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RNA_Seq analysis of localization along animal-vegetal axis of axolotl (Ambystoma mexicanum)

ABSTRACT: Asymmetrical localization of biomolecules inside the egg, results in uneven cell division and two daughter cells with different fates. This phenomenon is required for the establishment of many biological processes and is particularly responsible for the great variety of cell types formed during developmentand requires strict timing and positional control. The key molecules determining the body plan are the mRNAs, of which many examples have already been discovered to be asymmetrically localized during oogenesis and embryogenesis in both the amphibian and fish models. However, our knowledge about evolutionary conservation or differences of localized mRNAs is still limited to a few candidates. Our goal has been to compare localization profiles along the animal-vegetal axis of mature eggs of four diverse models, Xenopus laevis, Danio rerio, Ambystoma mexicanum and Acipenser ruthenus using the spatial expression analysis method called TOMO-Seq. Surprisingly, we revealed RNAs that code for many known important genes such as germ layer determinants, germ plasm factors and members of key signalling pathways, are localized in completely different profiles among the models and sometimes even missing in their genomes. We determined the transcriptome distribution and found a poor correlation between the vegetally localized genes but a relatively good correlation between the animally localized genes. These findings indicate that the regulation of embryonic development within the animal kingdom is highly diverse and cannot be deduced based on a single model.

ORGANISM(S): Ambystoma mexicanum

PROVIDER: GSE166916 | GEO | 2022/10/20

REPOSITORIES: GEO

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RNA_Seq analysis of localization along animal-vegetal axis of Danio rerio

Project description:Asymmetrical localization of biomolecules inside the egg, results in uneven cell division and two daughter cells with different fates. This phenomenon is required for the establishment of many biological processes and is particularly responsible for the great variety of cell types formed during developmentand requires strict timing and positional control. The key molecules determining the body plan are the mRNAs, of which many examples have already been discovered to be asymmetrically localized during oogenesis and embryogenesis in both the amphibian and fish models. However, our knowledge about evolutionary conservation or differences of localized mRNAs is still limited to a few candidates. Our goal has been to compare localization profiles along the animal-vegetal axis of mature eggs of four diverse models, Xenopus laevis, Danio rerio, Ambystoma mexicanum and Acipenser ruthenus using the spatial expression analysis method called TOMO-Seq. Surprisingly, we revealed RNAs that code for many known important genes such as germ layer determinants, germ plasm factors and members of key signalling pathways, are localized in completely different profiles among the models and sometimes even missing in their genomes. We determined the transcriptome distribution and found a poor correlation between the vegetally localized genes but a relatively good correlation between the animally localized genes. These findings indicate that the regulation of embryonic development within the animal kingdom is highly diverse and cannot be deduced based on a single model.

2022-10-20 | GSE166917 | GEO

Comparison of RNA localization during oogenesis within Acipenser ruthenus and Xenopus laevis [Acipenser ruthenus]

Project description:In this study we analyzed the spatial and temporal localization of maternal transcripts during oogenesis in Acipenser ruthenus. The occurrence of transcript asymmetry in A. ruthenus has been described at a global level only in matured eggs. However not much is known about the asymmetry during oogenesis. In this study we assessed the temporal establishment of the transcript localization at a global level for A. ruthenus. We were able to determine that there are many transcripts that show temporal variability in the establishment of their localization. We observed an early, predefined and also late pathways for both the vegetally and animally localized transcripts. Additionally, we showed that some maternal transcripts are dynamic during oogenesis with degradation and de novo production being observed. Our study showed that in additional to spatial orientation to the transcripts, there is a strong temporal factor. The discovery of these new temporal profiles should help to better understand the driving forces during embryogenesis.

2022-08-23 | GSE211412 | GEO

Microarray analysis of mRNAs enriched in the vegetal cortex of Xenopus oocytes

Project description:RNA localization is a fundamental mechanism for controlling the spatial regulation of protein synthesis within cells, as well as differential cell fates during early development. Localized RNAs are known to control critical aspects of early Xenopus development, but few have been studied in detail. We set out to identify novel transcripts localized to the vegetal cortex of Xenopus oocytes, one of the best-studied examples of RNA localization. We identified over 400 transcripts enriched in the vegetal cortex, compared with whole oocytes. Included were many novel genes, as well as known genes not thought to undergo RNA localization. These data suggest that the role of RNA localization in early development is extensive and will provide a resource for identifying candidate regulatory genes for early developmental processes. RNA was extracted from isolated vegetal cortices and compared with whole oocytes. Two biological replicates were used, each from a different donor female.

