Hazuki Takahashi

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 introduces nucCAGE and PRIME to identify active cis-regulatory elements with high sensitivity and applies them to create a cell-type-resolved CRE atlas.

The paper maps RNA-chromatin interactions in human prefrontal cortex, revealing co-regulatory changes linked to brain evolution and disease pathways.

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 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 CapTrap-seq, a method for full-length RNA transcript sequencing, and shows it produces highly accurate transcript models in human tissues.

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.

The paper investigates sequence, structure, and functional features of SINE-derived RNAs in SINEUP non-coding RNAs, showing their role in post-transcriptional gene regulation through interactions with RBPs and ribosomal RNAs.

The paper analyzes antisense lncRNAs in zebrafish development, identifying two groups with distinct expression patterns, localization, and regulatory features.

The paper introduces LQ-ssCAGE, a cost-effective CAGE method for low quantity RNA samples, and demonstrates its use in identifying novel enhancer and promoter-derived lncRNAs.

The paper investigates how SINEUP lncRNAs enhance translation by interacting with PTBP1 and HNRNPK to facilitate translational initiation complexes in HEK293T/17 cells.