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Genome Annotation [chapter]

Hideya Kawaji, Yoshihide Hayashizaki
2008 Msphere  
doi:10.1007/978-1-60327-159-2_6 pmid:18563372 fatcat:4nwvahclvrbndivcyqbnqnt5ze

dirHub: a trackHub configurator with directory structure projection [article]

Hideya Kawaji
2018 bioRxiv   pre-print
Summary: Track Data Hub is a mechanism enabling us to visualize genomics data as tracks along genome coordinates and share them over the Internet, relying on a web server hosting data files and genome browsers offering graphical representations. It requires an accessible configuration file specifying all graphical parameters and track hierarchy, in addition to the data files. Here dirHub is developed to assist generation of the configuration file by projection of a file directory structure,
more » ... h makes it possible to set up trackHub visualization mostly by file operations. Availability and implementation: It is implemented in ruby and the source code is available at https://github.com/hkawaji/dirHub/ . It is tested on the UCSC Genome Browser and the Hub Track Database Definition (v2).
doi:10.1101/314807 fatcat:cpsymgt4r5copnxbbthmdwoeiu

Exploration of Small RNAs

Hideya Kawaji, Yoshihide Hayashizaki
2008 PLoS Genetics  
F or several decades, only a limited number of noncoding RNAs, such as ribosomal and transfer RNA, have been studied in any depth. In recent years, additional species of noncoding RNAs have increasingly been discovered. Of these, small RNA species attract particular interest because of their essential roles in processes such as RNA silencing and modifications. Detailed analyses revealed several pathways associated with the function of small RNAs. Although these pathways show evolutional
more » ... tion, there are substantial differences. Advanced technologies to profile RNAs have accelerated the field further resulting in the discovery of an increasing number of novel species, suggesting that we are only just beginning to appreciate the complexity of small RNAs and their functions. Here, we review recent progress in novel small RNA exploration, including discovered small RNA species, their pathways, and devised technologies.
doi:10.1371/journal.pgen.0040022 pmid:18225959 pmcid:PMC2213711 fatcat:kgzctk37jvf47o5ymtnoathiti

CAGEd-oPOSSUM: motif enrichment analysis from CAGE-derived TSSs [article]

David J Arenillas, Alistair R.R. Forrest, Hideya Kawaji, Timo Lassman, Wyeth W. Wasserman, Anthony Mathelier
2016 bioRxiv   pre-print
Summary: With the emergence of large-scale Cap Analysis of Gene Expression (CAGE) data sets from individual labs and the FANTOM consortium, one can now analyze the cis-regulatory regions associated with gene transcription at an unprecedented level of refinement. By coupling transcription factor binding site (TFBS) enrichment analysis with CAGE-derived genomic regions, CAGEd-oPOSSUM can identify TFs that act as key regulators of genes involved in specific mammalian cell and tissue types. The
more » ... ool allows for the analysis of CAGE-derived transcription start sites (TSSs) either provided by the user or selected from ∼1,300 mammalian samples from the FANTOM5 project with pre-computed TFBS predicted with JASPAR TF binding profiles. The tool helps power insights into the regulation of genes through the study of the specific usage of TSSs within specific cell types and/or under specific conditions. Availability and implementation: The CAGEd-oPOSUM web tool is implemented in Perl, MySQL, and Apache and is available at http://cagedop.cmmt.ubc.ca/CAGEd_oPOSSUM. Supporting Information: Supplementary Text, Figures, and Data are available online at bioRxiv.
doi:10.1101/040667 fatcat:rv6kucg73ncy7bwwnb3yzuftii

Selective activation of alternative MYC core promoters by Wnt-responsive enhancers [article]

