A5085946915- RNA and protein synthesis mechanisms
- RNA Research and Splicing
- Reproductive Biology and Fertility
- Pluripotent Stem Cells Research
- Renal and related cancers
- RNA modifications and cancer
- RNA regulation and disease
- Machine Learning in Bioinformatics
- Animal Genetics and Reproduction
- Genomics and Phylogenetic Studies
- CRISPR and Genetic Engineering
- interferon and immune responses
- Epigenetics and DNA Methylation
- Chemical Synthesis and Analysis
- Neurogenesis and neuroplasticity mechanisms
- Natural Language Processing Techniques
- Photosynthetic Processes and Mechanisms
- DNA Repair Mechanisms
- Electrochemical Analysis and Applications
- Algorithms and Data Compression
- Cancer Genomics and Diagnostics
- Single-cell and spatial transcriptomics
- DNA and Biological Computing
- Pulmonary Hypertension Research and Treatments
- Nerve injury and regeneration
The University of Tokyo
2008-2024
Osaka University
2003-2024
Tokyo Medical and Dental University
2024
Kyoto University
2008-2016
Nara Institute of Science and Technology
2003-2012
National Institute of Advanced Industrial Science and Technology
2010-2012
Keio University
2012
Kindai University
1994-2011
Kyoto University Institute for Chemical Research
2008-2011
Doshisha University
2010
Pseudoknots found in secondary structures of a number functional RNAs play various roles biological processes. Recent methods for predicting RNA cover certain classes pseudoknotted structures, but only few them achieve satisfying predictions terms both speed and accuracy.We propose IPknot, novel computational method with pseudoknots based on maximizing expected accuracy predicted structure. IPknot decomposes structure into set pseudoknot-free substructures approximates base-pairing...
Highlights•WNT3 induces mesodermal factor T through β-CATENIN in epiblast-like cells•T is essential for primordial germ cell specification•T directly activates germline determinates Blimp1 and Prdm14 cells•BMP4 creates a permissive context to activate Prdm14SummaryGerm cells ensure reproduction heredity. In mice, (PGCs), the precursors spermatozoa oocytes, are induced pluripotent epiblast by BMP4 WNT3, yet underlying mechanism remains unclear. Here, using an vitro PGC specification system,...
Cohesin's Smc1 and Smc3 subunits form V-shaped heterodimers, the nucleotide binding domains (NBDs) of which bind C- N-terminal domains, respectively, α-kleisin subunit, forming a large tripartite ring within in sister DNAs are entrapped, thereby held together (sister chromatid cohesion). During replication, establishment stable cohesion is dependent on Eco1-mediated acetylation Smc3's NBD, thought to prevent dissociation from Smc3, locking shut "DNA exit gate." How Scc3 Pds5, regulatory...
Adenosine deaminase acting on RNA 1 (ADAR1), an enzyme responsible for adenosine-to-inosine editing, is composed of two isoforms: nuclear p110 and cytoplasmic p150. Deletion Adar1 or p150 genes in mice results embryonic lethality with overexpression interferon-stimulating (ISGs), caused by the aberrant recognition unedited endogenous transcripts melanoma differentiation-associated protein 5 (MDA5). However, among numerous editing sites, how many sites require especially ADAR1 p150, to avoid...
Abstract RNA structural elements called pseudoknots are involved in various biological phenomena including ribosomal frameshifts. Because it is infeasible to construct an efficiently computable secondary structure model pseudoknots, prediction methods considering not yet widely available. We developed IPknot, which uses heuristics speed up computations, but has remained difficult apply long sequences, such as messenger and viral RNA, because requires cubic computational time with respect...
Considerable attention has been focused on predicting RNA-RNA interaction since it is a key to identifying possible targets of non-coding small RNAs that regulate gene expression post-transcriptionally. A number computational studies have so far devoted joint secondary structures or binding sites under specific class interactions. In general, there trade-off between range type and efficiency prediction algorithm, thus efficient methods for comprehensive are still awaited.We present RactIP,...
