Intracellular and Intercellular Gene Regulatory Network Inference From Time-Course Individual RNA-Seq

Kashima, Makoto; Shida, Yuki; Yamashiro, Takashi; Hirata, Hiromi; Kurosaka, Hiroshi

doi:10.3389/fbinf.2021.777299

Cited by 7 publications

(2 citation statements)

References 63 publications

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“…RNA-seq was conducted according to the Lasy-Seq ver. 1.1 protocol ( https://sites.google.com/view/lasy-seq/ ) ( Kamitani et al, 2019 ; Kashima et al, 2021 ). Briefly, 18 ng of total RNA was reverse-transcribed with a RT primer and SuperScript IV Reverse Transcriptase (Thermo Fisher Scientific).…”

Section: Methodsmentioning

confidence: 99%

Activation of XBP1 but not ATF6α rescues heart failure induced by persistent ER stress in medaka fish

Jin,

Ishikawa,

Kashima

et al. 2023

Life Sci. Alliance

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The unfolded protein response is triggered in vertebrates by ubiquitously expressed IRE1α/β (although IRE1β is gut-specific in mice), PERK, and ATF6α/β, transmembrane-type sensor proteins in the ER, to cope with ER stress, the accumulation of unfolded and misfolded proteins in the ER. Here, we burdened medaka fish, a vertebrate model organism, with ER stress persistently from fertilization by knocking out theAXERgene encoding an ATP/ADP exchanger in the ER membrane, leading to decreased ATP concentration–mediated impairment of the activity of Hsp70- and Hsp90-type molecular chaperones in the ER lumen. ER stress and apoptosis were evoked from 4 and 6 dpf, respectively, leading to the death of allAXER-KO medaka by 12 dpf because of heart failure (medaka hatch at 7 dpf). Importantly, constitutive activation of IRE1α signaling—but not ATF6α signaling—rescued this heart failure and allowedAXER-KO medaka to survive 3 d longer, likely because of XBP1-mediated transcriptional induction of ER-associated degradation components. Thus, activation of a specific pathway of the unfolded protein response can cure defects in a particular organ.

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Section: Methodsmentioning

confidence: 99%

Activation of XBP1 but not ATF6α rescues heart failure induced by persistent ER stress in medaka fish

Jin,

Ishikawa,

Kashima

et al. 2023

Life Sci. Alliance

Self Cite

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“…The 3′ mRNA‐seq was conducted according to the Lasy‐Seq v1.1 protocol (https://sites.google.com/view/lasy-seq/) (Kamitani et al, 2019; Kashima et al, 2021). Briefly, total RNA was reverse transcribed using an reverse transcription primer with index and SuperScript IV reverse transcriptase (Thermo Fisher Scientific, Waltham, MA, USA).…”

Section: Methodsmentioning

confidence: 99%

A resource of single‐cell gene expression profiles in a planarian Dugesia japonica

Kashima,

Komura,

Sato

et al. 2023

Dev Growth Differ

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The freshwater planarian Dugesia japonica maintains an abundant heterogeneous cell population called neoblasts, which include adult pluripotent stem cells. Thus, it is an excellent model organism for stem cell and regeneration research. Recently, many single‐cell RNA sequencing (scRNA‐Seq) databases of several model organisms, including other planarian species, have become publicly available; these are powerful and useful resources to search for gene expression in various tissues and cells. However, only one scRNA‐Seq dataset for D. japonica that has limitation in the detected gene number has been available. Herein, we collected D. japonica cells, and conducted scRNA‐Seq analysis. A novel, automatic, iterative cell clustering strategy produced 3,404 cell dataset, which could be classified into 63 cell types based on gene expression profiles. We introduced two kinds of usage examples of the scRNA‐Seq dataset in this study using D. japonica. First, the dataset provided consistent results with previous studies as well as novel functionally relevant insights, i.e., the expression of DjMTA and DjP2X‐A genes in neoblasts that give rise to differentiated cells. Second, we conducted an integrative analysis of the scRNA‐Seq dataset and time‐course bulk RNA‐Seq of irradiated animals, demonstrating that the dataset can help interpret differentially expressed genes captured via bulk RNA‐Seq. Using the R package “Seurat” and GSE223927, researchers can easily access and utilize this dataset. (215/250 words)This article is protected by copyright. All rights reserved.

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Expression analysis of genes including Zfhx4 in mice and zebrafish reveals a temporospatial conserved molecular basis underlying craniofacial development

Liu,

Xu,

Kashima

et al. 2024

Developmental Dynamics

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BackgroundEmbryonic craniofacial development involves several cellular and molecular events that are evolutionarily conserved among vertebrates. Vertebrate models such as mice and zebrafish have been used to investigate the molecular and cellular etiologies underlying human craniofacial disorders, including orofacial clefts. However, the molecular mechanisms underlying embryonic development in these two species are unknown. Therefore, elucidating the shared mechanisms of craniofacial development between disease models is crucial to understanding the underlying mechanisms of phenotypes in individual species.ResultsWe selected mice and zebrafish as model organisms to compare various events during embryonic craniofacial development. We identified genes (Sox9, Zfhx3 and 4, Cjun, and Six1) exhibiting similar temporal expression patterns between these species through comprehensive and stage‐matched gene expression analyses. Expression analysis revealed similar gene expression in hypothetically corresponding tissues, such as the mice palate and zebrafish ethmoid plate. Furthermore, loss‐of‐function analysis of Zfhx4/zfhx4, a causative gene of human craniofacial anomalies including orofacial cleft, in both species resulted in deformed skeletal elements such as the palatine and ethmoid plate in mice and zebrafish, respectively.ConclusionsThese results demonstrate that these disease models share common molecular mechanisms, highlighting their usefulness in modeling craniofacial defects in humans.

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Intracellular and Intercellular Gene Regulatory Network Inference From Time-Course Individual RNA-Seq

Cited by 7 publications

References 63 publications

Activation of XBP1 but not ATF6α rescues heart failure induced by persistent ER stress in medaka fish

Activation of XBP1 but not ATF6α rescues heart failure induced by persistent ER stress in medaka fish

A resource of single‐cell gene expression profiles in a planarian Dugesia japonica

Expression analysis of genes including Zfhx4 in mice and zebrafish reveals a temporospatial conserved molecular basis underlying craniofacial development

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