A recent study published in Genome Biology used SLIM-seq technology to map the dynamics of RNA m6A modification during maternal-to-zygotic transition (MZT) in mice. The functions of m6A reading and writing on mouse preimplantation embryonic development were revealed through the integrated analysis of m6A sequencing, ultrasensitive proteome and translatome, and CRISPR/Cas13d-mediated gene knockdown.
This research was conducted by Zhen Liu's research group and Yidi Sun's research group at the Institute of Neuroscience, Center for Excellence in Brain Science and Intelligence Technology of the Chinese Academy of Sciences, in collaboration with Chen Li's research group at the Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine.
All animal embryos pass through the MZT which is a fundamental and conserved process, during which the maternal environment of the oocyte transitions to the zygotic genome driven expression program. This process reprograms the terminally differentiated oocyte and sperm to a state of totipotency. MZT is initiated by maternal mRNAs and proteins that are present during the period of zygotic genome quiescence after fertilization. This is followed by a gradual switch to the zygotic genome activation (ZGA) and is accompanied by the clearance of maternal RNAs and proteins.
A key question for embryonic development is how the MZT is regulated. N6-methyladenosine (m6A) is the most prevalent internal modification present in the messenger RNA (mRNA) across higher eukaryotes. It affects the stability and translation of modified transcripts, providing a mechanism for coordinated regulation of groups of transcripts mediated by writer, eraser, and reader proteins during cell fate maintenance and transitions.
Using the SLIM-seq recently developed by Dr. Haojian Zhang's group at Wuhan University (Yin et al., Cell Stem Cell, 2021), the researchers mapped RNA m6A dynamics during MZT in mice and found that m6A modifications can be maternally inherited or de novo gain during the ZGA. Analysis with translatome data published by Dr. Yi Zhang's group at Harvard University (Zhang et al., Sci Adv, 2022) showed that a group of maternally inherited and persistent m6A+ transcripts were significantly enriched for translational signaling.
With the rapid development of single-cell technologies in recent years, the single-cell or low-input genomic, transcriptomic and translatomic researches focused on mouse embryos are constantly emerging. However, the development of single-cell or low-input proteomic technologies is still relatively limited. Recently, Chen Li's research group at the Center for Single-Cell Omics, Shanghai Jiao Tong University School of Medicine developed a Comprehensive Solution of Ultrasensitive Proteome Technology (CS-UPT) for single-cell or low-input mouse embryo samples (Gu et al., bioRxiv, 2023). Here, with CS-UPT, researchers successfully identified 5,328 reliable proteins from only 20 embryos per sample. This proteomic depth is comparable to the latest embryonic proteomic resource generated from 8000 mouse embryos (Gao et al. Cell Reports, 2017). Using this deep proteomic dataset of mouse embryos, the researchers found that these m6A+ transcripts showed elevated protein abundance, thus suggesting that m6A modifications on these transcripts could potentially regulate MZT by maintaining RNA stability.
Furthermore, researchers screened for multiple m6A regulators in fertilized eggs of mouse using CRISPR/Cas13d technology, which has recently been shown to be used for embryonic gene silencing (Kushawah et al., Dev Cell, 2020), and found that knockdown of Ythdc1 and Ythdf2 significantly affected preimplantation embryonic development. Through transcriptome sequencing and RIP-qPCR experiments, the researchers confirmed that Ythdc1 can bind some maternal m6A+ transcripts and participate in their RNA stability regulation.
Figure 1. A group of maternally inherited m6A maintains mRNA stability and relates to protein translation.
This study reveals the dynamics of m6A modification during mouse MZT, identifies a few of m6A regulators involved in preimplantation embryonic development, preliminarily elucidates the possible involvement of Ythdc1 in the stability regulation of maternally inherited m6A+ transcripts, and exemplifies the importance of multi-omics analysis in embryonic development investigations.
This work entitled "Reading and writing of mRNA m6A modification orchestrate maternal-to-zygotic transition in mice" was published online in Genome Biology on April 6, 2023.
Dr. Wencheng Zhu, Dr. Yufeng Ding and graduate students Juan Meng and Wenjun Liu from the Center for Excellence in Brain Science and Intelligence Technology of the Chinese Academy of Sciences, and research assistant Lei Gu from the Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University School of Medicine are co-first authors of the paper. The research was supported by grants from the Ministry of Science and Technology, Chinese Academy of Sciences, Shanghai Municipality and China Postdoctoral Science Foundation.
Keywords: RNA m6A Dynamics; Maternal-To-Zygotic Transition; Multi-omics Analysis; Comprehensive Solution of Ultrasensitive Proteome Technology
Full-text link: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-023-02918-9
