LncRNA <i>XLOC-040580</i> targeted by <i>TPRA1</i> coordinate zygotic genome activation during porcine embryonic development

Long noncoding RNAs (lncRNAs) are crucial in porcine preimplantation embryonic development, yet their regulatory role during zygote genome activation (ZGA) is poorly understood. We analyzed transcriptome data from porcine fetal fibroblasts (PEF), induced pluripotent stem cells (iPS), and preimplantation embryos, identifying ZGA-specific lncRNAs like <i>XLOC-040580</i>, and further predicted its potentially interacting genes <i>TPRA1</i> and <i>BCL2L1</i> via co-expression network. <i>XLOC-040580</i> was knocked down by siRNA microinjection and the expression of ZGA-related genes was detected by qRT-PCR. After microinjecting siRNA targeting <i>TPRA1</i> and <i>BCL2L1</i> at the one-cell stage, we counted the blastocyst development rate. The blastocyst development rate was consistent with the results from si-XLOC-040580 after si-<i>TPRA1</i>. Through dual-luciferase reporter assays, we found that <i>XLOC-040580</i> was a downstream target of <i>TPRA1</i>. To further elucidate the mechanism of <i>XLOC-040580</i>, Single-cell mRNA sequencing after <i>XLOC-040580</i> knockdown revealed its regulatory network involved in embryonic developmental defects. Transcriptome analysis revealed that <i>XLOC-040580</i> was specifically expressed during zygote activation. Knockdown of <i>XLOC-040580</i> decreased the blastocyst development rate and reduced both the total blastocyst cell number and TE cell number. <i>TPRA1</i> and <i>BCL2L1 were</i> specifically co-expressed with <i>XLOC-040580</i> during ZGA stage, and <i>TPRA1</i> could interact with the promoter region of <i>XLOC-040580</i> and regulate its expression. Knockdown of <i>TPRA1</i> or <i>XLOC-040580</i> blocked porcine embryonic development by affecting the expression of ZGA-related genes. We found and validated that lncRNA <i>XLOC-040580</i> played a key role in the ZGA process, which was regulated by <i>TPRA1</i>. These results implied that the functional axis of <i>TPRA1</i>-<i>XLOC-040580</i>-downstream genes involved in ZGA-related functions also coordinated early embryonic development in porcine.