Chi Wai Yip

This study shows that knocking down DNAAF3-AS1 reduces gene-body H3K36me3, activates the p53 pathway, and alters promoter usage in apoptosis-related genes.

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 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 RNA-initiating sites at STRs and links them to gene expression, revealing regulatory roles and interactions with Alu repeats.

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 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.

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.

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.

The paper identifies cis-interacting lncRNAs and their targets using RNA-chromatin and Hi-C data across 18 human cell types.

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