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A single-cell map of maternal and zygotic mRNA dynamics during cell-type specification in zebrafish embryos [scSLAM-seq]

ABSTRACT: A single-cell map of maternal and zygotic mRNA dynamics during cell-type specification in zebrafish embryos [scSLAM-seq]

PROVIDER: PRJNA934545 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR23380800.fastq.gz	Fastqsanger.gz
	SRR23380801.fastq.gz	Fastqsanger.gz
	SRR23380802.fastq.gz	Fastqsanger.gz
	SRR23380803.fastq.gz	Fastqsanger.gz
	SRR23380804.fastq.gz	Fastqsanger.gz

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A single-cell map of maternal and zygotic mRNA dynamics during cell-type specification in zebrafish embryos [scSLAM-seq]

Project description:During early embryogenesis, embryos undergo a massive degradation of maternally inherited mRNAs and produce new zygotic transcripts. This maternal-to-zygotic transition requires a tight interplay of mRNA transcription and degradation, but distinguishing their unique contributions remains a challenge. Here, we dissect gene regulation during the zebrafish maternal-to-zygotic transition by combining single-cell RNA-sequencing with RNA metabolic labeling and nucleotide conversion within zebrafish embryos. We decompose single-cell transcriptomes into their new (zygotic) and old (maternal) mRNA components, and elicit critical information on gene regulation as it unfolds over both time and space. We show that most cell-type restricted expression arises by zygotic transcription, but distinguish a specific role for maternal transcripts in defining germ-cell and enveloping-layer identity, two earliest specified cell identities. We recover the underlying replacement between maternal and zygotic copies of embryonic genes with a relatively constant overall mRNA level, and associate a fast replacement with genes that has a restricted zygotic expression in either cell-type or time. Our study provides a valuable resource to investigate maternal and zygotic transcriptomes and reveals post-transcriptional events that control gene regulation during early embryogenesis.

2023-05-11 | GSE224918 | GEO

A single-cell map of maternal and zygotic mRNA dynamics during cell-type specification in zebrafish embryos [SLAM-seq]

2023-05-11 | GSE224113 | GEO

A single-cell map of maternal and zygotic mRNA dynamics during cell-type specification in zebrafish embryos

Project description:A single-cell map of maternal and zygotic mRNA dynamics during cell-type specification in zebrafish embryos

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A single-cell map of maternal and zygotic mRNA dynamics during cell-type specification in zebrafish embryos [SLAM-seq]

Project description:A single-cell map of maternal and zygotic mRNA dynamics during cell-type specification in zebrafish embryos [SLAM-seq]

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A low-input proteomic analysis of mouse maternal-to-zygotic transition

Project description:Maternal-to-zygotic transition (MZT) is a conserved and fundamental process during which the maternal environment of oocyte transits to the zygotic genome driven expression program, and terminally differentiated oocyte and sperm are reprogrammed to totipotency. It is initiated by maternal mRNAs and proteins during the period of zygotic genome quiescence after fertilization, followed by a gradual switch to zygotic genome activation and accompanied by clearance of maternal RNAs and proteins. A key question for embryonic development is how MZT process is regulated. Here we used a low-input proteomic analysis to measure the proteomic dynamics during early development of mouse maternal-to-zygotic transition.

2023-03-27 | PXD041023 | Pride

Quantitative proteomics reveals the dynamic proteome landscape of zebrafish embryos during maternal-to-zygotic transition and its relationship to zygotic genome activation

Project description:Upon fertilization, the embryonic genome remains transcriptionally inactive until the mid-blastula transition. Zygotic genome activation (ZGA) of vertebrate embryos has been extensively studied using nucleic acid-based strategies, but proteomics data are still scarce, impeding the full mechanistic understanding of how ZGA is executed during the maternal-to-zygotic transition (MZT). Here, we performed quantitative proteomics to decipher the proteome landscape of zebrafish embryos during the MZT, quantifying nearly 5,000 proteins across four embryonic stages. The stage-specific clustering based on protein expression pattern revealed that helicases (i.e., eif4a2 and ruvbl1) facilitate pluripotency factors (i.e., nanog, pou5f3, ctcf, and hmga1) triggering ZGA in zebrafish, accompanied by the maternal product decay with P-bodies and ubiquitin dependent proteolytic pathway. Dozens of transcription factors show wave-like expression patterns during MZT, implying their diverse functions in triggering the ZGA and modulating differentiation for organ development. The combination of morpholino knockdown and quantitative proteomics demonstrated that maternal Nanog is required for proper embryogenesis by regulating 1) interactions with other pluripotency factors, 2) F-actin band formation, 3) cell cycle checkpoints and 4) maternal product degradation. This study represents the most systematic proteomics survey of developmentally regulated proteins and their expression profiles accompanying MZT in zebrafish, which is a valuable proteome resource for understanding ZGA.