Jorge A Bardales, Evin Wieser, Hideya Kawaji, Yasuhiro Murakawa, Xavier Darzacq
2018 bioRxiv   pre-print
In Metazoans, transcription of most genes is driven through the use of multiple alternative promoters. Although the precise spatio-temporal regulation of alternative promoters is important for proper gene expression, the mechanism that mediates their differential utilization remains unclear. Here, we investigate how the two alternative promoters (P1, P2) that drive MYC expression are regulated. We find that P1 and P2 can be differentially regulated across cell-types, and that their selective
more » ... ge is largely mediated by distal regulatory sequences. Moreover, we show that in the colon carcinoma cell line HCT-116, Wnt-responsive enhancers preferentially upregulate transcription from the P1 promoter using both transgenic reporter assays and in the context of the endogenous Myc locus upon Wnt induction. In addition, multiple enhancer deletions using CRISPR/Cas9 corroborate the regulatory specificity of P1. Finally, we show that preferential activation between Wnt-responsive enhancers and the P1 promoter is influenced by distinct core promoter elements present in the two MYC promoters. Taken together, our results provide new insights into how enhancers can specifically target alternative promoters and suggest that formation of these selective interactions could allow more diverse combinatorial regulation of transcription initiation.
doi:10.1101/266387 fatcat:koxyp4ehyjbkrlulmocirssudi

Selective Activation of Alternative MYC Core Promoters by Wnt-Responsive Enhancers

Jorge Bardales, Evin Wieser, Hideya Kawaji, Yasuhiro Murakawa, Xavier Darzacq
2018 Genes  
In Metazoans, transcription of most genes is driven by the use of multiple alternative promoters. Although the precise regulation of alternative promoters is important for proper gene expression, the mechanisms that mediates their differential utilization remains unclear. Here, we investigate how the two alternative promoters (P1, P2) that drive MYC expression are regulated. We find that P1 and P2 can be differentially regulated across cell-types and that their selective usage is largely
more » ... d by distal regulatory sequences. Moreover, we show that in colon carcinoma cells, Wnt-responsive enhancers preferentially upregulate transcription from the P1 promoter using reporter assays and in the context of the endogenous Wnt induction. In addition, multiple enhancer deletions using CRISPR/Cas9 corroborate the regulatory specificity of P1. Finally, we show that preferential activation between Wnt-responsive enhancers and the P1 promoter is influenced by the distinct core promoter elements that are present in the MYC promoters. Taken together, our results provide new insight into how enhancers can specifically target alternative promoters and suggest that formation of these selective interactions could allow more precise combinatorial regulation of transcription initiation.
doi:10.3390/genes9060270 pmid:29882899 pmcid:PMC6027352 fatcat:py57win4d5bofk6l4kpnnxojne

SDRF2GRAPH – a visualization tool of a spreadsheet-based description of experimental processes

Hideya Kawaji, Yoshihide Hayashizaki, Carsten O Daub
2009 BMC Bioinformatics  
As larger datasets are produced with the development of genome-scale experimental techniques, it has become essential to explicitly describe the meta-data (information describing the data) generated by an experiment. The experimental process is a part of the metadata required to interpret the produced data, and SDRF (Sample and Data Relationship Format) supports its description in a spreadsheet or tab-delimited file. This format was primarily developed to describe microarray studies in
more » ... and it is being applied in a broader context in ISA-tab. While the format provides an explicit framework to describe experiments, increase of experimental steps makes it less obvious to understand the content of the SDRF files.
doi:10.1186/1471-2105-10-133 pmid:19422683 pmcid:PMC2689195 fatcat:6nm6zzryszc35bpsh77dvotqje

CAGEd-oPOSSUM: motif enrichment analysis from CAGE-derived TSSs

David J. Arenillas, Alistair R. R. Forrest, Hideya Kawaji, Timo Lassmann, Wyeth W. Wasserman, Anthony Mathelier
2016 Bioinformatics  
With the emergence of large-scale Cap Analysis of Gene Expression data sets from individual labs and the FANTOM consortium, one can now analyze the cis-regulatory regions associated with gene transcription at an unprecedented level of refinement. By coupling transcription factor binding site (TFBS) enrichment analysis with CAGE-derived cis-regulatory regions, CAGEd-oPOSSUM can identify TFs that act as key regulators of genes involved in specific mammalian cell and tissue types. The webtool
more » ... s for the analysis of CAGE-derived transcription start sites (TSSs) either (i) provided by the user or (ii) selected from ~1,300 mammalian samples from the FANTOM5 project with pre-computed TFBS predicted with JASPAR TF binding profiles. The tool can help power insights into the transcriptional regulation of genes through the study of the specific usage of TSSs within specific cell types and/or under specific conditions. Availability and implementation: The CAGEd-oPOSUM web tool is implemented in Perl, MySQL, and Apache and is available at
doi:10.1093/bioinformatics/btw337 pmid:27334471 pmcid:PMC5018375 fatcat:u6oscpafrjgkzl4yvn5nsb6wv4

