Hideya Kawaji

The human RNA-DNA interactome is cell type-specific and dynamic

The paper maps RNA-DNA interactions in 16 human cell types, showing cell-type-specific and dynamic networks that correlate with gene regulation and disease traits.

Dual Developmental Origins and Activity-dependent Specification of Mammalian Subplate Neurons

The paper identifies two distinct developmental origins of subplate neurons in mammals through comparative single-cell and spatial transcriptomics across amniotes.

BRCA2 loss triggers a downward spiral of genomic instability via ROS-dependent metabolic collapse

This paper shows BRCA2 loss causes genomic instability through ROS-dependent metabolic collapse, highlighting the role of glutathione metabolism and PARP inhibitors in cell death.

Anti-amyloid beta therapy resolves stroke recovery impairment caused by Alzheimer's disease

This study shows that anti-amyloid beta therapy improves stroke recovery in the presence of cerebral amyloid beta accumulation by resolving myeloid immunity impairment.

Drug-induced cis-regulatory elements in human hepatocytes affect molecular phenotypes associated with adverse reactions

The paper identifies drug-induced cis-regulatory elements in human hepatocytes that influence molecular phenotypes linked to adverse drug reactions.

Systematic assessment of long-read RNA-seq methods for transcript identification and quantification

Benchmarking six long-read RNA-seq protocol-platform combinations and 14 tools across human, mouse, and manatee shows read length and accuracy drive isoform detection, depth drives quantification.

Homologous recombination contributes to the repair of acetaldehyde-induced DNA damages.

This study investigates how acetaldehyde-induced DNA damage is repaired, finding that homologous recombination and TDP1/TDP2 play critical roles in repair efficiency.

mRNA-based generation of marmoset PGCLCs capable of differentiation into gonocyte-like cells

This study generates marmoset PGCLCs from iPSCs using mRNA transfection and shows their differentiation into gonocyte-like cells in xenoreconstituted testes.

Spatial transcriptome of developmental mouse brain reveals temporal dynamics of gene expressions and heterogeneity of the claustrum

This study uses spatial transcriptomics to analyze the developing mouse brain, identifying novel molecular markers and revealing heterogeneity in the claustrum.

Chromosomal-scale De novo Genome Assemblies of Cynomolgus Macaque and Common Marmoset

This study presents de novo chromosome-scale genome assemblies for cynomolgus macaque and common marmoset using long-read and Hi-C data, achieving high contiguity and accuracy.

Functional Annotation of Human Long Non-Coding RNAs via Molecular Phenotyping

The paper functionally annotates human long non-coding RNAs by systematically knocking down 285 lncRNAs and analyzing molecular phenotypes using CAGE sequencing.

Predicting cell-type-specific non-coding RNA transcription from genome sequence

The paper develops MENTR, a machine learning framework to predict cell-type-specific ncRNA transcription from genome sequence, identifying causal variants and ncRNAs associated with complex traits.

Assessment of mapping strategies for determining the 5'-end of mRNAs and long-noncoding RNAs with short read sequences

The paper evaluates mapping strategies for CAGE reads to determine 5'-end sequences of mRNAs and long-noncoding RNAs, finding that strategy choice affects alignment accuracy and biological interpretation.

DUX4 regulates oocyte to embryo transition in human

This study shows that DUX4 regulates the oocyte-to-embryo transition in humans by activating enhancers and promoting genome reprogramming.

Dynamics and Topology of Human Transcribed Cis-regulatory Elements

The paper develops NET-CAGE to detect nascent RNA 5-ends, identifies enhancer-promoter pairs, and reveals topological connections of cis-regulatory elements across cell types.

AGO1 in association with NEAT1 lncRNA contributes to nuclear and 3D chromatin architecture in human cells

This study shows AGO1 and NEAT1 lncRNA maintain 3D chromatin architecture by regulating TADs and A/B compartments in human cells.

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

The paper investigates how Wnt-responsive enhancers selectively activate alternative MYC promoters, showing their role in differential promoter usage and the influence of core promoter elements.

dirHub: a trackHub configurator with directory structure projection

dirHub generates configuration files for trackHub visualization by projecting directory structures, simplifying setup through file operations.

Integrative analysis of transcription factor occupancy at enhancers and disease risk loci in noncoding genomic regions

The paper integrates public ChIP-seq and DNase-seq data to identify transcription factor interactions and their association with disease risk loci in noncoding regions.

Shared activity patterns arising at genetic susceptibility loci reveal underlying genomic and cellular architecture of human disease.

The paper identifies shared expression patterns of genetic variants across tissues and cell types, enabling fine mapping of disease-associated variants and revealing key cell types involved in disease pathogenesis.

Linking FANTOM5 CAGE Peaks To Annotations With CAGEscan

The paper enhances the FANTOM5 expression atlas by associating gene-orphan promoter regions with their transcripts using CAGEscan.

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

CAGEd-oPOSSUM analyzes CAGE-derived TSSs to identify transcription factors regulating gene expression in specific cell types and conditions.

A role for YY1 in sex-biased transcription revealed through X-linked promoter activity and allelic binding analyses

The paper identifies YY1's role in X-linked gene escape from inactivation by analyzing promoter activity and allelic binding in human datasets.