Multi-omic meta-analysis of transcriptomes and the bibliome uncovers novel hypoxia-inducible genes

Ono, Yukiko; Bono, Hidemasa

doi:10.1101/2021.03.29.433661

Cited by 11 publications

(1 citation statement)

References 49 publications

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“…We previously performed a metaanalysis using RNA-Seq or genomic data derived from various studies and available in public databases. We used public RNA-Seq data related to hypoxia to identify new candidate genes induced by hypoxic stimulation [14]. New candidate genes related to oxidative stress and hypoxia were identified using public RNA-Seq data associated with these pathological processes.…”

Section: Introductionmentioning

confidence: 99%

Meta-analysis of the public RNA-Seq data of the Western honeybeeApis melliferato construct reference transcriptome data

Yokoi

Wakamiya

Bono

2022

Preprint

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The Western honeybee (Apis mellifera) is valuable in biological research and agriculture. Its genome sequence was published before those for other insect species. RNA-Seq data for A. mellifera have been applied in several recently published studies. Nevertheless, these data have not been prepared for use in subsequent meta-analyses. To promote A. mellifera transcriptome analysis, we constructed reference transcriptome data using the reference genome sequence and RNA-Seq data curated from about 1,000 runs of public databases. The new reference transcriptome data construct comprised 149,685 transcripts, and 194,174 protein sequences were predicted. About 50-60% of the predicted protein sequences were functionally annotated using the protein sequence data for several model and insect species. Novel candidate immune-related transcripts were searched by meta-analysis using immune response-related RNA-Seq and reference transcriptome data. Three to 20 candidate transcripts including autophagy related protein 3 were upregulated or downregulated in response to both viral and bacterial infections. The constructed reference transcriptome data may facilitate future transcriptome analyses of A. mellifera.

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Section: Introductionmentioning

confidence: 99%

Meta-analysis of the public RNA-Seq data of the Western honeybeeApis melliferato construct reference transcriptome data

Yokoi

Wakamiya

Bono

2022

Preprint

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Meta-Analysis of Public RNA Sequencing Data of Abscisic Acid-Related Abiotic Stresses inArabidopsis thaliana

Shintani¹,

Tamura

Bono

2023

Preprint

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Abiotic stresses such as drought, salinity, and cold negatively affect plant growth and crop productivity. Understanding the molecular mechanisms underlying plant responses to these stressors is essential for stress tolerance in crops. The plant hormone abscisic acid (ABA) is significantly increased upon abiotic stressors, inducing physiological responses to adapt to stress and regulate gene expression. Although many studies have examined the components of established stress signaling pathways, few have explored other unknown elements. Data-driven studies have the advantage of analyzing large and independent datasets, which can lead to the identification of novel research topics that are distinct from those that have already been extensively studied. This study aimed to identify novel stress-responsive genes in plants by performing a meta-analysis of public RNA sequencing (RNA-Seq) data on Arabidopsis thaliana from the NCBI Gene Expression Omnibus, focusing on five ABA-related stress conditions (ABA, Salt, Dehydration, Osmotic, and Cold). The meta-analysis of 216 paired datasets from five stress conditions was conducted, and differentially expressed genes were identified by introducing a new metric, called TN (stress-treated (T) and non-treated (N))-score. Enrichment analysis was performed to characterize differentially expressed genes, and genes that were commonly regulated under different stresses were also identified. The meta-analysis revealed that 14 genes were commonly upregulated and 8 genes were commonly downregulated across all five treatments, including some that were not previously associated with these stress responses. On the other hand, some genes regulated by salt, dehydration, and osmotic treatments were not regulated by exogenous ABA or cold stress, suggesting that they may be involved in the plant response to dehydration independent of ABA. Meta-analysis revealed a list of candidate genes with unknown molecular mechanisms in ABA-dependent and ABA-independent stress responses. The identified genes could be valuable resources for selecting genome editing targets and potentially contribute to the discovery of novel stress tolerance mechanisms and pathways in plants.

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Transcriptional Signatures of Domestication Revealed through Meta-Analysis of Pig, Chicken, Wild Boar, and Red Junglefowl Gene Expression Data

Uno,

Bono

2024

Animals

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Domesticated animals have undergone significant changes in their behavior, morphology, and physiological functions during domestication. To identify the changes in gene expression associated with domestication, we collected the RNA-seq data of pigs, chickens, wild boars, and red junglefowl from public databases and performed a meta-analysis. Gene expression was quantified, and the expression ratio between domesticated animals and their wild ancestors (DW-ratio) was calculated. Genes were classified as “upregulated”, “downregulated”, or “unchanged” based on their DW-ratio, and the DW-score was calculated for each gene. Gene set enrichment analysis revealed that genes upregulated in pigs were related to defense from viral infection, whereas those upregulated in chickens were associated with aminoglycan and carbohydrate derivative catabolic processes. Genes commonly upregulated in pigs and chickens are involved in the immune response, olfactory learning, epigenetic regulation, cell division, and extracellular matrix. In contrast, genes upregulated in wild boar and red junglefowl are related to stress response, cell proliferation, cardiovascular function, neural regulation, and energy metabolism. These findings provide valuable insights into the genetic basis of the domestication process and highlight potential candidate genes for breeding applications.

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Multi-omic meta-analysis of transcriptomes and the bibliome uncovers novel hypoxia-inducible genes

Cited by 11 publications

References 49 publications

Meta-analysis of the public RNA-Seq data of the Western honeybeeApis melliferato construct reference transcriptome data

Meta-analysis of the public RNA-Seq data of the Western honeybeeApis melliferato construct reference transcriptome data

Meta-Analysis of Public RNA Sequencing Data of Abscisic Acid-Related Abiotic Stresses inArabidopsis thaliana

Transcriptional Signatures of Domestication Revealed through Meta-Analysis of Pig, Chicken, Wild Boar, and Red Junglefowl Gene Expression Data

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