Novel Small Noncoding RNAs in Mouse Spermatozoa, Zygotes and Early Embryos

Mitsuoki Kawano, Hideya Kawaji, Valérie Grandjean, Jafar Kiani, Minoo Rassoulzadegan, Liang-Hu Qu
2012 PLoS ONE  
The recent discovery of a significant amount of RNA in spermatozoa contradicted the previously held belief that paternal contribution was limited to one copy of the genome. Furthermore, detection of RNA in sperm raised the intriguing question of its possible role in embryonic development. The possibility that RNAs may serve as epigenetic determinants was supported by experiments showing inheritance of epigenetic traits in mice mediated by RNA. We used high-throughput, large-scale sequencing
more » ... nology to analyze sperm RNA. The RNA sequences generated were diverse in terms of length and included mRNAs, rRNAs, piRNAs, and miRNAs. We studied two small noncoding RNAs enriched in mature sperm, designated sperm RNAs (spR) 212 and 213. They are both encoded in a piRNA locus on chromosome 17, but neither their length (20-21 nt), nor their sequences correspond to known piRNAs or miRNAs. They are resistant to periodate-oxidationmediated reaction, implying that they undergo terminal post-transcriptional modification. Both were detected in sperm and ovulated unfertilized oocytes, present in one-cell embryos and maintained in preimplantation stages, but not at later differentiation stages. These findings offer a new perspective regarding a possibly important role for gamete-specific small RNAs in early embryogenesis.
doi:10.1371/journal.pone.0044542 pmid:22984523 pmcid:PMC3440372 fatcat:anic5veok5g25mlvs5e2agbevm

Assessment of mapping strategies for determining the 5ʹ-end of mRNAs and long-noncoding RNAs with short read sequences [article]

Shuhei Noguchi, Hideya Kawaji, Takeya Kasukawa
2020 bioRxiv   pre-print
Genome mapping is an essential step in data processing for transcriptome analysis, and many previous studies have evaluated various methods and strategies for mapping RNA-seq data. Cap Analysis of Gene Expression (CAGE) is a sequencing-based protocol particularly designed to capture the 5'-ends of transcripts for quantitatively measuring the expression levels of transcription start sites genome-wide. Because CAGE analysis can also predict the activities of promoters and enhancers, this protocol
more » ... has been an essential tool in studies of transcriptional regulation. Typically, the same mapping software is used to align both RNA-seq data and CAGE reads to a reference genome, but which mapping software and options are most appropriate for mapping the 5'-end sequence reads obtained through CAGE has not previously been evaluated systematically. Here we assessed various strategies for aligning CAGE reads, particularly ~50-bp sequences, with the human genome by using the HISAT2, LAST, and STAR programs both with and without a reference transcriptome. One of the major inconsistencies among the tested strategies involves alignments to pseudogenes and parent genes: some of the strategies prioritized alignments with pseudogenes even when the read could be aligned with coding genes with fewer mismatches. Another inconsistency concerned the detection of exon-exon junctions. These preferences depended on the program applied and whether a reference transcriptome was included. Overall, the choice of strategy yielded different mapping results for approximately 2% of all promoters. Although the various alignment strategies produced very similar results overall, we noted several important and measurable differences. In particular, using the reference transcriptome in STAR yielded alignments with the fewest mismatches. In addition, the inconsistencies among the strategies were especially noticeable regarding alignments to pseudogenes and novel splice junctions. Our results indicate that the choice of alignment strategy is important because it might affect the biological interpretation of the data.
doi:10.1101/2020.03.14.982991 fatcat:id7dk2weh5fm7lymqautpbvcha

