title: Epigenetic modification with trichostatin A does not correct specific errors of somatic cell nuclear transfer at the transcriptomic level; highlighting the non-random nature of oocyte-mediated reprogramming errors.
abstract: BACKGROUND
  The limited duration and compromised efficiency of oocyte-mediated reprogramming, which occurs during the early hours following somatic cell nuclear transfer (SCNT), may significantly interfere with epigenetic reprogramming, contributing to the high incidence of ill/fatal transcriptional phenotypes and physiological anomalies occurring later during pre- and post-implantation events. A potent histone deacetylase inhibitor, trichostatin A (TSA), was used to understand the effects of assisted epigenetic modifications on transcriptional profiles of SCNT blastocysts and to identify specific or categories of genes affected.
  
  
  RESULTS
  TSA improved the yield and quality of in vitro embryo development compared to control (CTR-NT). Significance analysis of microarray results revealed that of 37,238 targeted gene transcripts represented on the microarray slide, a relatively small number of genes were differentially expressed in CTR-NT (1592 = 4.3 %) and TSA-NT (1907 = 5.1 %) compared to IVF embryos. For both SCNT groups, the majority of downregulated and more than half of upregulated genes were common and as much as 15 % of all deregulated transcripts were located on chromosome X. Correspondence analysis clustered CTR-NT and IVF transcriptomes close together regardless of the embryo production method, whereas TSA changed SCNT transcriptome to a very clearly separated cluster. Ontological classification of deregulated genes using IPA uncovered a variety of functional categories similarly affected in both SCNT groups with a preponderance of genes required for biological processes. Examination of genes involved in different canonical pathways revealed that the WNT and FGF pathways were similarly affected in both SCNT groups. Although TSA markedly changed epigenetic reprogramming of donor cells (DNA-methylation, H3K9 acetylation), reconstituted oocytes (5mC, 5hmC), and blastocysts (DNA-methylation, H3K9 acetylation), these changes did not recapitulate parallel marked changes in chromatin remodeling, and nascent mRNA and OCT4-EGFP expression of TSA-NT vs. CRT-NT embryos.
  
  
  CONCLUSIONS
  The results obtained suggest that despite the extensive reprogramming of donor cells that occurred by the blastocyst stage, SCNT-specific errors are of a non-random nature in bovine and are not responsive to epigenetic modifications by TSA.
authors.affiliation: Department of Reproduction and Development, Reproductive Biomedicine Centre, Royan Institute for Biotechnology, ACECR, Isfahan, Iran. smhosseini@royaninstitute.org.|Department of Genetics, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran. smhosseini@royaninstitute.org.
authors.forename: Sayyed Morteza
authors.initials: SM
authors.lastname: Hosseini
authors.affiliation: Department of Genetics, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran. Isabelle.Dufort@fsaa.ulaval.ca.
authors.forename: Isabelle
authors.initials: I
authors.lastname: Dufort
authors.affiliation: Department of Genetics, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran. julie.nieminen@fssa.ulaval.ca.
authors.forename: Julie
authors.initials: J
authors.lastname: Nieminen
authors.affiliation: Department of Reproduction and Development, Reproductive Biomedicine Centre, Royan Institute for Biotechnology, ACECR, Isfahan, Iran. f_moulavi@yahoo.com.
authors.forename: Fariba
authors.initials: F
authors.lastname: Moulavi
authors.affiliation: Department of Reproduction and Development, Reproductive Biomedicine Centre, Royan Institute for Biotechnology, ACECR, Isfahan, Iran. hamidghanai@yahoo.co.uk.
authors.forename: Hamid Reza
authors.initials: HR
authors.lastname: Ghanaei
authors.affiliation: Department of Reproduction and Development, Reproductive Biomedicine Centre, Royan Institute for Biotechnology, ACECR, Isfahan, Iran. mehdihajian2002@gmail.com.
authors.forename: Mahdi
authors.initials: M
authors.lastname: Hajian
authors.affiliation: Department of Reproduction and Development, Reproductive Biomedicine Centre, Royan Institute for Biotechnology, ACECR, Isfahan, Iran. farnoosh19792002@yahoo.com.
authors.forename: Farnoosh
authors.initials: F
authors.lastname: Jafarpour
authors.affiliation: Department of Reproduction and Development, Reproductive Biomedicine Centre, Royan Institute for Biotechnology, ACECR, Isfahan, Iran. mforozanfar@yahoo.com.
authors.forename: Mohsen
authors.initials: M
authors.lastname: Forouzanfar
authors.affiliation: Department of Genetics, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran. gourbai@royaninstitute.org.
authors.forename: Hamid
authors.initials: H
authors.lastname: Gourbai
authors.affiliation: Department of Genetics, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran. Shahverdi@royaninstitute.org.
authors.forename: Abdol Hossein
authors.initials: AH
authors.lastname: Shahverdi
authors.affiliation: Department of Reproduction and Development, Reproductive Biomedicine Centre, Royan Institute for Biotechnology, ACECR, Isfahan, Iran. mh.nasr-esfahani@royaninstitute.org.|Department of Genetics, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran, Iran. mh.nasr-esfahani@royaninstitute.org.
authors.forename: Mohammad Hossein
authors.initials: MH
authors.lastname: Nasr-Esfahani
authors.affiliation: Centre de Recherche en Biologie de la Reproduction, Faculté des Sciences de l'Agriculture et de l'Alimentation, Département des Sciences Animales, Pavillon INAF, Université Laval, Québec, QC, G1V 0A6, Canada. Marc-Andre.Sirard@fsaa.ulaval.ca.
authors.forename: Marc-André
authors.initials: MA
authors.lastname: Sirard
mesh_terms: D000818:Animals; D001755:Blastocyst / Q000187:drug effects; D002417:Cattle; D065150:Cellular Reprogramming / Q000187:drug effects / Q000235:genetics*; D042002:Chromatin Assembly and Disassembly / Q000187:drug effects / Q000235:genetics; D019175:DNA Methylation / Q000187:drug effects / Q000235:genetics*; D047108:Embryonic Development / Q000235:genetics; D044127:Epigenesis, Genetic / Q000235:genetics; D005307:Fertilization in Vitro; D006877:Hydroxamic Acids / Q000008:administration & dosage*; D046228:Microarray Analysis; D053652:Nuclear Transfer Techniques; D009865:Oocytes / Q000187:drug effects / Q000254:growth & development; D059467:Transcriptome / Q000235:genetics*; D060449:Wnt Signaling Pathway / Q000187:drug effects / Q000235:genetics
chemical_list: D006877:Hydroxamic Acids; C012589:trichostatin A