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

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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.

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Acknowledgements

Sincere appreciation is expressed to Dr. Rudi Appels for advice and editorial suggestions.

Funding

The support of the David H. and Norraine A. Baker Graduate Fellowship in Animal Sciences (HA Adams), NCI (Grant Number: 1R03CA143975), and NIH/NIDA (Grant Number: R21DA027548 and P30DA018310) (SL Rodriguez-Zas, BR Southey) are greatly appreciated.

Author information

Author notes

  1. Robin E. Everts

    Present address: SEQUENOM, Inc., San Diego, CA, USA

Authors and Affiliations

  1. Department of Animal Sciences, University of Illinois at Urbana–Champaign, Urbana, IL, USA

    Heather A. Adams, Robin E. Everts, Harris A. Lewin & Sandra L. Rodriguez-Zas

  2. Department of Chemistry, University of Illinois at Urbana–Champaign, Urbana, IL, USA

    Bruce R. Southey

  3. Department of Genetics, Yale University School of Medicine, New Haven, CT, USA

    Sadie L. Marjani

  4. Center for Regenerative Biology/Department of Animal Science, University of Connecticut, Storrs, CT, USA

    Cindy X. Tian

  5. Institute for Genomic Biology, University of Illinois at Urbana–Champaign, Urbana, IL, USA

    Harris A. Lewin & Sandra L. Rodriguez-Zas

  6. Department of Statistics, University of Illinois at Urbana–Champaign, Champaign, IL, USA

    Sandra L. Rodriguez-Zas

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  1. Heather A. Adams
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Corresponding author

Correspondence to Sandra L. Rodriguez-Zas.

Electronic supplementary materials

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Supplementary Materials Table 1

Comparison 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)

Supplementary Materials Table 2

Comparison 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)

Supplemental Material Table 3

Comparison 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)

Supplemental Material Table 4

Comparison 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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Adams, H.A., Southey, B.R., Everts, R.E. et al. Transferase activity function and system development process are critical in cattle embryo development. Funct Integr Genomics 11, 139–150 (2011). https://doi.org/10.1007/s10142-010-0189-9

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