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Introduction
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Publications
Publications (40)
[This corrects the article DOI: 10.1371/journal.pone.0213535.].
Background:
Read coverage of RNA sequencing data reflects gene expression and RNA processing events. Single-cell RNA sequencing (scRNA-seq) methods, particularly "full-length" ones, provide read coverage of many individual cells and have the potential to reveal cellular heterogeneity in RNA transcription and processing. However, visualization tool...
Single-cell RNA sequencing has enabled researchers to quantify the transcriptomes of individual cells, infer cell types and investigate differential expression among cell types, which will lead to a better understanding of the regulatory mechanisms of cell states. Transcript diversity caused by phenomena such as aberrant splicing events have been r...
The circadian clock drives gene expression rhythms, leading to daily changes in physiology and behavior. In mammals, Albumin D-site-Binding Protein (DBP) rhythmically activates transcription of various genes through a DNA cis-element, D-box. The DBP-dependent transactivation is repressed by competitive binding of E4BP4 to the D-box. Despite the ela...
Non-methanotrophic bacteria such as methylotrophs often coexist with methane-oxidizing bacteria (methanotrophs) by cross-feeding on methane-derived carbon. Methanol has long been considered a major compound that mediates cross-feeding of methane-derived carbon. Despite the potential importance of cross-feeding in the global carbon cycle, only a few...
The results of hypergeometric tests for overlaps of KEGG modules with (a) upregulated or (b) downregulated genes. The modules with FDR < 0.05 and > = 3 annotated M. caenitepidi Gela4 genes are shown according to the value of log10 (FDR).
(PDF)
KEGG pathway modules detected for M. marinum S8.
(XLSX)
Evaluation of cross mapping between M. caenitepidi Gela4 and M. marinum S8.
(XLSX)
Duplicated genes identified in the M. caenitepidi Gela4 genome (upper table) and M. marinum S8 genome (lower table) using 95% identity as a threshold.
(XLSX)
Pairwise comparison of gene expression levels for M. caenitepidi Gela4 cells in pure culture and co-culture.
(PDF)
Transcriptomics data of M. caenitepidi Gela4 grown in pure culture with methanol as well as in co-culture with M. marinum and methane.
(XLSX)
Expression profiles of major genes in the central metabolism of M. marinum S8 grown with M. caenitepidi Gela4.
(XLSX)
Schematic showing the transcriptome experiment.
(PDF)
KEGG pathway modules detected for M. caenitepidi Gela4.
(XLSX)
Number of duplicated genes in the M. marinum S8 genome.
(PDF)
Heat maps showing the expression levels of four xoxF genes of M. caenitepidi Gela4 in pure culture and co-culture with M. marinum S8.
Scaled RPKM was calculated as a z-score of RPKM values for each gene per culture.
(PDF)
Transcriptomics data of M. marinum S8 grown in co-culture with M. caenitepidi Gela4 and methane.
(XLSX)
Single-cell RNA sequencing has enabled researchers to quantify the transcriptomes of individual cells, infer cell types, and investigate differential expression among cell types, which will lead to a better understanding of the regulatory mechanisms of cell states. Transcript diversity caused by phenomena such as aberrant splicing events have been...
Background: Read coverage of RNA sequencing data reflects gene expression and RNA processing events. Single-cell RNA sequencing (scRNA-seq) methods, particularly "full-length" ones, provide read coverage of many individual cells and have the potential to reveal cellular heterogeneity in RNA transcription and processing. However, visualization tools...
Total RNA sequencing has been used to reveal poly(A) and non-poly(A) RNA expression, RNA processing and enhancer activity. To date, no method for full-length total RNA sequencing of single cells has been developed despite the potential of this technology for single-cell biology. Here we describe random displacement amplification sequencing (RamDA-s...
Background
Teleosts transiting from freshwater (FW) to seawater (SW) environments face an immediate osmotic stress from ion influxes and water loss, but some euryhaline species such as eels can maintain a stable plasma osmolality during early SW exposure. The time course changes in the gene expression, protein abundance, and localization of key ion...
Background and methods
Multiple Na+/K+-ATPase (NKA) α-subunit isoforms express differentially in response to salinity transfer in teleosts but we observed that the isoform nomenclature is inconsistent with the phylogenetic relationship of NKA α-genes. We cloned the catalytic NKA α-subunit isoforms in eels and medaka, analyzed the time course of the...
It has been proposed that the CLOCK-ARNTL (BMAL1) complex drives circadian transcription of thousands of genes, including Per and Cry family genes that encode suppressors of CLOCK-ARNTL-dependent transcription. However, recent studies demonstrated that 70-80% of circadian-oscillating mRNAs have no obvious rhythms in their de novo transcription, ind...
Background:
As a key mechanism of gene regulation, transcription factors (TFs) bind to DNA by recognizing specific short sequence patterns that are called DNA-binding motifs. A single TF can accept ambiguity within its DNA-binding motifs, which comprise both canonical (typical) and non-canonical motifs. Clarification of such DNA-binding motif ambi...
Primary piRNAs in Drosophila ovarian somatic cells arise from piRNA cluster transcripts and the 3' UTRs of a subset of mRNAs, including Traffic jam (Tj) mRNA. However, it is unclear how these RNAs are determined as primary piRNA sources. Here, we identify a cis-acting 100-nt fragment in the Tj 3' UTR that is sufficient for producing artificial piRN...
Teleost intestine is crucial for seawater acclimation by sensing osmolality of imbibed seawater and regulating drinking and water/ion absorption. Regulatory genes for transforming intestinal function have not been identified. A transcriptomic approach was used to search for such genes in the intestine of euryhaline medaka.
Quantitative RNA-seq by I...
Background
Understanding the genetic basis of adaptive evolution is one of the major goals in evolutionary biology. Recently, it has been revealed that gene copy number variations (GCNVs) constitute significant proportions of genomic diversities within natural populations. However, it has been unclear whether GCNVs are under positive selection and...
In mammalian circadian clockwork, the CLOCK-BMAL1 complex binds to DNA enhancers of target genes and drives circadian oscillation
of transcription. Here we identified 7,978 CLOCK-binding sites in mouse liver by chromatin immunoprecipitation-sequencing
(ChIP-Seq), and a newly developed bioinformatics method, motif centrality analysis of ChIP-Seq (MO...
RNA-binding proteins (RBPs) bind to their target RNA molecules by recognizing specific RNA sequences and structural contexts. The development of CLIP-seq and related protocols has made it possible to exhaustively identify RNA fragments that bind to RBPs. However, no efficient bioinformatics method exists to reveal the structural specificities of RB...
