A5078752284- RNA and protein synthesis mechanisms
- RNA modifications and cancer
- Genomics and Phylogenetic Studies
- RNA Research and Splicing
- Cancer-related molecular mechanisms research
- Machine Learning in Bioinformatics
- Microbial Natural Products and Biosynthesis
- Fungal and yeast genetics research
- RNA Interference and Gene Delivery
- Bacterial Genetics and Biotechnology
- Molecular Biology Techniques and Applications
- Microbial Metabolic Engineering and Bioproduction
- MicroRNA in disease regulation
- Advanced biosensing and bioanalysis techniques
- Plant Pathogens and Fungal Diseases
- CRISPR and Genetic Engineering
- Viral Infectious Diseases and Gene Expression in Insects
- Genomics and Chromatin Dynamics
- Plant Disease Resistance and Genetics
- RNA regulation and disease
- Mycotoxins in Agriculture and Food
- Endoplasmic Reticulum Stress and Disease
- Microbial Metabolism and Applications
- Probiotics and Fermented Foods
- Plant and fungal interactions
The University of Tokyo
1999-2024
Tokyo University of Science
1997-2023
Japan Science and Technology Agency
2023
National Institute of Advanced Industrial Science and Technology
2008-2017
Photonics Electronics Technology Research Association
2016
Instituto de Desarrollo Tecnológico para la Industria Química
2014
Instituto Tecnológico de Santo Domingo
2014
Niigata University
2011
Japan Biological Informatics Consortium
2007-2008
There are abundance of transcripts that code for no particular protein and remain functionally uncharacterized. Some these may have novel functions while others might be junk transcripts. Unfortunately, the experimental validation such to find functional non-coding RNA candidates is very costly. Therefore, our primary interest computationally mine candidate from a pool uncharacterized We introduce fRNAdb: database service hosts large collection including annotated/non-annotated sequences...
We developed a pair of databases that support two important tasks: annotation anonymous RNA transcripts and discovery novel non-coding RNAs. The database combo is called the Functional Database consists databases: rewrite original version (fRNAdb) latest UCSC GenomeBrowser for RNA. former sequence equipped with powerful search function hosts large collection known/predicted sequences acquired from existing as well novel/predicted reported by researchers Project. latter Genome Browser mirror...
Abstract RNA-binding proteins (RBPs) bind to their target RNA molecules by recognizing specific sequences and structural contexts. The development of CLIP-seq related protocols has made it possible exhaustively identify fragments that RBPs. However, no efficient bioinformatics method exists reveal the specificities RBP–RNA interactions using these data. We present CapR, an algorithm calculates probability each base position is located within secondary context. Using we demonstrate several...
Abstract Motivation: Ustiloxins A and B are toxic cyclic tetrapeptides, Tyr-Val/Ala-Ile-Gly (Y-V/A-I-G), that were originally identified from Ustilaginoidea virens, a pathogenic fungus affecting rice plants. Contrary to our report ustiloxin is ribosomally synthesized in Aspergillus flavus, recent suggested ustiloxins by non-ribosomal peptide synthetase U.virens. Thus, we analyzed the U.virens genome, identify responsible gene cluster. Results: The biosynthetic cluster was genome of based on...
Recent studies have revealed that large numbers of non-coding RNAs are transcribed in humans, but only a few them been identified with their functions. Identification the interaction target is an important step predicting The current experimental methods to identify RNA–RNA interactions, however, not fast enough apply whole human transcriptome. Therefore, computational predictions interactions desirable, this challenging task due huge costs involved. Here, we report comprehensive targets...
Abstract Motivation: The importance of RNA sequence analysis has been increasing since the discovery various types non-coding RNAs transcribed in animal cells. Conventional analyses have mainly focused on structured regions, which are stabilized by stacking energies acting adjacent base pairs. On other hand, recent findings regarding mechanisms small interfering (siRNAs) and transcription regulation microRNAs (miRNAs) indicate analyzing accessible regions where no pairs exist. So far,...
In the yeast Saccharomyces cerevisiae, terminator sequences not only terminate transcription but also affect expression levels of protein-encoded upstream terminator. The non-conventional Pichia pastoris (syn. Komagataella phaffii) has frequently been used as a platform for metabolic engineering knowledge regarding P. terminators is limited. To explore available to tune protein in pastoris, we created 'terminator catalog' by testing 72 sequences, including from S. cerevisiae or and synthetic...
