Evolutionary conservation of maternal RNA localization in fishes and amphibians revealed by TOMO-Seq

Naraine, Ravindra; Iegorova, Viktoriia; Abaffy, Pavel; Franěk, Roman; Soukup, Vladimír; Pšenička, Martin; Šindelka, Radek

doi:10.1016/j.ydbio.2022.06.013

Cited by 8 publications

(24 citation statements)

References 110 publications

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“…Transcripts coding pabpc4 (previously PABP ) , tubb (previously β-tubulin ) and nup93 (previously An4a ) were detected in the animal pole at VI stage only ( Yisraeli et al, 1990 ; Schroeder and Yost, 1996 ; reviewed by Schnapp et al, 1997 ). Contrary to the few animal transcripts that have been described in the past, many recent studies have demonstrated that there are in fact hundreds of animally localized transcripts ( Claußen et al, 2015 ; Owens et al, 2017 ; Sindelka et al, 2018 ; Naraine et al, 2022 ). Additionally, our recent study has shown that many of these maternal animal transcripts show a high level of conserved localization amongst diverse species ( D. rerio, A. ruthenus, X. laevis and Ambystoma mexicanum ) ( Naraine et al, 2022 ).…”

Section: Introductionmentioning

confidence: 84%

“…RNA-Seq reads were processed as previously described in Naraine et al (2022) . In brief, TrimmomaticPE (v. 0.36) ( Bolger et al, 2014 ) was used to remove adaptor sequences and low-quality reads, while SortMeRNA (v. 2.1b) ( Kopylova et al, 2012 ) was used to remove mtRNA reads (GenBank id: NC_001573.1 , KF153104.1 ) and any remaining rRNA reads.…”

Section: Methodsmentioning

confidence: 99%

“…The transcript counts for each section was summarized as a percentage relative to the total transcripts within the oocyte. These relative expression values were used to categorize the DLTs into localization profiles based on defined thresholds as previously defined ( Sindelka et al, 2018 ; Naraine et al, 2022 ). The profiles comprised of the extreme animal, animal, central, vegetal, and extreme vegetal profiles.…”

Section: Methodsmentioning

confidence: 99%

“…The profiles were verified manually and some clusters re-analyzed using optCluster (v. 1.3.0) with the “Diana” clustering algorithm ( Sekula et al, 2017 ). The transcripts were annotated using the annotations derived from the previous ortholog analysis done by Naraine et al (2022) . In brief, protein sequence similarity and gene symbol matching were used to find the most probable orthologs between the two models.…”

Section: Methodsmentioning

confidence: 99%

“…Contrary to the few animal transcripts that have been described in the past, many recent studies have demonstrated that there are in fact hundreds of animally localized transcripts (Claußen et al, 2015;Owens et al, 2017;Sindelka et al, 2018;Naraine et al, 2022). Additionally, our recent study has shown that many of these maternal animal transcripts show a high level of conserved localization amongst diverse species (D. rerio, A. ruthenus, X. laevis and Ambystoma mexicanum) (Naraine et al, 2022). We selected the two best models (easily accessible and early oocyte coloring reflecting A-V axis) to study RNA localization during oogenesis at the complete transcriptome level.…”

Section: Introductionmentioning

confidence: 98%

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

Iegorova

Naraine

Pšenička

et al. 2022

Front. Cell Dev. Biol.

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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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