RNA Sequencing of Stentor Cell Fragments Reveals Transcriptional Changes during Cellular Regeneration

Onsbring, Henning; Jamy, Mahwash; Ettema, Thijs J. G.

doi:10.1016/j.cub.2018.02.055

Cited by 17 publications

(30 citation statements)

References 39 publications

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“…Now that the Stentor coeruleus genome has been determined (Slabodnick, 2017) and RNA interference methods developed (Slabodnick, 2014b), molecular and genomic approaches enable new ways to explore this classic model system. It has been possible to use RNA sequencing to show that a portion of the genome becomes expressed during regeneration in Stentor Onsbring 2018;Wei 2020). These studies focused on two different regeneration paradigms.…”

Section: Introductionmentioning

confidence: 99%

Modular, Cascade-like Transcriptional Program of Regeneration inStentor

Sood

Lin

McGillivary

et al. 2021

Preprint

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The giant ciliate Stentor coeruleus is a classical model system for studying regeneration and morphogenesis at the level of a single cell. The anterior of the cell is marked by an array of cilia, known as the oral apparatus, which can be induced to shed and regenerate in a series of reproducible morphological steps, previously shown to require transcription. If a cell is cut in half, each half will regenerate an intact cell, including a new oral apparatus in the posterior half. We used RNAseq to assay the dynamic changes in Stentors transcriptome during regeneration, after both oral apparatus shedding and bisection, allowing us to identify distinct temporal waves of gene expression including kinases, RNA binding proteins, centriole biogenesis factors, and orthologs of human ciliopathy genes implicated in Meckel and Joubert syndromes. By comparing transcriptional profiles of different regeneration events in the same species, we were able to identify distinct modules of gene expression corresponding to oral apparatus regeneration, posterior holdfast regeneration, and recovery after wounding. By measuring gene expression in cells in which translation is blocked, we show that the sequential waves of gene expression involve a cascade mechanism in which later waves of expression are triggered by translation products of early-expressed genes. Among the early-expressed genes, we identified an E2F transcription factor and the conserved RNA binding protein Pumilio as potential regulators of regeneration based on the expression pattern of their predicted target genes. This work allows us to classify regeneration genes into groups based on their potential role for regeneration in distinct cell regeneration paradigms, and provides new insight into how a single cell can coordinate complex morphogenetic pathways to regenerate missing structures.

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Section: Introductionmentioning

confidence: 99%

Modular, Cascade-like Transcriptional Program of Regeneration inStentor

Sood

Lin

McGillivary

et al. 2021

Preprint

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“…For the confirmation of the relationship between obtained RquA sequences from Spirostomum spp., (in this study), a phylogenetic analysis was carried out with reported RquA sequences from Eukaryotes (Stairs et al, 2018) including additional identified RquA sequences obtained from the published transcriptomes [Spirostomum spp., Stentor polymorphus (Hines et al, 2018;Onsbring et al, 2018)] and genome of S. roeselii (PRJNA507905). We have also included additional RquA sequences from the transcriptome of B. undulans (SRR12647630) and B. musculus (SRR12647629).…”

Section: Phylogenetic Analysis Of Rquamentioning

confidence: 99%

Transcriptome Profiling Revealed Multiple rquA Genes in the Species of Spirostomum (Protozoa: Ciliophora: Heterotrichea)

Mukhtar

Wei

et al. 2021

Front. Microbiol.

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Adaptation to life at different oxygen tensions plays a role in protozoan ecology and controls the distribution of different species in anoxic habitats. The ciliate genus Spirostomum inhabiting fresh or low salinity water globally where these species are considered as bioindicators. Under anaerobic or low oxygen conditions, the rhodoquinol-dependent pathway has been reported in the species from the class Heterotrichea. With the help of RNA sequencing (RNAseq) data, Spirostomum spp., are suitable for deep molecular investigations on rquA for rhodoquinone (RQ) biosynthesis. In this study, Spirostomum ambiguum, Spirostomum subtilis, and Spirostomum teres collected from densely vegetated freshwater habitat in Fuzhou, China, explored the evidence of rquA. Based on transcriptome analysis, two to three RquA proteins were identified in S. ambiguum, S. teres, and S. subtilis, respectively. The presence of a key Motif-I of RquA and mitochondrial targeting signals (MTS), also confirmed the identity of these as RquA. Furthermore, Spirostomum RquA proteins could be sorted into two groups based on their conserved amino acid (CAA) residues. Phylogenetic analysis also exhibited RquA division into two subclades contained RquA1 and RquA2/RquA3 and supports two to three paralogs of rquA genes in the genomes Spirostomum spp. Additional transcriptomes and genomes analysis of Blepharisma spp., and Stentor spp., respectively, also revealed at least two paralogs of rquA in members of the class Heterotrichea. The present study provides evidence for the presence of RquA and rhodoquinol dependent fumarate reduction pathway in Spirostomum species potentially use to respire in the oxygen-depleted habitats and two to three diverse rquA genes.

