The maternal-to-zygotic transition (MZT), involving maternal RNA and protein depletion and zygotic genome activation (ZGA), is one of the most important events during early embryogenesis.  

In zebrafish, several factors have been indicated to be essential in regulating maternal mRNA decay through maternal and zygotic pathways. However, how the stability of maternally supplied transcripts are maintained during MZT remains largely unknown.  

5-Methylcytosine (m⁵C) is a prevalent mRNA modification. A joint study led by Prof. YANG Yungui from the Beijing Institute of Genomics (BIG) of the Chinese Academy of Sciences (CAS), Prof. LIU Feng from the Institute of Zoology of CAS and Prof. MA Jinbiao from Fudan University revealed that m⁵C maintained mRNA stability through the newly identified m⁵C binding protein Ybx1 during MZT. This work was published in Molecular Cell on August 6.  

The researchers illustrated the first single-base resolution RNA m⁵C landscape in zebrafish embryos. Based on the high-throughput sequencing analyses, they found that m⁵C-modified maternal mRNAs displayed higher stability than non-m⁵C-modified mRNAs during MZT.  

Using oligo-pulldown and IP-MS combined with ITC and protein crystallography technologies, they identified that the m⁵C binding protein Ybx1 preferentially recognized m⁵C-modified mRNAs through π-π interactions with a key residue, Trp45, in Ybx1’s cold shock domain (CSD).  

Furthermore, Ybx1 deficiency led to early gastrulation arrest. Through Co-IP, GST-pulldown and high-throughput sequencing, they found that poly(A)-binding protein Pabpc1a was an interactive partner of Ybx1 in zebrafish embryos. Consistent with the results of Ybx1 deficiency, Pabpc1a depletion led to similar defective phenotypes, and meanwhile, the stability of Ybx1 target mRNAs decreased significantly.  

Finally, they used single gene reporter system to verify that Ybx1 recruits Pabpc1a to maintain the stability of maternal m⁵C-modified mRNAs and facilitate zebrafish early embryonic development. 

This work demonstrated that m⁵C modification maintained maternal mRNA stability through its binding protein Ybx1 which recruited Pabpc1a and then facilitated maternal-to-zygotic transition. 

Schematic model of the dynamic regulation of maternal mRNA stability by m5C during zebrafish MZT (Image by YANG Yungui's group)