2009-12-30 | E-GEOD-17713 | biostudies-arrayexpress

Microarray analysis of mRNAs enriched in the vegetal cortex of Xenopus oocytes

2009-12-31 | GSE17713 | GEO

Maternal RNA localization during early development of the axolotl

Project description:The asymmetric localization of maternal biomolecules is critical for body plan development. One of the most popular model organisms for early embryogenesis studies is Xenopus laevis but there is a lack of information in other animal species. Here, we compare the early development of two amphibian species – the frog X. laevis and the axolotl Ambystoma mexicanum. This study aimed to identify asymmetrically localized RNAs along the animal-vegetal axis during the early development of A. mexicanum. For that purpose, we performed spatial transcriptome-wide analysis, which revealed dynamic changes along the animal-vegetal axis classified into the following categories: relocalization, de novo synthesis and degradation. Surprisingly, our results showed that many of the vegetally localized genes, which are important for germ cell development, are degraded during early development. Furthermore, we assessed the motif presence in UTRs of degraded mRNAs and revealed the enrichment of several motifs in RNAs of germ cell markers. Our results suggest novel reorganization of the transcriptome during embryogenesis of A. mexicanum to converge to the similar developmental pattern as the X. laevis.

2023-11-21 | GSE240796 | GEO

RNA-Seq analysis of localization along animal-vegetal axis of Xenopus laevis

Project description:We combined cryosectining of oocytes along the animal-vegetal axis (first developmental axis) and RNA-Seq to determine localization profiles of coding and noncoding RNAs. It provides complete view on RNA localization. We found that nearly all RNAs are localized, but only small percentage is actively transported during oogenesis.

2018-05-31 | GSE104848 | GEO

RNA_Seq analysis of localization along animal-vegetal axis of Acipenser ruthenus

Project description:We performed cryosectioning of oocytes along the animal-vegetal axis (first developmental axis, section A (first animal) to section E (last vegetal), followed by RNA-Seq to determine the localization profiles of coding and noncoding RNAs. The method allowed for a complete view on RNA localization. We found that nearly all RNAs are localized, but only a small percentage is actively transported during oogenesis.

2020-06-16 | GSE125819 | GEO

RNA_Seq analysis of localization along animal-vegetal axis of Acipenser ruthenus

Project description:RNA_Seq analysis of localization along animal-vegetal axis of Acipenser ruthenus

| PRJNA517649 | ENA

High Throughput Analysis Reveals Novel Maternal Germline RNAs Critical for PGC Preservation and Proper Migration

Project description:During oogenesis hundreds of RNAs are selectively localized to either the animal or vegetal cortical region. These maternal RNAs include determinants of both somatic and germline fates. Although microarray analysis has contributed to identifying localized determinants, it is not comprehensive and is limited to known transcripts. Here, we utilized high throughput RNA-sequencing analysis to comprehensively interrogate both animal and vegetal pole RNAs in the fully-grown Xenopus laevis oocyte. We identified 411 enriched RNAs at the vegetal pole, 198 of them annotated transcripts, and 27 RNAs enriched at the animal pole, 15 annotated. Of these, 90 were novel RNAs over 4-fold enriched at the vegetal pole and 6 over 10-fold at the animal pole. Unlike mRNAs, we found that microRNAs were not asymmetrically distributed. Whole mount in situ hybridization revealed all 17 selected RNAs were localized, confirming our data set. Biological function and network analysis of vegetally enriched transcripts identified protein-modifying enzymes, receptors, ligands, RNA binding proteins and 10 transcription factors or co-factors with 5 defining hubs linking 47 genes in a network. Initial functional studies of maternal vegetally-localized RNAs show, for the first time, that sox7 plays an important role in primordial germ cell (PGC) development and efnb1(ephrinB1), known to play important roles in migration/adhesion in the nervous system, is required for proper PGC migration. Based on our findings, we propose potential pathways operating at the vegetal pole that highlight where future investigations might be most fruitful.

2017-01-17 | GSE80971 | GEO

The Xenopus Primordial Germ Cell Transcriptome: Unexpected Role for sox7 in Early PGC Development

Project description:Xenopus primordial germ cells (PGCs) are determined by the presence of maternally derived germ plasm. Germ plasm components both protect PGCs from somatic differentiation and begin a unique gene expression program. Segregation of the germline from the endodermal lineage occurs during gastrulation and PGCs subsequently initiate zygotic transcription. However, the gene-networks that operate to both preserve the potential for totipotency and promote germline differentiation are poorly understood. Here, we utilized RNA-sequencing analysis to comprehensively interrogate PGC and neighboring endoderm cell RNAs after lineage segregation. We identified 1,865 transcripts enriched in PGCs compared to endoderm cells. Over 50% of maternal, vegetally-enriched transcripts were enriched in the PGC transcriptome, including sox7. PGC-directed sox7 knockdown and over-expression studies revealed an early requirement for sox7 in proper germ plasm localization, zygotic transcription, and PGC number. We identified oct60 as the most highly expressed and enriched OCT3/4 homologue in PGCs. Lastly, we compared the Xenopus PGC transcriptome with human PGC transcripts and showed that 80% of transcripts are conserved, identifying Xenopus as a relevant model system for understanding the gene-networks necessary for human germline development.

2017-08-01 | GSE102047 | GEO

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