Transcriptomic Features of Bovine Blastocysts Derived by Somatic Cell Nuclear Transfer.
Reprogramming incompletely occurs in most somatic cell nuclear transfer (SCNT) embryos, which results in misregulation of developmentally important genes and subsequent embryonic malfunction and lethality. Here we examined transcriptome profiles in single bovine blastocysts derived by in vitro fertilization (IVF) and SCNT. Different types of donor cells, cumulus cell and ear-skin fibroblast, were used to derive cSCNT and fSCNT blastocysts, respectively. SCNT blastocysts expressed 13,606 genes on average, similar to IVF (13,542). Correlation analysis found that both cSCNT and fSCNT blastocyst groups had transcriptomic features distinctive from the IVF group, with the cSCNT transcriptomes closer to the IVF ones than the fSCNT. Gene expression analysis identified 56 underrepresented and 78 overrepresented differentially expressed genes in both SCNT groups. A 400-kb locus harboring zinc-finger protein family genes in chromosome 18 were found coordinately down-regulated in fSCNT blastocysts, showing a feature of reprogramming-resistant regions. Probing into different categories of genes important for blastocyst development revealed that genes involved in trophectoderm development frequently were underrepresented, and those encoding epigenetic modifiers tended to be overrepresented in SCNT blastocysts. Our effort to identify reprogramming-resistant, differentially expressed genes can help map reprogramming error-prone loci onto the genome and elucidate how to handle the stochastic events of reprogramming to improve cloning efficiency.
Development and Differentiation Research Center, KRIBB, 125 Gwahak-ro, Yuseong-gu, Daejeon, 305-806, South Korea Department of Functional Genomics, University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, 305-350, South Korea.
Byungkuk
http://orcid.org/0000-0002-5419-6964
B
Min
Development and Differentiation Research Center, KRIBB, 125 Gwahak-ro, Yuseong-gu, Daejeon, 305-806, South Korea Department of Functional Genomics, University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, 305-350, South Korea.
Sunwha
S
Cho
Development and Differentiation Research Center, KRIBB, 125 Gwahak-ro, Yuseong-gu, Daejeon, 305-806, South Korea.
Jung Sun
JS
Park
Department of Bioinformatics, University of Science and Technology (UST), 217 Gajeong-ro Yuseong-gu, Daejeon, 305-350, South Korea Korean Bioinformation Center, KRIBB, 125 Gwahak-ro, Yuseong-gu, Daejeon, 305-806, South Korea.
Yun-Gyeong
YG
Lee
Department of Bioinformatics, University of Science and Technology (UST), 217 Gajeong-ro Yuseong-gu, Daejeon, 305-350, South Korea Korean Bioinformation Center, KRIBB, 125 Gwahak-ro, Yuseong-gu, Daejeon, 305-806, South Korea.
Namshin
N
Kim
Development and Differentiation Research Center, KRIBB, 125 Gwahak-ro, Yuseong-gu, Daejeon, 305-806, South Korea Department of Functional Genomics, University of Science and Technology (UST), 217 Gajeong-ro, Yuseong-gu, Daejeon, 305-350, South Korea ykkang@kribb.re.kr.
Yong-Kook
YK
Kang
D000818:Animals; D001755:Blastocyst / Q000378:metabolism*; D002417:Cattle; D065150:Cellular Reprogramming; D019976:Cloning, Organism; D016000:Cluster Analysis; D005307:Fertilization in Vitro; D020869:Gene Expression Profiling; D018507:Gene Expression Regulation, Developmental; D053652:Nuclear Transfer Techniques; D059467:Transcriptome
RNA-seq; SCNT; bovine blastocyst; development; transcriptomes