|
|
|
|
|
| RNA-Seq transcriptome analysis of porcine cloned and in vitro fertilized blastocysts |
| XU Wei-hua, LI Zi-cong, OUYANG Zhi-ping, YU Bo, SHI Jun-song, LIU De-wu, WU Zhen-fang |
1、National Engineering Research Center for Breeding Swine Industry, South China Agricultural University, Guangzhou 510642,P.R.China
2、College of Life Science, Longyan University, Longyan 364012, P.R.China
3、Wen’s Research Institute, Yunfu 527439, P.R.China |
|
|
|
摘要 Somatic nuclear transfer technology has become increasingly promising in biomedicine and agriculture. Whereas the approach remains inefficient and underlying mechanisms remain ambiguous. Although cloned embryos have similar in vitro developmental capacity as in vitro fertilized (IVF) embryos before implantation, they appeared to have much lower full-term developmental efficiency in pig and cattle, and thus it would be reasonable to postulate that profound distinction at the molecular level should exist between them. Herein, RNA sequencing technique was used to screen differentially expressed genes in cloned and IVF blastocysts, and in total 628 differentially expressed transcripts were obtained, among which, 280 transcripts are up-regulated and 348 transcripts are down-regulated in cloned blastocysts. Moreover, one statistically significant pathway associated with endoplasmic reticulum (ER) protein processing was enriched, and some ER-stress markers such as ATF4, ATF6, PDIA3, HSPA1B, HSP40 and HSP90 between cloned and IVF blastocysts were suggested. Additionally, some developmentally important genes such as lipid metabolism related genes (MGLL, DDHD2 and FADS2) and epigenetic modification genes (DNMT1, KDM5C and MBD3L5) were found differentially expressed between cloned and IVF embryos.
Abstract Somatic nuclear transfer technology has become increasingly promising in biomedicine and agriculture. Whereas the approach remains inefficient and underlying mechanisms remain ambiguous. Although cloned embryos have similar in vitro developmental capacity as in vitro fertilized (IVF) embryos before implantation, they appeared to have much lower full-term developmental efficiency in pig and cattle, and thus it would be reasonable to postulate that profound distinction at the molecular level should exist between them. Herein, RNA sequencing technique was used to screen differentially expressed genes in cloned and IVF blastocysts, and in total 628 differentially expressed transcripts were obtained, among which, 280 transcripts are up-regulated and 348 transcripts are down-regulated in cloned blastocysts. Moreover, one statistically significant pathway associated with endoplasmic reticulum (ER) protein processing was enriched, and some ER-stress markers such as ATF4, ATF6, PDIA3, HSPA1B, HSP40 and HSP90 between cloned and IVF blastocysts were suggested. Additionally, some developmentally important genes such as lipid metabolism related genes (MGLL, DDHD2 and FADS2) and epigenetic modification genes (DNMT1, KDM5C and MBD3L5) were found differentially expressed between cloned and IVF embryos.
|
|
Received: 03 April 2014
Accepted:
|
| Fund: This study was supported by a grant from the National study was supported by a grant from the National High-Technology Research and Development Program of China (2011AA100304), and two grants from Guangdong Provincial Department of Science and Technology, China (2011A090700016 and 2011A020102003). |
|
Corresponding Authors:
WU Zhen-fang, Tel/Fax: +86-20-85280369,E-mail: wzfemail@163.com
|
| About author: XU Wei-hua, Mobile: 13859594289, E-mail: xwh131@163.com;* These authors contributed equally to this work |
Cite this article:
XU Wei-hua, LI Zi-cong, OUYANG Zhi-ping, YU Bo, SHI Jun-song, LIU De-wu, WU Zhen-fang.
2015.
RNA-Seq transcriptome analysis of porcine cloned and in vitro fertilized blastocysts. Journal of Integrative Agriculture, 14(5): 926-938.