Dynamic usage of transcription start sites within core promoters

Hideya Kawaji, Martin C Frith, Shintaro Katayama, Albin Sandelin, Chikatoshi Kai, Jun Kawai, Piero Carninci, Yoshihide Hayashizaki
2006 Genome Biology  
Biology 2006, 7:R118 R118.8 Genome Biology 2006, Volume 7, Issue 12, Article R118 Kawaji et al. http://genomebiology.com/2006/7/12/R118 Genome Biology 2006, 7:R118  ...  et al. http://genomebiology.com/2006/7/12/R118 Genome Biology 2006, 7:R118 R118.6 Genome Biology 2006, Volume 7, Issue 12, Article R118 Kawaji et al. http://genomebiology.com/2006/7/12/R118 Genome  ... 
doi:10.1186/gb-2006-7-12-r118 pmid:17156492 pmcid:PMC1794431 fatcat:vyi7ckmfkfdnfnhvgviywevqmy

Hidden layers of human small RNAs

Hideya Kawaji, Mari Nakamura, Yukari Takahashi, Albin Sandelin, Shintaro Katayama, Shiro Fukuda, Carsten O Daub, Chikatoshi Kai, Jun Kawai, Jun Yasuda, Piero Carninci, Yoshihide Hayashizaki
2008 BMC Genomics  
Small RNA attracts increasing interest based on the discovery of RNA silencing and the rapid progress of our understanding of these phenomena. Although recent studies suggest the possible existence of yet undiscovered types of small RNAs in higher organisms, many studies to profile small RNA have focused on miRNA and/or siRNA rather than on the exploration of additional classes of RNAs. Results: Here, we explored human small RNAs by unbiased sequencing of RNAs with sizes of 19-40 nt. We provide
more » ... substantial evidences for the existence of independent classes of small RNAs. Our data shows that well-characterized non-coding RNA, such as tRNA, snoRNA, and snRNA are cleaved at sites specific to the class of ncRNA. In particular, tRNA cleavage is regulated depending on tRNA type and tissue expression. We also found small RNAs mapped to genomic regions that are transcribed in both directions by bidirectional promoters, indicating that the small RNAs are a product of dsRNA formation and their subsequent cleavage. Their partial similarity with ribosomal RNAs (rRNAs) suggests unrevealed functions of ribosomal DNA or interstitial rRNA. Further examination revealed six novel miRNAs. Conclusion: Our results underscore the complexity of the small RNA world and the biogenesis of small RNAs.
doi:10.1186/1471-2164-9-157 pmid:18402656 pmcid:PMC2359750 fatcat:3cdgijy76jhv7a62iksyo44swy

Identification of chromatin marks at TERRA promoter and encoding region

Yutaka Negishi, Hideya Kawaji, Aki Minoda, Kengo Usui
2015 Biochemical and Biophysical Research Communications - BBRC  
TERRA is a long non-coding RNA that is essential for telomere integrity. Although it is transcribed from subtelomeres and telomeres, how it is expressed in heterochromatic region is currently unknown. In this study, we focused our analysis on TERRA-encoding region TelBam3.4 and TelBam3.4-like sequences, and determined their transcription start sites, as well as enrichment of RNA polymerase II and histone modifications. We found that H3K4me3 and H3K9me3 are present at TERRA promoters, whereas
more » ... 27ac and H3K9me3 are present at telomeric repeats. Consistently, we show that presence of active histone modifications H3K4me3 and H3K27ac are correlated to TERRA expression. These results mark an important step towards understanding telomere maintenance and transcription.
doi:10.1016/j.bbrc.2015.09.176 pmid:26449455 fatcat:hssqzx4rznd7hk4zy7p4lglmkq

The FANTOM5 collection, a data series underpinning mammalian transcriptome atlases in diverse cell types

