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.

Sayyed Morteza Hosseini,Abdol Hossein Shahverdi,Hamid Reza Ghanaei,Fariba Moulavi,Mohammad Hossein Nasr-Esfahani,Farnoosh Jafarpour,Mohsen Forouzanfar,Mahdi Hajian,Marc-André Sirard,Hamid Gourbai,Isabelle Dufort,Julie Nieminen

doi:10.1186/s12864-015-2264-z

Abstract

BackgroundThe 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.ResultsTSA 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.ConclusionsThe 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-2264-z) contains supplementary material, which is available to authorized users.

Highlights

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
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 trichostatin A (TSA)
TSA treatment, but not the embryo production method, changed the distribution of cells in blastocysts as the proportion of cells allocated to the ICM and ICM/ TCN proportion, were both significantly higher in TSANT blastocysts compared to CTR-Nuclear transfer (NT) embryos

Summary

Introduction

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. Embryonic development in mammals begins in transcriptional silence [1] with an oocyte-mediated transcriptional reprogramming of parental gametes occurring during an across-the-board process of “erase-and-rebuild” [2] In this process, the parental transcription programs are erased long before (maternal) or soon after (paternal) fertilization to generate a relatively naïve zygotic chromatin upon which the transcription program of a new life cycle is rebuilt de novo after activation of the zygotic genome [2, 3]. The parental transcription programs are erased long before (maternal) or soon after (paternal) fertilization to generate a relatively naïve zygotic chromatin upon which the transcription program of a new life cycle is rebuilt de novo after activation of the zygotic genome [2, 3] Any perturbation in this process will result in ill or fatal transcriptional phenotypes of the resultant embryos [4]. It would be interesting to determine how small transcriptional aberrations translate into broad epigenetic anomalies or vice versa

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