|
| Ahner A, Brodsky J L. 2004. Checkpoints in ER-associateddegradation: excuse me, which way to the proteasome?Trends in Cell Biology, 14, 474-478Audic S, Claverie J M 1997. The significance of digital geneexpression profiles. Genome Research, 7, 986-995Bauer B K, Isom S C, Spate L D, Whitworth K M, Spollen W G,Blake S M, Springer G K, Murphy C N, Prather R S 2010.Transcriptional profiling by deep sequencing identifiesdifferences in mRNA transcript abundance in in vivo-derivedversus in vitro-cultured porcine blastocyst stage embryos.Biology of Reproduction, 83, 791-798Bendixen E, Danielsen M, Larsen K, Bendixen C. 2010.Advances in porcine genomics and proteomics-A toolboxfor developing the pig as a model organism for molecularbiomedical research. Briefings in Functional Genomics, 9,208-219Bermejo A P, Lonergan P, Rath D, Gutiérrez A A, Rizos D. 2010.Developmental kinetics and gene expression in male andfemale bovine embryos produced in vitro with sex-sortedspermatozoa. Reproduction, Fertility and Development,22, 426-436Bernardini C, Fantinati P, Zannoni A, Forni M, Tamanini C,Bacci M L. 2004. Expression of HSP70/HSC70 in swineblastocysts: effects of oxidative and thermal stress.Molecular Reproduction and Development, 69, 303-307Betthauser J, Forsberg E, Augenstein M, Childs L, EilertsenK, Enos J, Forsythe T, Golueke P, Jurgella G, KoppangR, Lesmeister T, Mallon K, Mell G, Misica P, Pace M,Pfister-Genskow M, Strelchenko N, Voelker G, Watt S,Thompson S, et al. 2000. Production of cloned pigs fromin vitro systems. Nature Biotechnology, 18, 1055-1059Brodsky J L, Wojcikiewicz R J. 2009. Substrate-specificmediators of ER associated degradation (ERAD). CurrentOpinion Cell Biology, 21, 516-521Burton G J, Yung H W, Cindrova-Davies T, Charnock-JonesD S. 2009. Placental endoplasmic reticulum stress andoxidative stress in the pathophysiology of unexplainedintrauterine growth restriction and early onset preeclampsia.Placenta, 30(Suppl A), S43-48Canepa M J, Mucci N, Kaiser G, Mutto A. 2011. Stress indicatorgenes expression pattern in bovine blastocysts productionby in vitro fertilization and somatic cell nuclear transfer.Reproduction, Fertility and Development, 24, 159.Chae J I, Lee K S, Kim D J, Han Y M, Lee D S, Lee K K, KooD B. 2009. Abnormal gene expression in extraembryonic tissue from cloned porcine embryos. Theriogenology, 71,323-333Chan M M, Smith Z D, Egli D, Regev A, Meissner A. 2012.Mouse ooplasm confers context-specific reprogrammingcapacity. Nature Genetics, 44, 978-980Ciccone D N, Su H, Hevi S, Gay F, Lei H, Bajko J, Xu G, LiE, Chen T. 2009. KDM1B is a histone H3K4 demethylaserequired to establish maternal genomic imprints. Nature,461, 415-418Esfandiari N, Falcone T, Goldberg J M, Agarwal A, Sharma RK. 2007. Heat-shock proteins modulate the incidence ofapoptosis and oxidative stress in preimplantation mouseembryos. Fertility and Sterility, 87, 1214-1217Feng C, Chen M, Xu C J, Bai L, Yin X R, Li X, Allan A C,Ferguson I B, Chen K S. 2012. Transcriptomic analysisof Chinese bayberry (Myrica rubra) fruit development andripening using RNA-Seq. BMC Genomics, 13, 19.Gil M A, Cuello C, Parrilla I, Vazquez J M, Roca J, MartinezE A. 2010. Advances in swine in vitro embryo productiontechnologies. Reproduction in Domestic Animals, 45(Suppl.2), 40-48Howell C Y, Bestor T H, Ding F, Latham K E, Mertineit C, TraslerJ M, Chaillet J R. 2001. Genomic imprinting disrupted bya maternal effect mutation in the Dnmt1 gene. Cell, 104,829-838Inoue K, Kohda T, Sugimoto M, Sado T, Ogonuki N, MatobaS, Shiura H, Ikeda R, Mochida K, Fujii T, Sawai K, OtteA P, Tian X C, Yang X , Ishino F, Abe K, Ogura A. 2010.Impeding Xist