Hideya Kawaji, Takeya Kasukawa, Alistair Forrest, Piero Carninci, Yoshihide Hayashizaki
2017 Scientific Data  
The latest project from the FANTOM consortium, an international collaborative effort initiated by RIKEN, generated atlases of transcriptomes, in particular promoters, transcribed enhancers, and long-noncoding RNAs, across a diverse set of mammalian cell types. Here, we introduce the FANTOM5 collection, bringing together data descriptors, articles and analyses of FANTOM5 data published across the Nature Research journals. Associated data are openly available for reuse by all. Our genomes contain
more » ... the complete set of information necessary to specify our development from a single totipotent cell to a complex multicellular organism, composed of hundreds of specialized cell types able to respond to environmental changes. In each of these cell types, and their responding states, different sets of genes are expressed through transcription. Determining the transcriptome, including the set of genes expressed, is fundamental to understanding cellular identity, gene regulation and human disease. The FANTOM (Functional Annotation of Mammalian Genomes) project was launched to provide a comprehensive catalogue of transcripts encoded in mammalian genomes (http://fantom.gsc.riken.jp). With the full-length cDNA technology developed at RIKEN 1 , the first, second and third rounds of the FANTOM projects surveyed the mammalian transcriptome landscape by sequencing a large collection of full-length cDNAs. This improved our catalog of protein coding genes, but also revealed the new world of long non-protein coding RNAs 2-7 (a major novel class of genes that had been overlooked). The captrapper reaction, initially used to select full-length cDNAs, was later used to develop CAGE (Cap Analysis Gene Expression) that quantifies transcription starting sites (TSSs) at single base-pair resolution 8 . With this method, the FANTOM3 project globally mapped TSSs in the mouse genome. This helped classify mammalian promoters into broad-CpG and sharp-TATA associated promoter architectures 9 . Subsequently the FANTOM4 project used CAGE and predicted proximal promoter transcription factor binding motifs to decipher the transcriptional regulatory network of a myeloid leukemia cell line undergoing differentiation 10 . Additionally, the new CAGE data revealed that a large fraction of the transcriptome initiates from retrotransposon derived sequences, and these exhibit exquisite tissue specificity 6 . Most recently the FANTOM5 11-13 project aimed at comprehensive maps of transcription initiation activities across the most diverse collection of cell types studied to date. A focus on normal, primary cells differentiated FANTOM5 from previous transcriptome studies. Most other broad studies had focused on 1
doi:10.1038/sdata.2017.113 pmid:28850107 pmcid:PMC5574373 fatcat:5ooytyc2lndm3gvkx4kv6atvgy

Designing Database Systems for Efficient Analyses in Breeding Tests of Plants

Etsuko INOUE, Takuya YOSHIHIRO, Hideya KAWAJI, Keiichi NEGORO, Hiromi HANADA, Manabu WANAKA, Masaru NAKAGAWA
2007 Joho Chishiki Gakkaishi  
全国の農業試験場などで実施されている育種・栽培試験のデータの管理および分析支援を実現するデー タベースシステムを構築した.育種・栽培試験の現場では,植物を生育する労力だけでなく,データ分析の労 力も無視できない.そこで,現場の研究者へのヒアリングや試験事例の文献調査により,育種・栽培試験デー タをモデル化した.また,このモデルを用いて分析支援システムを構築し,分析作業にかかるデータの可視化 作業の効率化を実現した.本システムは,ユーザの利便性を第一に設計し,現場の研究者が普段より使用し ている表計算ソフトのファイルを用いて容易にデータベースへのデータ登録が行える.また,Web ブラウザ上で 容易にグラフ表示などの可視化を行えるほか,特定条件のデータのみをダウンロードする機能などにより,現 場の分析作業を支援する.本研究では,試験事例である文献を対するモデルの適用性の調査と,実際の育 種・栽培試験のデータ分析へのシステムの適用実験により評価を行った. We developed a database system to store and analyze crop data which
more » ... re obtained in breeding tests of various plants. In operating breeding tests, researchers pay considerable labor not only for cultivating but also analyzing obtained data. To improve it, we performed a data-modeling of crop data through investigating a number of 論文
doi:10.2964/jsik.17.2 fatcat:npqy7zxjinb6xiuhu7ajodxrlm
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