Regulation of zygotic gene activation by chromatin structure and epigenetic factors

Funaya, Satoshi; Aoki, Fugaku

doi:10.1262/jrd.2017-058

Cited by 17 publications

(10 citation statements)

References 60 publications

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“…Studies have shown that when chromatin reprogramming happens, regulatory factors that are associated with gene transcription and DNA recombination are recruited by chromatin [87, 88], and simultaneously the stability of nucleosome is altered [89]. During zygote gene activation, the activity of open chromatin is increased, in parallel with activities of cis -regulatory factors, which confirms that cis -regulatory elements play a significant role in early development [90, 91]. ATAC-seq has been used, together with the CRISP/Cas-9 technology, to detect mouse preimplantation embryos [61].…”

Section: Summary Of the Atac-seq Methodsmentioning

confidence: 90%

Detect accessible chromatin using ATAC-sequencing, from principle to applications

2019

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Background Chromatin accessibility is crucial for gene expression regulation in specific cells and in multiple biological processes. Assay for Transposase Accessible Chromatin with high-throughput sequencing (ATAC-seq) is an effective way to reveal chromatin accessibility at a genome-wide level. Through ATAC-seq, produced reads from a small number of cells reflect accessible regions that correspond to nucleosome positioning and transcription factor binding sites, due to probing hyperactive Tn5 transposase to DNA sequence. Conclusion In this review, we summarize both principle and features of ATAC-seq, highlight its applications in basic and clinical research. ATAC-seq has generated comprehensive chromatin accessible maps, and is becoming a powerful tool to understand dynamic gene expression regulation in stem cells, early embryos and tumors.

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Section: Summary Of the Atac-seq Methodsmentioning

confidence: 90%

Detect accessible chromatin using ATAC-sequencing, from principle to applications

2019

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“…Following fertilization, the zygotic genome is globally demethylated 6 , and this loss of DNA methylation coincides with global decreases in repressive histone modifications 5,7 . Overall, epigenetic factors linked to relaxed chromatin are more abundant in mouse zygotes, whereas factors implicated in chromatin compaction become more prevalent during EGA 8 , pointing to a more permissive chromatin landscape in pre-EGA embryos. Indeed, mouse zygotes present increased histone mobility 9 , highly dispersed chromatin 10 , and lack chromocenters (congregations of pericentromeric heterochromatin) 11,12 .…”

mentioning

confidence: 98%

Chromatin remodeling in bovine embryos indicates species-specific regulation of genome activation

Halstead

Zhou

et al. 2020

Nat Commun

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The shift from maternal to embryonic control is a critical developmental milestone in preimplantation development. Widespread transcriptomic and epigenetic remodeling facilitate this transition from terminally differentiated gametes to totipotent blastomeres, but the identity of transcription factors (TF) and genomic elements regulating embryonic genome activation (EGA) are poorly defined. The timing of EGA is species-specific, e.g., the timing of murine and human EGA differ significantly. To deepen our understanding of mammalian EGA, here we profile changes in open chromatin during bovine preimplantation development. Before EGA, open chromatin is enriched for maternal TF binding, similar to that observed in humans and mice. During EGA, homeobox factor binding becomes more prevalent and requires embryonic transcription. A cross-species comparison of open chromatin during preimplantation development reveals strong similarity in the regulatory circuitry underlying bovine and human EGA compared to mouse. Moreover, TFs associated with murine EGA are not enriched in cattle or humans, indicating that cattle may be a more informative model for human preimplantation development than mice.

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“…Minor ZGA that occurs at the one-cell stage is promiscuous and over 90% of genes (including extensive intergenic regions) are transcribed, mainly with poor splicing and 3ʹ processing. Major ZGA takes place at the two-cell stage, where less than 80% of genes are selectively transcribed, probably due to a condensed chromatin state [60]. Recently, it was confirmed that minor ZGA is critical for mouse PED [61].…”

Section: Discussionmentioning

confidence: 99%

Atypical GATA protein TRPS1 plays indispensable roles in mouse two-cell embryo

Liu

Lian

et al. 2019

Cell Cycle

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Zygotic genome activation (ZGA) is one of the most critical events at the beginning of mammalian preimplantation embryo development (PED). The mechanisms underlying mouse ZGA remain unclear although it has been widely studied. In the present study, we identified that tricho-rhinophalangeal syndrome 1 (TRPS1), an atypical GATA family member, is an important factor for ZGA in mouse PED. We found that the Trps1 mRNA level peaked at the one-cell stage while TRPS1 protein did so at the two/four-cell stage. Knockdown of Trps1 by the microinjection of Trps1 siRNA reduced the developmental rate of mouse preimplantation embryos by approximately 30%, and increased the expression of ZGA marker genes MuERV-L and Zscan4d via suppressing the expression of major histone markers H3K4me3 and H3K27me3. Furthermore, Trps1 knockdown decreased the expression of Sox2 but increased Oct4 expression. We conclude that TRPS1 may be indispensable for zygotic genome activation during mouse PED.

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Regulation of zygotic gene activation by chromatin structure and epigenetic factors

Cited by 17 publications

References 60 publications

Detect accessible chromatin using ATAC-sequencing, from principle to applications

Detect accessible chromatin using ATAC-sequencing, from principle to applications

Chromatin remodeling in bovine embryos indicates species-specific regulation of genome activation

Atypical GATA protein TRPS1 plays indispensable roles in mouse two-cell embryo

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