Jane A. Skok

The paper identifies a developmentally regulated long-range enhancer-promoter contact that is critical for SOX2 expression and neuroectodermal differentiation in human neural development.

This study shows that DNA damage in glioblastoma cells leads to long-term chromatin changes and gene expression reprogramming, affecting cellular function and tumor outcomes.

The paper shows cohesin collisions maintain ordered nucleosome architecture at CTCF sites and promoters, independent of CTCF occupancy or cohesin levels.

This study shows that chromatin architecture and physical constriction together drive phenotype switching and metastasis in melanoma by altering CTCF positioning and heterochromatin structure.

This study identifies HOXD13 as a driver of a developmental program in melanoma that promotes angiogenesis and suppresses T-cell infiltration through a gene regulatory axis involving VEGFA, SEMA3A, and CD73.

The paper uses nano-NOMe-seq to phase single-molecule chromatin states and link them to transcriptional activity, revealing heterogeneity in enhancer-promoter interactions.

The paper creates a database of multi-target CRISPR-Cas9 guide-RNAs with on- and off-target scores and provides a web tool for selecting these guide-RNAs.

The paper investigates how CTCF mutations affect chromatin accessibility, cohesin binding, and gene regulation through multivariate modeling and mutant perturbations.

The paper investigates how CTCF, cohesin, and TFs influence nucleosome repositioning and chromatin insulation across cell states using mouse and human data.

This study introduces C.Origami, a deep learning model that predicts cell type-specific 3D chromatin organization, enabling in silico genetic screening to identify genomic regions affecting chromatin structure.

The paper identifies new therapeutic targets in CRLF2-overexpressing B-ALL by analyzing TF-gene regulatory interactions using network inference and experimental validation.

CRISPR-Decryptr analyzes noncoding CRISPR screens to infer regulatory elements by accounting for experimental design and validating on published data.

The paper investigates the distinct and combined roles of CTCF and CTCFL in chromosome organization and transcription by analyzing their binding sites and functional domains.

EpiMethylTag combines ATAC-seq or ChIP-seq with bisulfite conversion to simultaneously assess chromatin accessibility/TF binding and DNA methylation.

The paper shows NSD2 overexpression alters chromatin structure and gene expression by affecting CTCF and H3K27ac in specific chromatin domains.

This study shows that reducing EHMT1/2 activity during reprogramming with ascorbic acid impairs iPSC formation and viability, highlighting the role of H3K9 methylation in reprogramming efficiency.

The paper shows that CTCF's RNA-binding ability is crucial for its chromatin association and insulation function.

The paper demonstrates a two-step mechanism of PRC2-mediated repressive domain formation through nucleation sites and long-range spreading of H3K27me2/3.

The paper introduces 4Tran, a method to study transposon interactions in the genome, revealing their role in chromatin organization and gene regulation.