Long noncoding RNAs (lncRNAs) play a key role in normal tissue differentiation and cancer development through their tissue-specific expression the human transcriptome. Recent investigations of macromolecular interactions have shown that lncRNAs form base-pairing with various mRNAs associated tissue-differentiation, suggesting specificity is an important factor controlling lncRNA-mRNA interactions.Here, we report specificities by using RNA-seq data across tissues as well computational...
The identification of novel miRNAs has significant biological and clinical importance. However, none the known miRNA features alone is sufficient for accurately detecting miRNAs. aim this paper to integrate these in a straightforward manner with better accuracy. Since most regions are highly conserved among vertebrates ability form stable hairpin structures, we implemented hidden Markov model that outputs multidimensional feature vectors composed both evolutionary secondary structural ones....
RNA secondary structure around translation initiation sites strongly affects the abundance of expressed proteins in Escherichia coli. However, detailed structural features governing protein remain elusive. Recent advances high-throughput DNA synthesis and experimental systems enable us to obtain large amounts data. Here, we evaluated six types using two large-scale datasets. We found that accessibility, which is probability a given region start codon has no base-paired nucleotides, showed...
Summary In our previous study, we serendipitously discovered that protein secretion in the methylotrophic yeast Pichia pastoris is enhanced by a mutation (V50A) mating factor alpha (MFα) prepro‐leader signal derived from Saccharomyces cerevisiae . present investigated 20 single‐amino‐acid substitutions, including V50A, located within MFα peptide, indicating V50A and several single mutations alone provided significant increase production of secreted proteins. addition to hydrophobicity index...
The filamentous fungus Aspergillus oryzae is widely used for secondary metabolite production by heterologous expression; thus, a wide variety of promoter tools necessary to broaden the application this species. Here we built procedure survey A. flavus genes constitutively highly expressed in 83 transcriptome datasets obtained under various conditions affecting production, find promoters useful expression oryzae. To test ability top 6 induce fungal metabolite, ustiloxin B, inserted before...
Expression of secreted recombinant proteins burdens the protein secretion machinery, limiting production. Here, we describe an approach to improving production by non-conventional yeast Komagataella phaffii comprised genome-wide screening for effective gene disruptions, combining them in a single strain, and recovering growth reduction adaptive evolution. For screen, designed multiwell-formatted, streamlined workflow high-throughput assay single-chain small antibody, which is cumbersome...
We report on chemically modified PCR primers that enable the design of flexible sticky ends by introducing a photo-cleavable group at phosphate moiety. DNA fragments synthesized using these can be ligated with higher efficiency.
Umbelopsis isabellina is a fungus in the subdivision Mucoromycotina, many members of which have been shown to be oleaginous and become important organisms for producing oil because their high level intracellular lipid accumulation from various feedstocks. The genome sequence U. NBRC 7884 was determined annotated, this information might provide insights into properties fungus.
Ustilaginoidea virens is a rice pathogenic fungus that causes false smut disease, disease seriously damages the yield and quality of grain. Analysis U. IPU010 33.6-Mb genome sequence will aid in understanding pathogenicity strain, particularly regard to effector proteins secondary metabolic genes.
An important problem in synthetic biology is to design a nucleotide sequence of an mRNA that confers desirable expression level target protein. The secondary structure protein-coding sequences (CDSs) one potential factor could have both positive and negative effects on protein production. To elucidate the role CDSs, algorithms for manipulating should be developed.We developed algorithm designing CDS with most stable among all possible ones translated into same protein, implemented it as...
MicroRNA (miRNA) precursor hairpins have a unique secondary structure, nucleotide length, and content that are in most cases evolutionarily conserved. The aim of this study was to utilize position-specific features miRNA improve their identification. To end, we defined the evolutionary structurally conserved each position with heuristically derived values, which were successfully integrated using probabilistic framework. Our method, miRRim2, can not only accurately detect hairpins, but infer...
Abstract Motivation Enhancing expression levels of a target protein is an important goal in synthetic biology. A widely used strategy to integrate multiple copies genes encoding into host organism genome. Integrating highly similar sequences, however, can induce homologous recombination between them, resulting the ultimate reduction number integrated genes. Results We propose method for designing protein-coding sequences (i.e. CDSs) that are unlikely recombination, while same protein. The...