Despite the clinical impact of DNMT3A mutation on acute myeloid leukaemia, molecular mechanisms regarding how this causes leukaemogenesis in vivo are largely unknown. Here we show that, murine transplantation experiments, recipients transplanted with mutant-transduced cells exhibit aberrant haematopoietic stem cell (HSC) accumulation. Differentiation-associated genes downregulated without accompanying changes methylation status their promoter-associated CpG islands stem/progenitor cells,...
Adenosine-to-inosine RNA editing is an essential post-transcriptional modification catalyzed by adenosine deaminase acting on (ADAR)1 and ADAR2 in mammals. For numerous sites coding sequences (CDS) microRNAs, highly conserved has significant biological consequences, for example, altering amino acid residues target recognition. However, no comprehensive quantitative studies have been undertaken to determine how specific ADARs contribute vivo. Here, we amplified each region with site(s)...
The methyltransferase-like 3 (METTL3)-/METTL14-containing complex predominantly catalyzes N6-methyladenosine (m6A) modification, which affects mRNA stability. Although the METTL14 R298P mutation is found in multiple cancer types, its biological effects are not completely understood. Here, we show that heterozygous promotes cell proliferation, whereas homozygous reduces proliferation. Methylated RNA immunoprecipitation sequencing analysis indicates m6A modification at canonical motifs....
Abstract Background RNA secondary structure prediction is one major task in bioinformatics, and various computational methods have been proposed so far. Pseudoknot of the typical substructures appearing several RNAs, plays an important role some biological processes. Prediction with pseudoknots still challenging since problem NP-hard when arbitrary are taken into consideration. Results We introduce a new method predicting based on integer programming. In our formulation, we aim at minimizing...
Abstract Motivation: It is well known that the accuracy of RNA secondary structure prediction from a single sequence limited, and thus comparative approach predicts common aligned sequences better choice if homologous with reliable alignments are available. However, correct information needed to produce sequences. To tackle this dilemma, we require fast accurate aligner takes structural into consideration yield alignments, which suitable for prediction. Results: We develop DAFS, novel...
A key virulence factor of enterohaemorrhagic Escherichia coli (EHEC) is the bacteriophage-encoded Shiga toxin (Stx). Stxs are classified into two types, Stx1 and Stx2, Stx2-producing strains thought to cause more severe infections than producing only Stx1. Although O26 : H11 second most prevalent EHEC following O157 H7, majority produce alone. However, have increasingly been detected worldwide. Through a large-scale genome analysis, we present global phylogenetic overview evolutionary...
Global alignment of complex pseudotime trajectories between different single-cell RNA-seq datasets is challenging, as existing tools mainly focus on linear trajectories. Here we present CAPITAL (comparative analysis trajectory inference with tree alignment), a method for comparing whereby branching can be automatically compared. Computational tests synthetic and authentic bone marrow cells indicate that has achieved accurate robust alignments trees, revealing various gene expression dynamics...
The nuclei of mouse trophectoderm cells were found to have developmental totipotency like inner cell mass after serial nuclear transfer. Single or from expanded blastocysts synchronized with the cycle by treatment nocodazole and aphidicolin G1 stage injected into perivitelline space enucleated metaphase II oocytes together Sendai virus. All given three electrical pulses induce fusion activation (first transfer). Aphidicolin was present in all media used until fusion. When reconstituted...
Summary. Mouse two-cell embryos were cultured in a medium supplemented with nocodazole or colcemid for 12·5–14·5 h vitro, and development after elimination of these drugs was examined. All stopped at the metaphase second cell cycle. When removed, almost all divided to normal four-cell stage within 1 then developed into blastocysts (98%). The proportion that young transfer recipients not significantly different from control (35 versus 36%), but developmental ability treated reduced,...