams B A, Mccue K, Schaeffer L, Wold B. 2008. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nature Methods, 5, 621–628.
Munro S K, Farquhar C M, Mitchell M D, Ponnampalam A P. 2010. Epigenetic regulation of endometrium during the menstrual cycle. Molecular Human Reproduction, 16, 297–310.
NRC (National Research Council). 2007. Nutrient Requirements of Small Ruminants. Sheep, Goats, Cervids and New World Camelids. National Academy Press, Washington, D.C.
Petar G, Panagiotis P, Rajewsky N. 2014. circBase: A database for circular RNAs. RNA, 20, 1666–1670.
Pfenning A R, Kim T K, Spotts J M, Hemberg M, Su D, West A E. 2010. Genome-wide identification of calcium-response factor (CaRF) binding sites predicts a role in regulation of neuronal signaling pathways. PLoS ONE, 5, e10870.
Pietras R J, Szego C M. 1975. Endometrial cell calcium and oestrogen action. Nature, 253, 357–359.
Poliseno L, Salmena L, Zhang J, Carver B, Haveman W J, Pandolfi P P. 2010. A coding-independent function of gene and pseudogene mRNAs regulates tumour biology. Nature, 465, 1033–1038.
Rogers P A, Murphy C R. 1992. Morphometric and freeze fracture studies of human endometrium during the peri-implantation period. Reproduction Fertility & Development, 4, 265–269.
Rybak-Wolf A, Stottmeister C, Gla?ar P, Jens M, Pino N, Giusti S, Hanan M, Behm M, Bartok O, Ashwal-Fluss R. 2015. Circular RNAs in the mammalian brain are highly abundant, conserved, and dynamically expressed. Molecular Cell, 58, 870–885.
Salzman J, Chen R E, Olsen M N, Wang P L, Brown P O. 2013. Cell-type specific features of circular RNA expression. PLoS Genetics, 9, 119–129.
Song Y, An X, Zhang L, Fu M, Peng J, Han P, Hou J, Zhou Z, Cao B. 2015. Identification and profiling of microRNAs in goat endometrium during embryo implantation. PLoS ONE, 10, e0122202.
Song Y X, Zhang L, Liu X R, Niu M X, Cui J Z, Che S C, Liu Y X, An X P, Cao B Y. 2019. Analyses of circRNA profiling during the development from pre-receptive to receptive phases in the goat endometrium. Journal of Animal Science and Biotechnology, 10, 16.
Tao H, Xiong Q, Zhang F, Zhang N, Liu Y, Suo X J, Li X F, Yang Q P, Chen M X. 2018. Circular RNA profiling reveals chi_circ_0008219 function as microRNA sponges in pre-ovulatory ovarian follicles of goats (Capra hircus). Genomics, 110, 257–266.
Tao X, West A E, Chen W G, Corfas G, Greenberg M E. 2002. A calcium-responsive transcription factor, carf, that regulates neuronal activity-dependent expression of BDNF. Neuron, 33, 383–395.
Trapnell C, Williams B A, Pertea G, Mortazavi A, Kwan G, Van Baren M J, Salzberg S L, Wold B J, Pachter L. 2010. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nature Biotechnology, 28, 511–515.
Wang Y, Xue S, Liu X, Liu H, Hu T, Qiu X, Zhang J, Lei M. 2016. Analyses of long non-coding RNA and mRNA profiling using RNA sequencing during the pre-implantation phases in pig endometrium. Scientific Reports, 6, 20238.
Wira C R, Ghosh F M, Patel M V, Hickey D K, Ochiel D O. 2010. Sex Hormone regulation of innate immunity in the female reproductive tract: The role of epithelial cells in balancing reproductive potential with protection against sexually transmitted pathogens. American Journal of Reproductive Immunology, 63, 544–565.
You X, Vlatkovic I, Babic A, Will T, Epstein I, Tushev G, Akbalik G, Wang M, Glock C, Quedenau C. 2015. Neural circular RNAs are derived from synaptic genes and regulated by development and plasticity. Nature Neuroscience, 18, 603–610.