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“…In line with this, most significantly enriched DEGs are involved in developmental, organelle, and microtubule-based processes. Previously, Onsbring et al [76] studied the regeneration of Stentor polymorphus and identified several eukaryotic cell cycle-related biological processes and homologs known for their roles in eukaryotic cell division. Serine/threonine kinase at the D stage was most significantly enriched in our study ( Figure 4C), in agreement with the results of Onsbring et al [76], indicating the overlap of expressed genes in regeneration and cell division processes.…”

Section: Comparisons With Previous Studies Focusing On the Cell Cyclementioning

confidence: 99%

“…Previously, Onsbring et al [76] studied the regeneration of Stentor polymorphus and identified several eukaryotic cell cycle-related biological processes and homologs known for their roles in eukaryotic cell division. Serine/threonine kinase at the D stage was most significantly enriched in our study ( Figure 4C), in agreement with the results of Onsbring et al [76], indicating the overlap of expressed genes in regeneration and cell division processes. Furthermore, MAPK genes, closely related to cell proliferation, were up-regulated at the D stage in Pseudokeronopsis erythrina ( Supplementary Table S3), as well as at the alternative splicing stage in the conjugation cell cycle of Tetrahymena thermophila [9].…”

Section: Comparisons With Previous Studies Focusing On the Cell Cyclementioning

confidence: 99%

Comparative Transcriptome Analyses during the Vegetative Cell Cycle in the Mono-Cellular Organism Pseudokeronopsis erythrina (Alveolata, Ciliophora)

Shen

Gentekaki

et al. 2020

Microorganisms

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Studies focusing on molecular mechanisms of cell cycles have been lagging in unicellular eukaryotes compared to other groups. Ciliates, a group of unicellular eukaryotes, have complex cell division cycles characterized by multiple events. During their vegetative cell cycle, ciliates undergo macronuclear amitosis, micronuclear mitosis, stomatogenesis and somatic cortex morphogenesis, and cytokinesis. Herein, we used the hypotrich ciliate Pseudokeronopsis erythrina, whose morphogenesis has been well studied, to examine molecular mechanisms of ciliate vegetative cell cycles. Single-cell transcriptomes of the growth (G) and cell division (D) stages were compared. The results showed that (i) More than 2051 significantly differentially expressed genes (DEGs) were detected, among which 1545 were up-regulated, while 256 were down-regulated at the D stage. Of these, 11 randomly picked DEGs were validated by reverse transcription quantitative polymerase chain reaction (RT-qPCR); (ii) Enriched DEGs during the D stage of the vegetative cell cycle of P. erythrina were involved in development, cortex modifications, and several organelle-related biological processes, showing correspondence of molecular evidence to morphogenetic changes for the first time; (iii) Several individual components of molecular mechanisms of ciliate vegetative division, the sexual cell cycle and cellular regeneration overlap; and (iv) The P. erythrina cell cycle and division have the same essential components as other eukaryotes, including cyclin-dependent kinases (CDKs), cyclins, and genes closely related to cell proliferation, indicating the conserved nature of this biological process. Further studies are needed focusing on detailed inventory and gene interactions that regulate specific ciliated cell-phase events.

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RNA Sequencing of Stentor Cell Fragments Reveals Transcriptional Changes during Cellular Regeneration

Cited by 17 publications

References 39 publications

Modular, Cascade-like Transcriptional Program of Regeneration inStentor

Modular, Cascade-like Transcriptional Program of Regeneration inStentor

Transcriptome Profiling Revealed Multiple rquA Genes in the Species of Spirostomum (Protozoa: Ciliophora: Heterotrichea)

Comparative Transcriptome Analyses during the Vegetative Cell Cycle in the Mono-Cellular Organism Pseudokeronopsis erythrina (Alveolata, Ciliophora)

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