Trajectory Mapping of the Early Drosophila Germline Reveals Controls of Zygotic Activation and Sex Differentiation
Ontology highlight
ABSTRACT:
ORGANISM(S): Drosophila melanogaster
PROVIDER: GSE150568 | GEO | 2020/09/10
REPOSITORIES: GEO
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Project description:Early embryogenesis is characterized by the maternal to zygotic transition (MTZ), in which maternally deposited messenger RNAs are translated and subsequently degraded while zygotic transcription begins. Posttranscriptional gene regulation by RNA-binding proteins (RBPs) is a dominant force controlling pre-zygotic gene expression. Here we describe the first in vivo mRNA-bound proteome in early Drosophila melanogaster embryos. mRNA interactome capture using conventional (254nm) and photoactivatable ribonucleoside-enhanced UV-crosslinking (365nm) was applied to detect RBPs bound to maternal and early zygotic polydenylated transcripts within the first two hours of embryogenesis. We identified a high confidence set of 476 putative RBPs and confirmed RNA-binding activity for most of the tested candidates. The majority of the identified proteins in the early fly mRNA interactome were known RBPs, harboring canonical RBPs features. Nearly hundred of the identified proteins were previously not known to bind RNA. Interestingly, mRNAs encoding RBPs and TFs exhibit time specific expression modules, in which RBPs dominate the first hours of embryonic development. Using fly-FISH data, we could show enriched RBP localization in the posterior embryo during these first hours of fly embryogenesis, suggesting general importance germ cell maturation.
2016-04-26 | PXD002992 | Pride
Project description:These data from sperm were generated to demonstrate detection of post-zygotic mutations in the male germline. This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute please see http://www.sanger.ac.uk/datasharing/
| EGAS00001001700 | EGA
Project description: Not available
| S-EPMC8168578 | biostudies-literature
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
Project description:Trajectory Mapping of the Early Drosophila Germline Reveals Controls of Zygotic Activation and Sex Differentiation
| PRJNA632835 | ENA
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
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
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 | GSE224113 | GEO
Project description:One of the earliest and most significant events in embryonic development is zygotic genome activation (ZGA). In several species, bulk transcription begins at the midblastula transition (MBT) when, after a certain number of cleavages, the embryo attains a particular nuclear-to-cytoplasmic (N/C) ratio, maternal repressors become sufficiently diluted, and the cell cycle slows down. Here we resolve the frog ZGA in time and space by profiling RNA polymerase II (RNAPII) engagement and its transcriptional readout. We detect a gradual increase in both the quantity and the length of RNAPII elongation before the MBT, revealing that >1,000 zygotic genes disregard the N/C timer for their activation and that the sizes of newly transcribed genes are not necessarily constrained by cell cycle duration. We also find that Wnt, Nodal, and BMP signaling together generate most of the spatiotemporal dynamics of regional ZGA, directing the formation of orthogonal body axes and proportionate germ layers.
2019-05-14 | GSE122551 | GEO
Project description:[PROJECT] After fertilization the embryonic genome is inactive until transcription is initiated during the maternal-zygotic transition (MZT). This universal process coincides with the formation of pluripotent cells, which in mammals can be used to generate embryonic stem (ES) cells. To study the changes in chromatin structure that accompany zygotic genome activation and pluripotency, we mapped the genomic locations of histone H3 modifications before and after MZT in zebrafish embryos. Repressive H3 lysine 27 trimethylation (H3K27me3) and activating H3 lysine 4 trimethylation (H3K4me3) are only detected after MZT. H3K4me3 marks more than 80% of genes, including many developmental regulatory genes that are also occupied by H3K27me3. Sequential chromatin immunoprecipitation demonstrates that both methylation marks occupy the same promoter regions, revealing that the bivalent chromatin domains found in cultured ES cells also exist in embryos. In addition, we find a large group of genes that are monovalently marked by H3K4me3 but not H3K27me3. These H3K4me3 monovalent genes are neither expressed nor stably bound by RNA polymerase II. Closer inspection of in vitro data sets reveals similar monovalent H3K4me3 domains in ES cells. The analysis of an inducible transgene indicates that H3K4me3 domains can form in the absence of sequence-specific transcriptional activators or stable association with RNA pol II. These results suggest that bivalent and monovalent domains might poise embryonic genes for activation and that the chromatin profile associated with pluripotency is established during MZT. [SAMPLES] ChIPchip analysis of histone modifications (H3K4me3, H3K27me3, H3K36me3) and RNA polymerase II in pre MZT (256-cell) and post MZT (4hpf; dome/30% epiboly) wt zebrafish embryos. H3K4me3, H3K27me3, H3K36me3 and PolII ChIP-chip at 256 cell stage (one replicate) and 4hpf (dome/30% epiboly) (two replicates)
2010-01-25 | E-GEOD-20023 | biostudies-arrayexpress