Iegorova V et al. (2022), Comparison of RNA localization during oogenesis...

XB-ART-59386

Front Cell Dev Biol 2022 Jan 01;10:982732. doi: 10.3389/fcell.2022.982732.

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

Iegorova V , Naraine R , Psenicka M , Zelazowska M , Sindelka R .

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The oocyte is a unique cell, from which develops a complex organism comprising of germ layers, tissues and organs. In some vertebrate species it is known that the asymmetrical localization of biomolecules within the oocyte is what drives the spatial differentiation of the daughter cells required for embryogenesis. This asymmetry is first established to produce an animal-vegetal (A-V) axis which reflects the future specification of the ectoderm, mesoderm, and endoderm layers. Several pathways for localization of vegetal maternal transcripts have already been described using a few animal models. However, there is limited information about transcripts that are localized to the animal pole, even though there is accumulating evidence indicating its active establishment. Here, we performed comparative TOMO-Seq analysis on two holoblastic cleavage models: Xenopus laevis and Acipenser ruthenus oocytes during oogenesis. We found that there were many transcripts that have a temporal preference for the establishment of localization. In both models, we observed vegetal transcript gradients that were established during either the early or late oogenesis stages and transcripts that started their localization during the early stages but became more pronounced during the later stages. We found that some animal gradients were already established during the early stages, however the majority were formed during the later stages of oogenesis. Some of these temporally localized transcripts were conserved between the models, while others were species specific. Additionally, temporal de novo transcription and also degradation of transcripts within the oocyte were observed, pointing to an active remodeling of the maternal RNA pool.

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Species referenced: Xenopus laevis
GO keywords: RNA localization [+]

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	FIGURE 1. Schematic of the methodological workflow.
	FIGURE 2. Summary of the different oocyte sizes assessed for each of the models. Shown for the X. laevis model are the schematic drawings for the equivalent stages for the given oocyte as derived from *Carotenuto and Tussellino (2018). Stage classification of the X. laevis oocytes are from Dumont (1972).
	FIGURE 3. PCA plot showing the top 500 most variable genes for each of the different oocyte sizes from the models. (A) Principle component 2 showing variation in transcript as a function of oocyte size. (B) Principle component 1 showing variation in transcript across segment and size. The sections correspond to the regions of the oocyte that were cryosectioned, whereby sections A - extremely animal, B - animal, C - central, D - vegetal, E - extremely vegetal.
	FIGURE 4. Unique groups representing the significant transcript sub-cellular alterations between the different oocyte sizes of the Xenopus laevis. Four groups of localization profiles were observable, early vegetal, late vegetal, late animal and polar. The following subgroups were observed: same profile - similar profile in early and late stages; predefined - profile already established in the early stages; homogeneous very small/small - profile is ubiquitous in the small/very small stage; homogeneous vs., s - profile is ubiquitous in both the small and very small stage. The sections correspond to the regions of the oocyte that were cryosectioned, whereby sections A - extremely animal, B - animal, C - central, D - vegetal, E - extremely vegetal.
	FIGURE 5. Unique groups representing the significant sub-cellular transcript alterations between the different oocyte sizes of the Acipenser ruthenus. Five groups of localization profiles were observable, early vegetal, late vegetal, early animal, late animal and polar. The following subgroups were observed: same profile - similar profile in early and late stages; predefined small - profile already established in the early stage; homogeneous small - profile is ubiquitous in the small stage; polar smallâprofile shows maximum expression in the polar regions of the oocyte; early animalâprofile shows animal distribution in the early stage. The sections correspond to the regions of the oocyte that were cryosectioned, whereby sections A - extremely animal, B - animal, C - central, D - vegetal, E - extremely vegetal.
	FIGURE 6. Unique profiles representing the significant total transcript count alterations between the different oocyte sizes of the Xenopus laevis and Acipenser ruthenus. The sections correspond to the regions of the oocyte that were cryosectioned, whereby sections A - extremely animal, B - animal, C - central, D - vegetal, E - extremely vegetal.
	FIGURE 7. Vegetal and animal transcripts with similar temporal sub-cellular profiles in Xenopus laevis and Acipenser ruthenus. Heatmap is based on the Z-score of the transcript expression relative to the oocyte stage of the model. The Gene Ontology terms are those found associated with the given group of transcripts. Transcripts were filtered to include only those with either limited (early vegetal < â¼1.5x) or enhanced (late pathways > â¼1.2x) fold differences between stage sections of interest. The sections correspond to the regions of the oocyte that were cryosectioned, whereby sections A - extremely animal, B - animal, C - central, D - vegetal, E - extremely vegetal.
	FIGURE 8. List of transcripts with a reduced or over abundance during the oocyte development between the Xenopus laevis and Acipenser ruthenus. Heatmap is based on the Z-score of the percentage mean transcript expression relative to each model. Representative transcripts show a minimum of â¼1.5x change relative to a given oocyte stage.

References [+] :

Bolger, Trimmomatic: a flexible trimmer for Illumina sequence data. 2014, Pubmed