Tong Wu

Mechanosensitive Endothelial METTL7A Regulates Internal m7G mRNA Methylation and Protects Against Atherosclerosis

This study identifies METTL7A as a mechanosensitive methyltransferase that regulates internal m7G methylation in endothelial cells, protecting against atherosclerosis through stabilization of anti-inflammatory transcripts.

Quantitative analysis of cis-regulatory elements in transcription with KAS-ATAC-seq

This study introduces KAS-ATAC-seq to quantitatively analyze cis-regulatory elements in transcription, showing improved identification of functional CREs compared to standard ATAC-seq.

5-hydroxymethylcytosine profiling of cell-free DNA identifies bivalent genes that are prognostic of survival in high-risk neuroblastoma.

The paper identifies bivalent genes in neuroblastoma cell-free DNA associated with poor prognosis in high-risk patients.

The chromatin landscape of the euryarchaeon Haloferax volcanii

This study uses ATAC-seq to map the chromatin accessibility of Haloferax volcanii and finds that promoter accessibility does not correlate with transcriptional activity, and archaeal chromatin is similarly accessible to eukaryotic chromatin.

KAS-pipe2: a flexible toolkit for exploring KAS-seq and spKAS-seq data

KAS-pipe2 is a toolkit for analyzing KAS-seq and spKAS-seq data, offering quality control, alignment, differential activity analysis, and novel features for studying transcription and R-loops.

The chromatin organization of a chlorarachniophyte nucleomorph genome

This study maps open chromatin, transcription, and 3D organization of the nucleomorph genome in Bigelowiella natans, revealing its highly accessible and transcribed state with strong nucleosome positioning and telomeric chromosome interactions.

Direct profiling of genome-wide dCas9 and Cas9 specificity using ssDNA mapping (CasKAS)

The paper introduces a method to profile off-target specificity of CRISPR enzymes using ssDNA mapping, applicable to both catalytically dead and active Cas9 variants.