Hiromi Nishiyori-Sueki

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.

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.

CapTrap-Seq: A platform-agnostic and quantitative approach for high-fidelity full-length RNA transcript sequencing

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

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.

Discovery of widespread transcription initiation at microsatellites predictable by sequence-based deep neural network.

The paper identifies widespread transcription initiation at microsatellites across species and develops deep learning models to predict STR-associated transcription and its impact on disease variants.

Low Quantity single strand CAGE (LQ-ssCAGE) maps regulatory enhancers and promoters

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.

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.