Accurate Classification of Differential Expression Patterns in a Bayesian Framework With Robust Normalization for Multi-Group RNA-Seq Count Data

Osabe, Takayuki; Shimizu, Kentaro; Kadota, Koji

doi:10.1177/1177932219860817

Cited by 17 publications

(11 citation statements)

References 34 publications

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“…The TCC+baySeq (ver. 2.18.0) method with a false discovery rate of 0.01 was used for the identification of the DEGs among the synergid, egg, and central cells of the wild type [ 34 ]. Gene Ontology (GO) enrichment analysis was performed using g:Profiler (g:COSt; https://biit.cs.ut.ee/gprofiler/gost ).…”

Section: Methodsmentioning

confidence: 99%

Dynamics of the cell fate specifications during female gametophyte development in Arabidopsis

et al. 2021

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The female gametophytes of angiosperms contain cells with distinct functions, such as those that enable reproduction via pollen tube attraction and fertilization. Although the female gametophyte undergoes unique developmental processes, such as several rounds of nuclear division without cell plate formation and final cellularization, it remains unknown when and how the cell fate is determined during development. Here, we visualized the living dynamics of female gametophyte development and performed transcriptome analysis of individual cell types to assess the cell fate specifications in Arabidopsis thaliana. We recorded time lapses of the nuclear dynamics and cell plate formation from the 1-nucleate stage to the 7-cell stage after cellularization using an in vitro ovule culture system. The movies showed that the nuclear division occurred along the micropylar–chalazal (distal–proximal) axis. During cellularization, the polar nuclei migrated while associating with the forming edge of the cell plate, and then, migrated toward each other to fuse linearly. We also tracked the gene expression dynamics and identified that the expression of MYB98pro::GFP–MYB98, a synergid-specific marker, was initiated just after cellularization in the synergid, egg, and central cells and was then restricted to the synergid cells. This indicated that cell fates are determined immediately after cellularization. Transcriptome analysis of the female gametophyte cells of the wild-type and myb98 mutant revealed that the myb98 synergid cells had egg cell–like gene expression profiles. Although in myb98, egg cell–specific gene expression was properly initiated in the egg cells only after cellularization, but subsequently expressed ectopically in one of the 2 synergid cells. These results, together with the various initiation timings of the egg cell–specific genes, suggest complex regulation of the individual gametophyte cells, such as cellularization-triggered fate initiation, MYB98-dependent fate maintenance, cell morphogenesis, and organelle positioning. Our system of live-cell imaging and cell type–specific gene expression analysis provides insights into the dynamics and mechanisms of cell fate specifications in the development of female gametophytes in plants.

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Section: Methodsmentioning

confidence: 99%

Dynamics of the cell fate specifications during female gametophyte development in Arabidopsis

et al. 2021

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“…The TCC+baySeq (ver. 2.18.0) method with a false discovery rate < 0.01 was used for the identification of the differentially expressed genes among the synergid, egg, and central cells of the wild type (Osabe et al, 2019). Hierarchical clustering of the gene expression data was carried out using phylogram package (https://github.com/rambaut/figtree/).…”

Section: Methodsmentioning

confidence: 99%

Dynamics of the cell fate specifications during female gametophyte development inArabidopsis

Susaki

Suzuki

Maruyama

et al. 2020

Preprint

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The female gametophytes of angiosperms contain cells with distinct functions, such as those that enable reproduction via pollen tube attraction and fertilization. Although the female gametophyte undergoes unique developmental processes, such as several rounds of nuclear division without cell plate formation, and the final cellularization, it remains unknown when and how the cell fate is determined during their development. Here, we visualized the living dynamics of female gametophyte development and performed transcriptome analysis of its individual cell types, to assess the cell fate specifications in Arabidopsis thaliana. We recorded time lapses of the nuclear dynamics and cell plate formation from the one-nucleate stage to the seven-cell stage after cellularization, using the in vitro ovule culture system. The movies showed that the nuclear division occurred along the micropylar-chalazal axis. During cellularization, the polar nuclei migrated while associating with forming edge of the cell plate. Then, each polar nucleus migrated to fuse linearly towards each other. We also tracked the gene expression dynamics and identified that the expression of the MYB98pro::GFP, a synergid-specific marker, was initiated before cellularization, and then restricted to the synergid cells after cellularization. This indicated that cell fates are determined immediately after cellularization. Transcriptome analysis of the female gametophyte cells of the wild type and myb98 mutant, revealed that the myb98 synergid cells had the egg cell-like gene expression profile. Although in the myb98, the egg cell-specific gene expressions were properly initiated only in the egg cells after cellularization, but subsequently expressed ectopically in one of the two synergid cells. These results, together with the various initiation timings of the egg cell-specific genes suggest the complex regulation of the individual gametophyte cells, such as cellularization-triggered fate initiation, MYB98-dependent fate maintenance, cell morphogenesis, and organelle positioning. Our system of live-cell imaging and cell-type-specific gene expression analysis provides insights into the dynamics and mechanisms of cell fate specifications in the development of female gametophytes in plants.

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“…RNA sequencing (RNA-seq) is a common tool for obtaining data related to gene expression (Mortazavi et al, 2008 ). Identification of genes exhibiting differential expression (DE) in different groups or conditions is critical to analysis of RNA-seq data (Osabe et al, 2019 ). Recently, Vieth et al ( 2019 ) evaluated a total of 3,000 possible single-cell RNA-seq (scRNA-seq) analysis pipelines, encompassing the entire analytical process—from library preparation protocols to identification of DE genes.…”

mentioning

confidence: 99%

Commentary: A Systematic Evaluation of Single Cell RNA-Seq Analysis Pipelines

Kadota

Shimizu

2020

Front. Genet.

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Accurate Classification of Differential Expression Patterns in a Bayesian Framework With Robust Normalization for Multi-Group RNA-Seq Count Data

Cited by 17 publications

References 34 publications

Dynamics of the cell fate specifications during female gametophyte development in Arabidopsis

Dynamics of the cell fate specifications during female gametophyte development in Arabidopsis

Dynamics of the cell fate specifications during female gametophyte development inArabidopsis

Commentary: A Systematic Evaluation of Single Cell RNA-Seq Analysis Pipelines

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