Biology subjects

Cabrera Quio, L. E.

Publications and source records attributed to Cabrera Quio, L. E..

3 recordsLinked to original sources

bioRxiv2022

SLAMseq resolves the kinetics of maternal and zygotic gene expression in early zebrafish embryogenesis

The maternal-to-zygotic transition (MZT) is a key developmental process in metazoan embryos that involves the activation of zygotic transcription (ZGA) and degradation of maternal transcripts. We employed metabolic mRNA sequencing (SLAMseq) to deconvolute the compound embryonic transcriptome in zebrafish. While mitochondrial zygotic transcripts prevailed prior to MZT, we uncover the spurious transcription of hundreds of short and intron-poor nuclear genes as early as the 2-cell stage. Upon ZGA, most zygotic transcripts originate from thousands of maternal-zygotic (MZ) genes that are transcribed at rates comparable to those of hundreds of purely zygotic genes and replenish maternal mRNAs at distinct timescales. Rapid replacement of MZ transcripts involves transcript decay features unrelated to major maternal degradation pathways and promotes de novo synthesis of the core gene expression machinery by increasing poly(A)-tail length and translation efficiency. SLAMseq hence provides unprecedented insights into the timescales, molecular features and regulation of MZT during zebrafish embryogenesis.

developmental biology↗

bioRxiv2021

Reciprocal zebrafish-medaka hybrids reveal maternal control of zygotic genome activation timing

The sperm and egg contribute unequally to the newly formed zygote. While the sperm provides mainly paternal DNA, the egg provides both maternal DNA and the bulk of the future embryonic cytoplasm. Most embryonic processes like the onset of zygotic transcription are thought to depend on maternal cytoplasmic components, but this has not been tested rigorously. Here we report the establishment of a reciprocal zebrafish-medaka hybrid system which enables unequivocal distinction between maternal and paternal gene products. By combining expression of zebrafish Bouncer on the medaka egg with artificial egg activation, we demonstrate the in vitro generation of paternal zebrafish/maternal medaka (reripes) hybrid embryos. These hybrids complement the previously reported paternal medaka/maternal zebrafish (latio) hybrid embryos1, providing a versatile tool to dissect parental control mechanisms during early development. With this system, we investigated maternal vs. paternal control of zygotic genome activation (ZGA) timing. RNA-seq and ATAC-seq analyses of the purebred fish species and hybrids revealed that the onset of ZGA is primarily governed by the egg. Combining these datasets with proteome-wide analysis of early medaka and zebrafish embryogenesis highlights new potential regulators of ZGA, including Znf281b. Overall, our study establishes the reciprocal zebrafish-medaka hybrid system as a versatile tool to study parent-of-origin effects in vertebrate embryos.

developmental biology↗

bioRxiv2020

Zebrafish Ski7 tunes RNA levels during the oocyte-to-embryo transition

Post-transcriptional mechanisms are crucial for the regulation of gene expression. These mechanisms are particularly important during rapid developmental transitions such as the oocyte-to-embryo transition, which is characterized by dramatic changes to the developmental program in the absence of nuclear transcription. Under these conditions, changes to the RNA content are solely dependent on RNA degradation. Although several mechanisms that promote RNA decay during embryogenesis have been identified, it remains unclear which cellular machineries contribute to remodeling the maternal transcriptome during the oocyte-to-embryo transition. Here, we focused on the auxiliary 3-to-5 degradation factor Ski7 in zebrafish as its mRNA peaks during this time frame. Homozygous ski7 mutant fish were viable and developed into morphologically normal adults, yet they had decreased fertility. Consistent with the idea that Ski7 participates in remodeling the transcriptome during the oocyte-to-embryo transition, transcriptome profiling identified stage-specific mRNA targets of Ski7. Genes upregulated in ski7 mutants were generally lowly expressed in wild type, suggesting that Ski7 maintains low transcript levels for this subset of genes. GO enrichment analyses of genes mis-regulated in ski7 mutants implicated Ski7 in the regulation of redox processes. This was confirmed experimentally by an increased resistance of ski7 mutant embryos to reductive stress. Overall, our results provide first insights into the physiological role of vertebrate Ski7 as an important post-transcriptional regulator during the oocyte-to-embryo transition.

developmental biology↗