2024-05-01 | PXD036678 | Pride

Nanog, SoxB1 and Pou5f1/Oct4 regulate widespread zygotic gene activation during the maternal-to-zygotic transition

Project description:Upon fertilization, maternal factors direct development in a transcriptionally silent embryo. At the maternal-to-zygotic transition (MZT), a universal step in animal development, unknown maternal factors trigger zygotic genome activation (ZGA). In zebrafish, ZGA is required for gastrulation and clearance of maternal mRNAs, which is achieved in part by the conserved microRNA miR-430. However, the precise factors that activate the zygotic program remain largely unknown. Here we show that Nanog, Pou5f1 and SoxB1 are required for genome activation in zebrafish. We identified several hundred genes directly activated by maternal factors, thus constituting the first wave of zygotic transcription in zebrafish. Ribosome profiling in the pre-MZT embryo revealed that nanog, sox19b and pou5f1 are the most highly translated transcription factor mRNAs. Combined loss of function for Nanog, SoxB1 and Pou5f1 resulted in developmental arrest prior to gastrulation, and a failure to activate >75% of zygotic genes. Furthermore, we found that Nanog binds the miR-430 locus and together with Pou5f1 and SoxB1 initiate miR-430 expression and activity. Our results demonstrate that maternal Nanog, Pou5f1 and SoxB1 are required to initiate the zygotic developmental program and in turn trigger the clearance of the maternal program by activating miR-430 expression. Wild type and loss-of-function total mRNA sequencing of embryonic transcriptomes pre- and post-MZT; ribosome profiling pre-MZT

2013-09-22 | E-GEOD-47558 | biostudies-arrayexpress

Transcriptome analysis of wild-type and maternal zygotic double mutant of nup85;nup133 zebrafish embryos during early development

Project description:To study the function of zebrafish nuclear pores during early embryogenesis, we generated maternal zygotic double mutant of nup85;nup133 (MZnup85;nup133) using CRISPR/Cas9 and report the transcriptome-wide changes in comparison to wild-type (WT) embryos. Our analysis reveals a dramatic delay of maternal mRNA degradation and zygotic genome activation in MZnup85;nup133 embryos during maternal-to-zygotic transition.

2023-03-04 | GSE146394 | GEO

Germ cell-specific eIF4E1b regulates maternal mRNA translation to ensure zygotic genome activation

Project description:Translation of maternal mRNAs is detected before transcription of zygotic genes and is essential for mammalian embryo development. How certain maternal mRNAs are selected for translation instead of degradation and how this burst of translation affects zygotic genome activation remain unknown. Using gene-edited mice, we document that the oocyte-specific eukaryotic translation initiation factor 4E family member 1b (eIF4E1b) is the regulator of maternal mRNA expression that ensures subsequent reprogramming of the zygotic genome. In oocytes, eIF4E1b binds to transcripts encoding translation machinery proteins, chromatin remodelers, and reprogramming factors to promote their translation in zygotes and protect them from degradation. The protein products are thought to establish an open chromatin landscape in one-cell zygotes to enable transcription of genes required for cleavage stage development. Our results define a program for rapid resetting of the zygotic epigenome that is regulated by maternal mRNA expression and provide new insights into the mammalian maternal-to-zygotic transition. This SuperSeries is composed of the SubSeries listed below.

2023-06-07 | GSE180218 | GEO

Ultrasensitive proteomics depicted an in-depth landscape for the very early stage of mouse maternal-to-zygotic transition

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