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In brief
How and when embryonic transcription begins following fertilization remains elusive. Asami et al. generate a high-resolution time course to reveal a
transcription program initiating within 4 h of fertilization in mouse one-cell embryos. The program predicts embryonic and cancer-associated pathway expression, and inhibiting inferred regulators acutelyblocks transcription and development.



A gene expression program, iEGA, initiates within 4 h of mouse fertilization

•Upregulated genes are normatively spliced, protein coded, and soon downregulated

•iEGA genes predict cancer-associated pathways and transcription regulators

•Inhibiting predicted transcription regulators acutely disrupts iEGA and development

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The initiation of mammalian embryonic transcription

: to begin at the biginning

Perry, A.C.F., Asami, M., Lam, B., Yeo, G.S.H.


Trends in Cell Biology


  • Our high-resolution single-cell RNA-sequencing revealed that in human embryos, transcription initiates at the one-cell stage, earlier than widely thought.

  • The new findings suggest that fertilization itself triggers transcription [embryonic genome activation (EGA)] by activating maternal transcription factors.

  • EGA mostly utilizes canonical promoters and produces normatively spliced, protein-coding transcripts.

  • The first genes expressed in the embryo predict upregulation by cancer-associated transcription factors, including MYC and MYCN, linking the onset of embryogenesis to cancer.

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Human embryonic genome activation initiates

at the one-cell stage

Asami, M*., Lam, B*., Ma, M.K., Rainbow, K., Braun, S., VerMilyea, M.D., Yeo, G.S.H. and Perry, A.C.F. 


Cell Stem Cell

In human embryos, the initiation of transcription (embryonic genome activation, EGA) occurs by the eight-cell stage, but its exact timing and profile are unclear. To address this, we profiled gene expression at depth in human metaphase II oocytes and bipronuclear (2PN) one-cell embryos. High resolution single-cell RNA sequencing revealed previously inaccessible oocyte-to-embryo gene expression changes. This confirmed transcript depletion following fertilization (maternal RNA degradation) but also uncovered low-magnitude upregulation of hundreds of spliced transcripts. Gene expression analysis predicted embryonic processes including cell cycle progression and chromosome maintenance, and transcriptional activators that included cancer-associated gene regulators. Transcription was disrupted in abnormal monopronuclear (1PN) and tripronuclear (3PN) one-cell embryos. These findings indicate that human embryonic transcription initiates at the one-cell stage, sooner than previously thought.

The pattern of gene upregulation promises to illuminate processes involved at the onset of human development, with implications for epigenetic inheritance, stem-cell-derived embryos and cancer.

GA Asami et al 2021.png

Genomic imprinting in mouse blastocysts is

predominantly associated with H3K27me3

Santini K*, Halbritter F*, Titz-Teixeira F, Suzuki T, Asami M, Ramesmayer J, Ma X, Lackner A, Warr N, Pauler F, Hippenmeyer S, Laue E, Farlik M, Bock C, Beyer A, Perry ACF & Leep M.


Nat Commun 12, 3804 (2021).

In mammalian genomes, differentially methylated regions (DMRs) and histone marks including trimethylation of histone 3 lysine 27 (H3K27me3) at imprinted genes are asymmetrically inherited to control parentally-biased gene expression. However, neither parent-of-origin-specific transcription nor imprints have been comprehensively mapped at the blastocyst stage of preimplantation development. Here, we address this by integrating transcriptomic and epigenomic approaches in mouse preimplantation embryos. We find that seventy-one genes exhibit previously unreported parent-of-origin-specific expression in blastocysts (nBiX: novel blastocyst-imprinted expressed). Uniparental expression of nBiX genes disappears soon after implantation. Micro-whole-genome bisulfite sequencing (µWGBS) of individual uniparental blastocysts detects 859 DMRs. We further find that 16% of nBiX genes are associated with a DMR, whereas most are associated with parentally-biased H3K27me3, suggesting a role for Polycomb-mediated imprinting in blastocysts. nBiX genes are clustered: five clusters contained at least one published imprinted gene, and five clusters exclusively contained nBiX genes. These data suggest that early development undergoes a complex program of stage-specific imprinting involving different tiers of regulation.

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Comparison of differential DNA methylation in uniparental blastocysts (y-axis) and parent-of-origin-specific gene expression (x-axis). Published and novel imprinted genes (nBiX and nBsX) are indicated in colour and other genes in grey. Each dot represents one gene associated with its closest DMR. Selected genes are labelled.

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Mice produced by mitotic reprogramming of sperm injected into haploid parthenogenotes

Toru Suzuki, Maki Asami, Martin Hoffmann, Xin Lu, Miodrag Guzˇvic´,

Christoph A. Klein& Anthony C.F. Perry

Nat Commun 7 (2016)

Sperm are highly differentiated and the activities that reprogram them for embryonic development during fertilization have historically been considered unique to the oocyte.

We here challenge this view and demonstrate that mouse embryos in the mitotic cell cycle can also directly reprogram sperm for full-term development. Developmentally incompetent haploid embryos (parthenogenotes) injected with sperm developed to produce healthy offspring at up to 24% of control rates, depending when in the embryonic cell cycle injection took place. This implies that most of the first embryonic cell cycle can be bypassed in sperm genome reprogramming for full development. Remodelling of histones and genomic 50-methylcytosine and 50-hydroxymethylcytosine following embryo injection were distinct from remodelling in fertilization and the resulting 2-cell embryos consistently possessed abnormal transcriptomes. These studies demonstrate plasticity in the reprogramming of terminally differentiated sperm nuclei and suggest that different epigenetic pathways or kinetics can establish totipotency.

A two cell embryo created using phICSI.

Fluorescence image (BrdU, maternal genome; PI, both genomes) show 2+1 class of nuclear configuration 14h after the first mitotic division (1C --> 2C) in phICSI-13 embryo.

White arrowhead: paternal chromatin.

A program of successive gene expression in mouse one-cell embryos

Maki Asami, Brian Y.H. Lam, Martin Hoffmann, Toru Suzuki, Xin Lu, Naoko Yoshida, Marcella K. Ma,
Kara Rainbow, Miodrag Guzvic, Matthew D. VerMilyea, Giles S.H. Yeo, Christoph A. Klein

and Anthony C.F. Perry


Cell Reports

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