Zhang L, An X P, Liu X R, Fu M Z, Han P, Peng J Y, Hou J X, Zhou Z Q, Cao B Y, Song Y X. 2015. Characterization of the transcriptional complexity of the receptive and pre-receptive endometria of dairy goats. Scientific Reports, 5, 14244.
Zhang L, Liu X, Liu J, Ma L, Zhou Z, Song Y, Cao B. 2017a. The developmental transcriptome landscape of receptive endometrium during embryo implantation in dairy goats. Gene, 633, 82–95.
Zhang L, Liu X, Liu J, Ma X, Zhou Z, Song Y, Cao B. 2017b. MiR-26a promoted endometrial epithelium cells (EECs) proliferation and induced stromal cells (ESCs) apoptosis via the PTEN-PI3K/AKT pathway in dairy goats. Journal of Cellular Physiology, 233, 4688–4706.
Zhang L, Liu X, Liu J, Zhou Z, Song Y, Cao B, An X. 2017c. miR-182 aids in receptive endometrium development in dairy goats by down-regulating PTN expression. PLoS ONE, 12, e0179783.
Zhang L, Liu X, Ma X, Liu Y, Che S, Cui J, An X, Cao B, Song Y. 2018. Testin was regulated by circRNA3175-miR182 and inhibited endometrial epithelial cell apoptosis in pre-receptive endometrium of dairy goats. Journal of Cellular Physiology, 233, 6965–6974.
Zhang L, Liu X R, Che S C, Cui J Z, Ma X N, An X P, Cao B Y, Song Y X. 2019. Endometrial epithelial cell apoptosis is inhibited by a ciR8073-miR181a-neurotensis pathway during embryo implantation. Molecular Therapy-Nucleic Acids, 14, 262–273.
Zhang L, Liu X R, Han P, Zhou Z Q, Cao B Y, Song Y X. 2017d. The study of endometrium at gestational days 5 and 15 in dairy goats (Capra hircus). Czech Journal of Animal Science, 62, 358–367.
Zhang L, Liu X R, Liu J Z, Song Y X, Zhou Z Q, Cao B Y. 2017e. miR-182 selectively targets HOXA10 in goat endometrial epithelium cells in vitro. Reproduction in Domestic Animals, 52, 1081–1092.
Zhang L, Zhou Z Q, Li G, Fu M Z. 2013. The effect of deposition Se on the mRNA expression levels of GPxs in goats from a Se-enriched county of China. Biological Trace Element Research, 156, 111–123.
Zhang R J, Zou L B, Zhang D, Tan Y J, Wang T T, Liu A X, Qu F, Meng Y, Ding G L, Lu Y C. 2011. Functional expression of large-conductance calcium-activated potassium channels in human endometrium: A novel mechanism involved in endometrial receptivity and embryo implantation. Journal of Clinical Endocrinology & Metabolism, 97, 543–553.
Zhang S, Lin H, Kong S, Wang S, Wang H, Wang H, Armant D R. 2013. Physiological and molecular determinants of embryo implantation. Molecular Aspects of Medicine, 34, 939–980.
Zhang X O, Wang H B, Zhang Y, Lu X, Chen L L, Yang L. 2014. Complementary sequence-mediated exon circularization. Cell, 159, 134–147.
Zhao W, Cheng Y, Zhang C, You Q, Shen X, Guo W, Jiao Y. 2017. Genome-wide identification and characterization of circular RNAs by high throughput sequencing in soybean. Scientific Reports, 7, 5636.
Zheng Q, Bao C, Guo W, Li S, Chen J, Chen B, Luo Y, Lyu D, Li Y, Shi G. 2016. Circular RNA profiling reveals an abundant circHIPK3 that regulates cell growth by sponging multiple miRNAs. Nature Communications, 7, 11215.
Zheng Y, Hui T, Yue C, Sun J, Bai W. 2020. Comprehensive analysis of circRNAs from cashmere goat skin by next generation RNA sequencing (RNA-seq). Scientific Reports, 10, 516.
Zuin J, Casali V, Pozojevic J, Kolovos P, van den Hout M, van Ijcken W F J, Parenti I, Braunholz D, Baron Y, Watrin E, Kaiser F J, Wendt K S. 2017. Regulation of the cohesin-loading factor NIPBL: Role of the lncRNA NIPBL-AS1 and identification of a distal enhancer element. PLoS Genetics, 13, 24.

相关文章 0

编辑推荐

Metrics