expression from the active X chromosomeimproves mouse somatic cell nuclear transfer. Science,330, 496-499Isom S C, Stevens J R, Li R, Spollen W G, Cox L, Spate L D,Murphy C N, Prather R S. 2013. Transcriptional profilingby RNA-Seq of peri-attachment porcine embryos generatedby a variety of assisted reproductive technologies.Physiological Genomics, 45, 577-589Iwase S, Lan F, Bayliss P, de la Torre-Ubieta L, Huarte M, QiH H, Whetstine J R, Bonni A, Roberts T M, Shi Y. 2007.The X-linked mental retardation gene SMCX/JARID1Cdefines a family of histone H3 lysine 4 demethylases. Cell,128, 1077-1088Jiang L, Lai L, Samuel M, Prather R S, Yang X, Tian X C. 2008.Expression of X-linked genes in deceased neonates andsurviving cloned female piglets. Molecular Reproductionand Development, 75, 265-273Kurome M, Geistlinger L, Kessler B, Zakhartchenko V, KlymiukN, Wuensch A, Richter A, Baehr A, Kraehe K, BurkhardtK, Flisikowski K, Flisikowska T, Merkl C, Landmann M,Durkovic M, Tschukes A, Kraner S, Schindelhauer D, PetriT, Kind A, et al. 2013. Factors influencing the efficiencyof generating genetically engineered pigs by nucleartransfer: multi-factorial analysis of a large data set. BMCBiotechnology, 13, 43.Lian I A, Løset M, Mundal S B, Fenstad M H, Johnson M P, EideI P, Bjørge L, Freed K A, Moses E K, Austgulen R. 2011.Increased endoplasmic reticulum stress in decidual tissuefrom pregnancies complicated by fetal growth restrictionwith and without pre-eclampsia. Placenta, 32, 823-829Li R, Yu C, Li Y, Lam T W, Yiu S M, Kristiansen K, Wang J.2009. SOAP2: An improved ultrafast tool for short readalignment. Bioinformatics, 25, 1966-1967Li Z, Shi J, Liu D, Zhou R, Zeng H, Zhou X, Mai R, ZengS, Luo L, Yu W, Zhang S, Wu Z. 2013. Effects of donorfibroblast cell type and transferred cloned embryo numberon the efficiency of pig cloning. Cellular Reprogramming,15, 35-42Macháty Z, Day B N, Prather R S. 1998. Development ofearly porcine embryos in vitro and in vivo. Biology ofReproduction, 59, 451-455Matoba S, Inoue K, Kohda T, Sugimoto M, Mizutani E, OgonukiN, Nakamura T, Abe K, Nakano T, Ishino F, Ogura A. 2011.RNAi-mediated knockdown of Xist can rescue the impairedpostimplantation development of cloned mouse embryos.Proceedings of the National Academy of Sciences of theUnited States of America, 108, 20621-20626McKeegan P J, Sturmey R G. 2011. The role of fatty acidsin oocyte and early embryo development. Reproduction,Fertility and Development, 24, 59-67Mortazavi A, Williamsm B A, McCue K, Schaeffer L, Wold B.2008. Mapping and quantifying mammalian transcriptomesby RNA-Seq. Nature Methods, 5, 621-628Onishi A, Iwamoto M, Akita T, Mikawa S, Takeda K, Awata T,Hanada H, Perry A C. 2000. Pig cloning by microinjectionof fetal fibroblast nuclei. Science, 289, 1188-1190Ooi S K, Qiu C, Bernstein E, Li K, Jia D, Yang Z, Erdjument-Bromage H, Tempst P, Lin S P, Allis C D, Cheng X, BestorT H. 2007. DNMT3L connects unmethylated lysine 4 ofhistone H3 to de novo methylation of DNA. Nature, 448,714-717Peat J R, Reik W. 2012. Incomplete methylation reprogrammingin SCNT embryos. Nature Genetics, 44, 965-966Pfister-Genskow M, Strelchenko N, Voelker G, Watt S,Thompson S, Bishop M. 2000. Production of cloned pigsfrom in vitro systems. Nature Biotechnology, 18, 1055-1059Polejaeva I A, Chen S H, Vaught T D, Page R L, Mullins J, Ball S,Dai Y, Boone J, Walker S, Ayares D L, Colman A, CampbellK H. 2000. Cloned pigs produced by nuclear transfer fromadult somatic cells. Nature, 407, 86-90Prather R S, Hawley R J, Carter D B, Lai L, Greenstein J L.2003. Transgenic swine for biomedicine and agriculture.Theriogenology, 59, 115-123Somfai T, Ozawa M, Noguchi