title: Transcriptome profiling of bovine inner cell mass and trophectoderm derived from in vivo generated blastocysts.
abstract: BACKGROUND
  This study describes the generation and analysis of the transcriptional profile of bovine inner cell mass (ICM) and trophectoderm (TE), obtained from in vivo developed embryos by using a bovine-embryo specific array (EmbryoGENE) containing 37,238 probes.
  
  
  RESULTS
  A total of 4,689 probes were differentially expressed between ICM and TE, among these, 2,380 and 2,309 probes were upregulated in ICM and TE tissues, respectively (P ≤ 0.01, FC ≥ 2.0, FDR: 2.0). Ontological classification of the genes predominantly expressed in ICM emerged a range of functional categories with a preponderance of genes involved in basal and developmental signaling pathways including P53, TGFβ, IL8, mTOR, integrin, ILK, and ELF2 signalings. Cross-referencing of microarray data with two available in vitro studies indicated a marked reduction in ICM vs. TE transcriptional difference following in vitro culture of bovine embryos. Moreover, a great majority of genes that were found to be misregulated following in vitro culture of bovine embryos were known genes involved in epigenetic regulation of pluripotency and cell differentiation including DNMT1, GADD45, CARM1, ELF5 HDAC8, CCNB1, KDM6A, PRDM9, CDX2, ARID3A, IL6, GADD45A, FGFR2, PPP2R2B, and SMARCA2. Cross-species referencing of microarray data revealed substantial divergence between bovine and mouse and human in signaling pathways involved in early lineage specification.
  
  
  CONCLUSIONS
  The transcriptional changes occur during ICM and TE lineages specification in bovine is greater than previously understood. Therefore, this array data establishes a standard to evaluate the in vitro imprint on the transcriptome and to hypothesize the cross-species differences that allow in vitro acquisition of pluripotent ICM in human and mice but hinder that process in bovine.
authors.affiliation: Department of Reproductive Biotechnology, Reproductive Biomedicine Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran. smhosseini@royaninstitute.org.|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. smhosseini@royaninstitute.org.
authors.forename: S M
authors.initials: SM
authors.lastname: Hosseini
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. Isabelle.dufort@fsaa.ulaval.ca.
authors.forename: I
authors.initials: I
authors.lastname: Dufort
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. Julieta.caballero.1@ulaval.ca.
authors.forename: J
authors.initials: J
authors.lastname: Caballero
authors.affiliation: Department of Reproductive Biotechnology, Reproductive Biomedicine Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran. f_moulavi@yahoo.com.
authors.forename: F
authors.initials: F
authors.lastname: Moulavi
authors.affiliation: Department of Reproductive Biotechnology, Reproductive Biomedicine Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran. hamidghanai@yahoo.co.uk.
authors.forename: H R
authors.initials: HR
authors.lastname: Ghanaei
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: M A
authors.initials: MA
authors.lastname: Sirard
mesh_terms: D000818:Animals; D053624:Blastocyst Inner Cell Mass / Q000166:cytology*; D002417:Cattle; D002454:Cell Differentiation / Q000235:genetics; D019070:Cell Lineage; D004475:Ectoderm / Q000166:cytology* / Q000196:embryology; D004622:Embryo, Mammalian / Q000196:embryology; D047108:Embryonic Development / Q000235:genetics; D005260:Female; D020869:Gene Expression Profiling; D018507:Gene Expression Regulation, Developmental / Q000235:genetics*; D046228:Microarray Analysis; D016133:Polymerase Chain Reaction; D014158:Transcription, Genetic / Q000235:genetics; D015533:Transcriptional Activation / Q000235:genetics; D059467:Transcriptome / Q000235:genetics*; D014327:Trophoblasts / Q000166:cytology*