Tsukasa Kouno

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.

ASCL1 primes medullary thymic epithelial cell programs required for central tolerance

The paper identifies ASCL1 as a key regulator of mTEC function and central tolerance by analyzing single-cell RNA sequencing data from thymoma patients and mouse models.

A genome-wide, machine learning-guided exploration of the cis-regulatory code involved in neuronal differentiation

The paper develops a machine learning method to identify cis-regulatory element profiles and their sequence features during neuronal differentiation using single-cell ATAC-seq and RNA-seq data.

Genomic codes governing enhancer RNA fate

This paper introduces CFC-seq and SALA to sequence non-poly(A) RNAs, identifies 39,425 novel transcriptional units, and reveals a genomic code governing enhancer RNA fate based on promoter architecture.

Single-cell analysis of human diversity in circulating immune cells

The paper presents AIDA, a diverse single-cell RNA-seq atlas of immune cells, revealing sub-continental diversity impacts on immune cell properties and identifying functional genetic variants.

A single-cell atlas of transcribed cis-regulatory elements in the human genome

The paper constructs a single-cell atlas of transcribed cis-regulatory elements in the human genome, revealing gene regulation patterns and trait-gene relationships across cell populations.

Antisense oligonucleotide-mediated perturbation of long non-coding RNA reveals functional features in stem cells and across cell types

The paper performs knockdown of 200 lncRNAs in human iPS cells, identifies 36 with growth inhibition, and finds molecular phenotypes in 29.3% of cases, with higher agreement in molecular than cell growth phenotypes across cell types.

Microglia integration into human midbrain organoids leads to increased neuronal maturation and functionality.

This study integrates human iPSC-derived microglia into midbrain organoids, enhancing neuronal maturation and functionality through effects on synaptic remodeling and excitability.

Autism in a dish: ES cell models of autism with copy number variations reveal cell-type-specific vulnerability

The paper establishes genetically modified mouse embryonic stem cell lines for autism spectrum disorder research and uses single-cell RNA sequencing to identify cell-type and CNV-specific molecular features.

Profiling of transcribed cis-regulatory elements in single cells

This paper introduces sc-end5-seq and SCAFE to profile transcribed cis-regulatory elements in single cells, showing tCREs improve prediction of CRE interactions and disease heritability.

LETR1 is a lymphatic endothelial-specific lncRNA that governs cell proliferation and migration through KLF4 and SEMA3C

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.

Brainstem organoids from human pluripotent stem cells contain neural crest population

This study develops human brainstem organoids containing neural crest cells and various neuron types, validated by single-cell RNA sequencing, proteomics, and electrophysiology.

Decoding neuronal diversity by single-cell Convert-seq

This study introduces Convert-seq, a method combining scRNA-seq and ectopic gene expression to identify gene regulatory networks during cell reprogramming.

C1 CAGE detects transcription start sites and enhancer activity at single-cell resolution

C1 CAGE detects transcription start sites and enhancer activity in lung cancer cells, revealing subpopulations with distinct responses to TGF-β and enhancer RNA dynamics.

Single-cell transcriptomes of fluorescent, ubiquitination-based cell cycle indicator cells

The paper generates a single-cell RNA-seq dataset of HeLa cells labeled with Fucci reporters and provides an open workflow for data processing and quality control.