J, Kaneko H, Karja N W, FahrudinM, Nakai M, Maedomari N, Dinnyés A, Nagai T, Kikuchi K.2008. In vitro development of polyspermic porcine oocytes:Relationship between early fragmentation and excessivenumber of penetrating spermatozoa. Animal ReproductionScience, 107, 131-147Song B S, Kim J S, Yoon S B, Lee K S, Koo D B, Lee D S,Choo Y K, Huh J W, Lee S R, Kim S U, Kim S H, Kim H M,Chang K T. 2011. Inactivated Sendai-virus-mediated fusionimproves early development of cloned bovine embryosby avoiding endoplasmic-reticulum-stress-associated apoptosis. Reproduction, Fertility and Development, 23,826-836Sturmey R G, Reis A, Leese H J, McEvoy T G. 2009. Role offatty acids in energy provision during oocyte maturationand early embryo development. Reproduction in DomesticAnimals, 44(Suppl 3), 50-58Szegezdi E, Logue S E, Gorman A M, Samali A. 2006. Mediatorsof endoplasmic reticulum stress-induced apoptosis. EMBOReports, 7, 880-885Travers K J, Patil C K, Wodicka L, Lockhart D J, WeissmanJ S, Walter P. 2000. Functional and genomic analysesreveal an essential coordination between the unfoldedprotein response and ER-associated degradation. Cell,101, 249-258Van M G, Voelker D R, Feigenson G W. 2008. Membrane lipids:where they are and how they behave. Nature ReviewsMolecular Cell Biology, 9, 112-124Whitworth K M, Agca C, Kim J G, Patel R V, Springer G K,Bivens N J, Forrester L J, Mathialagan N, Green J A, PratherR S. 2005. Transcriptional profiling of pig embryogenesisby using a 15-K member unigene set specific for pigreproductive tissues and embryos. Biology of Reproduction,72, 1437-1451Whitworth K M, Prather R S. 2010. Somatic cell nucleartransfer efficiency: how can it be improved through nuclearremodeling and reprogramming? Molecular Reproductionand Development, 77, 1001-1015Whitworth K M, Spate L D, Li R, Rieke A, Sutovsky P, GreenJ A, Prather R S. 2010. Activation method does not alterabnormal placental gene expression and development incloned pigs. Molecular Reproduction and Development,77, 1016-1030Whyte J J, Prather R S. 2011. Genetic modifications of pigsfor medicine and agriculture. Molecular Reproduction andDevelopment, 78, 879-891Wu L L, Russell D L, Norman R J, Robker R L. 2012.Endoplasmic reticulum (ER) stress in cumulus-oocytecomplexes impairs pentraxin-3 secretion, mitochondrialmembrane potential (ΔΨm), and embryo development.Molecular Endocrinology, 26, 562-573Xu W, Li Z, Yu B, He X, Shi J, Zhou R, Liu D, Wu Z. 2013.Effects of DNMT1 and HDAC inhibitors on gene-specificmethylation reprogramming during porcine somatic cellnuclear transfer. PLOS ONE, 8, e64705.Yang X, Smith S L, Tian X C, Lewin H A, Renard J P, WakayamaT. 2007. Nuclear reprogramming of cloned embryos andits implications for therapeutic cloning. Nature Genetics,39, 295-302Yang A S, Estécio M R, Doshi K, Kondo Y, Tajara E H, IssaJ P. 2004. A simple method for estimating global DNAmethylation using bisulfite PCR of repetitive DNA elements.Nucleic Acids Research, 32, e38.Yoshioka K, Suzuki C, Itoh S, Kikuchi K, Iwamura S, RodriguezM H. 2003. Production of piglets derived from in vitroproducedblastocysts fertilized and cultured in chemicallydefined media: effects of theophylline, adenosine, andcysteine during in vitro fertilization. Biology of Reproduction,69, 2092-2099Zhang J Y, Diao Y F, Oqani R K, Han R X, Jin D I. 2012.Effect of endoplasmic reticulum stress on porcine oocytematuration and parthenogenetic embryonic developmentin vitro. Biology of Reproduction, 86, 128. |
| No Suggested Reading articles found! |
|
|
Viewed |
|
|
|
Full text
|
|
|
|
|
Abstract
|
|
|
|
|
Cited |
|
|
|
|
| |
Shared |
|
|
|
|
| |
Discussed |
|
|
|
|
