Masaki Kato

The paper identifies repeat element-anchored enhancer-promoter interactions (REEPIs) in hormone-resistant breast cancer and links them to transcriptional adaptation and regulatory reprogramming.

The paper identifies new gene products and transcript isoforms in macrophage differentiation and activation, revealing how alternative promoters influence innate immune functions.

The paper integrates enhancer-promoter interactions and RNA-DNA contacts to show RNA's role in modulating cis-regulatory networks during neural differentiation.

The paper identifies hypoacetylation-defined enhancers in luminal breast cancer cells and links them to subtype-specific gene regulation and patient classification.

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.

The paper identifies trans-contacting intronic RNAs (TIRs) in neuronal cells that form nuclear scaffolds called introsomes, influencing 3D genome organization and gene expression.

The paper identifies 3UTR-derived capped RNAs, showing they are abundant and originate from AGO2-mediated cleavage at G-quadruplexes, with implications for APP protein regulation.

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.

The paper introduces RADIP, a new technology for mapping RNA-chromatin interactions mediated by H3K27me3, and demonstrates its application in mouse embryonic stem cells.