Allelic reprogramming of chromatin states in human early embryos

Shenli Yuan; Lei Gao; Wenrong Tao; Jianhong Zhan; Gang Lu; Jingye Zhang; Chuanxin Zhang; Lizhi Yi; Zhenbo Liu; Zhenzhen Hou; Min Dai; Han Zhao; Zi-Jiang Chen; Jiang Liu; Keliang Wu

doi:10.1093/nsr/nwad328

Allelic reprogramming of chromatin states in human early embryos

Natl Sci Rev. 2024 Jan 2;11(3):nwad328. doi: 10.1093/nsr/nwad328. eCollection 2024 Mar.

Authors

Shenli Yuan^{1

2

3

4}, Lei Gao², Wenrong Tao^{1

5}, Jianhong Zhan^{2

3}, Gang Lu⁴, Jingye Zhang^{1

5}, Chuanxin Zhang^{1

5}, Lizhi Yi², Zhenbo Liu², Zhenzhen Hou^{1

5}, Min Dai³, Han Zhao^{1

5}, Zi-Jiang Chen^{1

5

6}, Jiang Liu^{2

3

7}, Keliang Wu^{1

5}

Affiliations

¹ Center for Reproductive Medicine, Shandong University, Jinan 250012, China.
² CAS Key Laboratory of Genome Sciences and Information, Collaborative Innovation Center of Genetics and Development, Beijing Institute of Genomics, and China National Center for Bioinformation, Chinese Academy of Sciences, Beijing 100101, China.
³ University of Chinese Academy of Sciences, Beijing 100049, China.
⁴ CUHK-SDU Joint Laboratory on Reproductive Genetics, School of Biomedical Sciences, the Chinese University of Hong Kong, Hong Kong, China.
⁵ Key Laboratory of Reproductive Endocrinology of the Ministry of Education, Shandong University, Jinan 250012, China.
⁶ Center for Reproductive Medicine, Ren Ji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200135, China.
⁷ CAS Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China.

Abstract

The reprogramming of parental epigenomes in human early embryos remains elusive. To what extent the characteristics of parental epigenomes are conserved between humans and mice is currently unknown. Here, we mapped parental haploid epigenomes using human parthenogenetic and androgenetic embryos. Human embryos have a larger portion of genome with parentally specific epigenetic states than mouse embryos. The allelic patterns of epigenetic states for orthologous regions are not conserved between humans and mice. Nevertheless, it is conserved that maternal DNA methylation and paternal H3K27me3 are associated with the repression of two alleles in humans and mice. In addition, for DNA-methylation-dependent imprinting, we report 19 novel imprinted genes and their associated germline differentially methylated regions. Unlike in mice, H3K27me3-dependent imprinting is not observed in human early embryos. Collectively, allele-specific epigenomic reprogramming is different in humans and mice.

Keywords: DNA methylation; H3K27me3; chromatin accessibility; epigenetics reprogramming; human embryo.