Functional & Integrative Genomics

, Volume 11, Issue 1, pp 139–150 | Cite as

Transferase activity function and system development process are critical in cattle embryo development

  • Heather A. Adams
  • Bruce R. Southey
  • Robin E. Everts
  • Sadie L. Marjani
  • Cindy X. Tian
  • Harris A. Lewin
  • Sandra L. Rodriguez-Zas
Original Paper

Abstract

Microarray gene expression experiments often consider specific developmental stages, tissue sources, or reproductive technologies. This focus hinders the understanding of the cattle embryo transcriptome. To address this, four microarray experiments encompassing three developmental stages (7, 25, 280 days), two tissue sources (embryonic or extra-embryonic), and two reproductive technologies (artificial insemination or AI and somatic cell nuclear transfer or NT) were combined using two sets of meta-analyses. The first set of meta-analyses uncovered 434 genes differentially expressed between AI and NT (regardless of stage or source) that were not detected by the individual-experiment analyses. The molecular function of transferase activity was enriched among these genes that included ECE2, SLC22A1, and a gene similar to CAMK2D. Gene POLG2 was over-expressed in AI versus NT 7-day embryos and was under-expressed in AI versus NT 25-day embryos. Gene HAND2 was over-expressed in AI versus NT extra-embryonic samples at 280 days yet under-expressed in AI versus NT embryonic samples at 7 days. The second set of meta-analyses uncovered enrichment of system, organ, and anatomical structure development among the genes differentially expressed between 7- and 25-day embryos from either reproductive technology. Genes PRDX1and SLC16A1 were over-expressed in 7- versus 25-day AI embryos and under-expressed in 7- versus 25-day NT embryos. Changes in stage were associated with high number of differentially expressed genes, followed by technology and source. Genes with transferase activity may hold a clue to the differences in efficiency between reproductive technologies.

Keywords

Embryo development Gene expression Extra-embryonic tissue Cattle Reproductive technologies Meta-analysis 

Supplementary material

10142_2010_189_MOESM1_ESM.pdf (275 kb)
Supplementary Materials Table 1Comparison of gene expression between AI and NT from the individual-experiment analyses of 7-day embryos (d7E), 25-day embryos (d25E), 25-day extra-embryonic samples (d25X), and 280-day extra-embryonic samples (d280X) in the first set of meta-analyses. (PDF 275 kb)
10142_2010_189_MOESM2_ESM.pdf (224 kb)
Supplementary Materials Table 2Comparison of gene expression between AI and NT from the study-level meta-analysis (study) and sample-level meta-analysis (sample) in the first set of meta-analyses. (PDF 223 kb)
10142_2010_189_MOESM3_ESM.pdf (308 kb)
Supplemental Material Table 3Comparison of gene expression between developmental stages 7 and 25 days within AI embryos (7vs25d_AI_E), between 7 and 25 days within NT embryos (7vs25d_NT_E), between 25 and 280 days within AI extra-embryonic samples (25vs280d_AI_X), and between 25 and 280 days within NT extra-embryonic samples (25vs280d_NT_X) from the second set of meta-analyses. (PDF 307 kb)
10142_2010_189_MOESM4_ESM.pdf (222 kb)
Supplemental Material Table 4Comparison of gene expression between embryonic and extra-embryonic AI samples at 25 days (EvsX_AI_25d) and between embryonic and extra-embryonic NT samples at 25 days (EvsX_NT_25d) from the second set of meta-analyses. (PDF 221 kb)

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Copyright information

© Springer-Verlag 2010

Authors and Affiliations

  • Heather A. Adams
    • 1
  • Bruce R. Southey
    • 2
  • Robin E. Everts
    • 1
    • 3
  • Sadie L. Marjani
    • 4
  • Cindy X. Tian
    • 5
  • Harris A. Lewin
    • 1
    • 6
  • Sandra L. Rodriguez-Zas
    • 1
    • 6
    • 7
  1. 1.Department of Animal SciencesUniversity of Illinois at Urbana–ChampaignUrbanaUSA
  2. 2.Department of ChemistryUniversity of Illinois at Urbana–ChampaignUrbanaUSA
  3. 3.SEQUENOM, Inc.San DiegoUSA
  4. 4.Department of GeneticsYale University School of MedicineNew HavenUSA
  5. 5.Center for Regenerative Biology/Department of Animal ScienceUniversity of ConnecticutStorrsUSA
  6. 6.Institute for Genomic BiologyUniversity of Illinois at Urbana–ChampaignUrbanaUSA
  7. 7.Department of StatisticsUniversity of Illinois at Urbana–ChampaignChampaignUSA

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