Nuclear transfer efficiency in the pig is low and is thought to be caused by inadequate nuclear reprogramming. The objective of this study was to identify differentially represented transcripts in pig in vivo derived (BLIVV), in vitro fertilized (BLIVF), or nuclear transfer derived (NT, three different activation methods) blastocyst stage embryos and the donor cell line by microarray analysis, and to determine if treatment of reconstructed embryos with the histone deacetylase inhibitor, Scriptaid (NTS), for 14 h postactivation would correct gene expression in a subset of the identified aberrantly reprogrammed transcripts. There were 1481 differentially expressed transcripts when comparing all six treatment groups (p < 0.05). Transcripts that were different between BLIVV and NT (p < 0.20) and significantly different from donor cells (p < 0.05) were classified as being aberrantly reprogrammed (179 transcripts). Fourteen transcripts were chosen to determine the effect of Scriptaid treatment. After real-time PCR relative gene expression was compared among BLIVV, NT pool, cells, and NTS by the comparative Ct method, statistical analysis was performed in SAS 9.1 (p < 0.05). NTS embryos had three transcripts returning to the same level as BLIVV (H3F3A, CAPG, and SEPT7). Half of the transcripts (7/14) were not affected by NTS treatment, for example, SIRT1 and H1F0. Scriptaid treatment resulted high expression of COX5A and very low expression of GPD1L, EIF3E, and GSTA3. Scriptaid also reduced the number of 5-Methylcytidine-positive nuclei in blastocyst stage embryos (p < 0.0003). Scriptaid treatment significantly affected gene expression in 7 of the 14 transcripts evaluated and returned 3 genes to BLIVV levels.
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