Accession PRJCA001013
Title RNA m5C prevents maternal mRNA decay during zebrafish embryogenesis
Relevance Model organism
Data Types Epigenomics
Transcriptome or Gene expression
Organisms Danio rerio
Description The maternal-to-zygotic transition (MZT) is a conserved and fundamental progression during which the embryos undergoes dramatic reprogramming to convert the maternal environment to embryonic-driven programing. However, how the maternally supplied transcripts are dynamically regulated during MZT remains largely unknown. Herein, through genome-wide profiling of RNA 5-methylcytosine (m5C) in zebrafish early embryos, we show that m5C methylated maternal mRNAs display higher stability during MZT. We identify the Y box-binding protein 1 (Ybx1) as a novel m5C reader specifically binding to m5C-modified mRNAs through the vital amino acid Trp45 in its cold shock domain (CSD). Ybx1 is essential for maternal mRNA stability and early embryogenesis in zebrafish. Cooperated with an mRNA stabilizer Pabpc1a, Ybx1 promotes the stability of its target mRNAs in an m5C-dependent manner. Our study demonstrates a novel mechanism of RNA m5C methylation-regulated maternal mRNA stability during zebrafish MZT, highlighting the critical role of m5C mRNA methylation in early development.
Sample scope Multispecies
Release date 2019-06-12
Agency program Grant ID Grant title
National Natural Science Foundation of China (NSFC) General Program 3177079
Submitter sun    baofa  (
Organization Beijing Institute of Genomics, Chinese Academy of Sciences
Submission date 2018-08-30

Project Data

Resource name Description
BioSample (56) -
SAMC067648 RIP-BS_3hpf_Ybx1-RIP-BisSeq
SAMC067647 RIP-BS_0hpf_Ybx1-RIP-BisSeq
SAMC067646 RIP-INPUT_2hpf_rep2_Ybx1-RIP
SAMC067645 RIP-INPUT_2hpf_rep1_Ybx1-RIP
SAMC067644 RIP-INPUT_0hpf_rep2_Ybx1-RIP
SAMC067643 RIP-INPUT_0hpf_rep1_Ybx1-RIP
SAMC067642 RIP_2hpf_rep2_Ybx1-RIP
SAMC067641 RIP_2hpf_rep1_Ybx1-RIP
SAMC067640 RIP_0hpf_rep2_Ybx1-RIP
SAMC067639 RIP_0hpf_rep1_Ybx1-RIP
SAMC067638 ribo-WT_4hpf_rep2_RNA-seq
SAMC067637 ribo-WT_4hpf_rep1_RNA-seq
SAMC067636 ribo-amanitin_6hpf_rep2_RNA-seq
SAMC067635 ribo-amanitin_6hpf_rep1_RNA-seq
SAMC067634 ribo-amanitin_4hpf_rep2_RNA-seq
SAMC067633 ribo-amanitin_4hpf_rep1_RNA-seq
SAMC067632 ribo-amanitin_2hpf_rep2_RNA-seq
SAMC067631 ribo-amanitin_2hpf_rep1_RNA-seq
SAMC047056 MOpabpc1a_6hpf_rep2_RNA-seq
SAMC047055 MOpabpc1a_6hpf_rep1_RNA-seq
SAMC047054 MOpabpc1a_4hpf_rep2_RNA-seq
SAMC047053 MOpabpc1a_4hpf_rep1_RNA-seq
SAMC045548 iCLIP_4hpf_rep2_Ybx1-iCLIP
SAMC045547 iCLIP_4hpf_rep1_Ybx1-iCLIP
SAMC045546 RIP_4hpf_rep2_Ybx1-RIP
SAMC045545 RIP_4hpf_rep1_Ybx1-RIP
SAMC045544 MO_6hpf_rep2_RNA-seq
SAMC045543 MO_6hpf_rep1_RNA-seq
SAMC045542 MO_4hpf_rep2_RNA-seq
SAMC045541 MO_4hpf_rep1_RNA-seq
SAMC045540 MO_3hpf_rep2_RNA-seq
SAMC045539 MO_3hpf_rep1_RNA-seq
SAMC045538 WT_6hpf_rep2_RNA-seq
SAMC045537 WT_6hpf_rep1_RNA-seq
SAMC045536 WT_4hpf_rep2_RNA-seq
SAMC045535 WT_4hpf_rep1_RNA-seq
SAMC045534 WT_3hpf_rep2_RNA-seq
SAMC045533 WT_3hpf_rep1_RNA-seq
SAMC045532 WT_2hpf_rep2_RNA-seq
SAMC045531 WT_2hpf_rep1_RNA-seq
SAMC045530 WT_0hpf_rep2_RNA-seq
SAMC045529 WT_0hpf_rep1_RNA-seq
SAMC045528 MIX_homo_2hpf_rep2_m5C_RNA-BisSeq
SAMC045527 MIX_homo_2hpf_rep1_m5C_RNA-BisSeq
SAMC045526 MO_4hpf_rep2_m5C_RNA-BisSeq
SAMC045525 MO_4hpf_rep1_m5C_RNA-BisSeq
SAMC045524 WT_6hpf_rep2_m5C_RNA-BisSeq
SAMC045523 WT_6hpf_rep1_m5C_RNA-BisSeq
SAMC045522 WT_4hpf_rep2_m5C_RNA-BisSeq
SAMC045521 WT_4hpf_rep1_m5C_RNA-BisSeq
SAMC045520 WT_3hpf_rep2_m5C_RNA-BisSeq
SAMC045519 WT_3hpf_rep1_m5C_RNA-BisSeq
SAMC045518 WT_2hpf_rep2_m5C_RNA-BisSeq
SAMC045517 WT_2hpf_rep1_m5C_RNA-BisSeq
SAMC045516 WT_0hpf_rep2_m5C_RNA-BisSeq
SAMC045515 WT_0hpf_rep1_m5C_RNA-BisSeq
GSA (1) -
CRA001080 RNA m5C prevents maternal mRNA decay during zebrafish embryogenesis