Single cell RNA-seq reveals genes vital to in vitro fertilized embryos and parthenotes in pigs

Abstract Successful early embryo development requires the correct reprogramming and configuration of gene networks by the timely and faithful execution of zygotic genome activation (ZGA). However, the regulatory principle of molecular elements and circuits fundamental to embryo development remains l...

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Autores principales:	Zhi-Qiang Du, Hao Liang, Xiao-Man Liu, Yun-Hua Liu, Chonglong Wang, Cai-Xia Yang
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/7a4f98bb1bc14779aeb4d09e34ad330b
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spelling	oai:doaj.org-article:7a4f98bb1bc14779aeb4d09e34ad330b2021-12-02T15:33:12ZSingle cell RNA-seq reveals genes vital to in vitro fertilized embryos and parthenotes in pigs10.1038/s41598-021-93904-32045-2322https://doaj.org/article/7a4f98bb1bc14779aeb4d09e34ad330b2021-07-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-93904-3https://doaj.org/toc/2045-2322Abstract Successful early embryo development requires the correct reprogramming and configuration of gene networks by the timely and faithful execution of zygotic genome activation (ZGA). However, the regulatory principle of molecular elements and circuits fundamental to embryo development remains largely obscure. Here, we profiled the transcriptomes of single zygotes and blastomeres, obtained from in vitro fertilized (IVF) or parthenogenetically activated (PA) porcine early embryos (1- to 8-cell), focusing on the gene expression dynamics and regulatory networks associated with maternal-to-zygote transition (MZT) (mainly maternal RNA clearance and ZGA). We found that minor and major ZGAs occur at 1-cell and 4-cell stages for both IVF and PA embryos, respectively. Maternal RNAs gradually decay from 1- to 8-cell embryos. Top abundantly expressed genes (CDV3, PCNA, CDR1, YWHAE, DNMT1, IGF2BP3, ARMC1, BTG4, UHRF2 and gametocyte-specific factor 1-like) in both IVF and PA early embryos identified are of vital roles for embryo development. Differentially expressed genes within IVF groups are different from that within PA groups, indicating bi-parental and maternal-only embryos have specific sets of mRNAs distinctly decayed and activated. Pathways enriched from DEGs showed that RNA associated pathways (RNA binding, processing, transport and degradation) could be important. Moreover, mitochondrial RNAs are found to be actively transcribed, showing dynamic expression patterns, and for DNA/H3K4 methylation and transcription factors as well. Taken together, our findings provide an important resource to investigate further the epigenetic and genome regulation of MZT events in early embryos of pigs.Zhi-Qiang DuHao LiangXiao-Man LiuYun-Hua LiuChonglong WangCai-Xia YangNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-13 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Zhi-Qiang Du Hao Liang Xiao-Man Liu Yun-Hua Liu Chonglong Wang Cai-Xia Yang Single cell RNA-seq reveals genes vital to in vitro fertilized embryos and parthenotes in pigs
description	Abstract Successful early embryo development requires the correct reprogramming and configuration of gene networks by the timely and faithful execution of zygotic genome activation (ZGA). However, the regulatory principle of molecular elements and circuits fundamental to embryo development remains largely obscure. Here, we profiled the transcriptomes of single zygotes and blastomeres, obtained from in vitro fertilized (IVF) or parthenogenetically activated (PA) porcine early embryos (1- to 8-cell), focusing on the gene expression dynamics and regulatory networks associated with maternal-to-zygote transition (MZT) (mainly maternal RNA clearance and ZGA). We found that minor and major ZGAs occur at 1-cell and 4-cell stages for both IVF and PA embryos, respectively. Maternal RNAs gradually decay from 1- to 8-cell embryos. Top abundantly expressed genes (CDV3, PCNA, CDR1, YWHAE, DNMT1, IGF2BP3, ARMC1, BTG4, UHRF2 and gametocyte-specific factor 1-like) in both IVF and PA early embryos identified are of vital roles for embryo development. Differentially expressed genes within IVF groups are different from that within PA groups, indicating bi-parental and maternal-only embryos have specific sets of mRNAs distinctly decayed and activated. Pathways enriched from DEGs showed that RNA associated pathways (RNA binding, processing, transport and degradation) could be important. Moreover, mitochondrial RNAs are found to be actively transcribed, showing dynamic expression patterns, and for DNA/H3K4 methylation and transcription factors as well. Taken together, our findings provide an important resource to investigate further the epigenetic and genome regulation of MZT events in early embryos of pigs.
format	article
author	Zhi-Qiang Du Hao Liang Xiao-Man Liu Yun-Hua Liu Chonglong Wang Cai-Xia Yang
author_facet	Zhi-Qiang Du Hao Liang Xiao-Man Liu Yun-Hua Liu Chonglong Wang Cai-Xia Yang
author_sort	Zhi-Qiang Du
title	Single cell RNA-seq reveals genes vital to in vitro fertilized embryos and parthenotes in pigs
title_short	Single cell RNA-seq reveals genes vital to in vitro fertilized embryos and parthenotes in pigs
title_full	Single cell RNA-seq reveals genes vital to in vitro fertilized embryos and parthenotes in pigs
title_fullStr	Single cell RNA-seq reveals genes vital to in vitro fertilized embryos and parthenotes in pigs
title_full_unstemmed	Single cell RNA-seq reveals genes vital to in vitro fertilized embryos and parthenotes in pigs
title_sort	single cell rna-seq reveals genes vital to in vitro fertilized embryos and parthenotes in pigs
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/7a4f98bb1bc14779aeb4d09e34ad330b
work_keys_str_mv	AT zhiqiangdu singlecellrnaseqrevealsgenesvitaltoinvitrofertilizedembryosandparthenotesinpigs AT haoliang singlecellrnaseqrevealsgenesvitaltoinvitrofertilizedembryosandparthenotesinpigs AT xiaomanliu singlecellrnaseqrevealsgenesvitaltoinvitrofertilizedembryosandparthenotesinpigs AT yunhualiu singlecellrnaseqrevealsgenesvitaltoinvitrofertilizedembryosandparthenotesinpigs AT chonglongwang singlecellrnaseqrevealsgenesvitaltoinvitrofertilizedembryosandparthenotesinpigs AT caixiayang singlecellrnaseqrevealsgenesvitaltoinvitrofertilizedembryosandparthenotesinpigs
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Single cell RNA-seq reveals genes vital to in vitro fertilized embryos and parthenotes in pigs

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