東京大学 · Biochemistry, Genetics and Molecular Biology
류이치로 나카토 교수의 연구실은 에피제놈 연구를 중심으로, 히스톤 변형과 단백질-DNA 상호작용을 고분해능 유전자 분석 기법을 통해 세포 정체성, 발달 및 질병 메커니즘을 규명하는 데 집중하고 있습니다. 특히 ChIP-seq를 활용한 대량 스크리닝과 고해상도 게놈 구조 분석을 통해 조절 염기서열의 기능적 역할을 밝혀내는 데 주력하고 있으며, 핵내 상피체 형성과 유전자 발현 조절의 관계를 탐구하고 있습니다. 연구는 실험 설계, 데이터 품질 관리, 고성능 계산 분석까지 종합적인 접근을 통해 진행됩니다.
표시된 성과는 수집된 데이터 기준으로 산출되며, 일부 차이가 있을 수 있습니다.
Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is a central method in epigenomic research. Genome-wide analysis of histone modifications, such as enhancer analysis and genome-wide chromatin state annotation, enables systematic analysis of how the epigenomic landscape contributes to cell identity, development, lineage specification, and disease. In this review, we first present a typical ChIP-seq analysis workflow, from quality assessment to chromatin-state annotation. We focus o
Chromatin immunoprecipitation followed by sequencing (ChIP-seq) analysis can detect protein/DNA-binding and histone-modification sites across an entire genome. Recent advances in sequencing technologies and analyses enable us to compare hundreds of samples simultaneously; such large-scale analysis has potential to reveal the high-dimensional interrelationship level for regulatory elements and annotate novel functional genomic regions de novo. Because many experimental considerations are relevant
Chromatin immunoprecipitation with high-throughput sequencing (ChIP-seq) can identify genomic regions that bind proteins involved in various chromosomal functions. Although the development of next-generation sequencers offers the technology needed to identify these protein-binding sites, the analysis can be computationally challenging because sequencing data sometimes consist of >100 million reads/sample. Herein, we describe a cost-effective and time-efficient protocol that is generally applicab
This comprehensive analysis of epigenome characterization of EC types reveals diverse transcriptional regulation across human vascular systems. These datasets provide a valuable resource for understanding the vascular system and associated diseases.
Supplementary data are available at Bioinformatics online.
NUP98 and NUP214 form chimeric fusion proteins that assemble into phase-separated nuclear bodies containing CRM1, a nuclear export receptor. However, these nuclear bodies' function in controlling gene expression remains elusive. Here, we demonstrate that the nuclear bodies of NUP98::HOXA9 and SET::NUP214 promote the condensation of mixed lineage leukemia 1 (MLL1), a histone methyltransferase essential for the maintenance of HOX gene expression. These nuclear bodies are robustly associated with M
Cohesin regulates gene expression through context-specific chromatin folding mechanisms such as enhancer-promoter looping and topologically associating domain (TAD) formation by cooperating with factors such as cohesin loaders and the insulation factor CTCF. We developed a computational workflow to explore how three-dimensional (3D) structure and gene expression are regulated collectively or individually by cohesin and related factors. The main component is CustardPy, by which multi-omics datase
Eukaryotic genomes are organized in a three-dimensional spatial structure. In this regard, the development of chromosome conformation capture methods has enabled studies of chromosome organization on a genomic scale. Hi-C, the high-throughput chromosome conformation capture method, can reveal a population-averaged, hierarchical chromatin structure. The typical Hi-C analysis uses a two-dimensional (2D) contact matrix that indicates contact frequencies between all possible genomic position pairs.
Cgaln is not only fast and memory efficient but also effective in coping with genomic rearrangements. Our results show that Cgaln is very effective for comparison of large genomes, especially of intact chromosomal sequences. We believe that Cgaln provides novel viewpoint for reducing computational complexity and will contribute to various fields of genome science.
