Miao Yu

The paper integrates 4D Nucleome data to analyze 3D genome structure and function in human cells, revealing chromatin domains, loops, and interactions, and showing how genetic variants affect genome folding.

The paper maps chromatin interactions in mouse fetal tissues and links them to gene expression and disease risk variants in humans.

This study identifies ZNHIT1's role in meiotic progression by regulating H2A.Z deposition and gene expression during pachytene in male meiosis.

This study investigates how chromatin-associated RNA interacts with 3D genome organization in human cells, revealing a feedback loop between RNA distribution and chromatin structure.

SnapHiC-D identifies differential chromatin contacts between two scHi-C datasets with high sensitivity and accuracy, showing correlation with cell-type-specific gene expression and epigenomic features.

CRISPRpath enables parallel characterization of cis-regulatory elements for multiple genes in a pathway, identifying functional enhancers and distinguishing their impact on gene expression.

This study shows that chromatin organization remains largely intact in mouse embryonic stem cells after acute CTCF depletion, despite reduced cell growth and changes in chromatin loop interactions and cohesin occupancy.

SnapHiC identifies high-resolution chromatin loops from scHi-C data and demonstrates cell-type-specific chromatin architecture in mouse and human cells.

This study investigates how CTCF binding sites mediate transcriptional insulation in mouse embryonic stem cells, showing that insulation depends on CTCF site number, sequence context, and TAD boundary location.

This study shows that CTCF depletion in mESCs weakens TAD boundaries and INs but only affects a small subset of enhancer-promoter contacts, highlighting CTCF's role in promoting long-range gene regulation.

The paper identifies cell type-specific enhancer-promoter connectivity in the human brain and links these to disease risk variants in Alzheimer's and psychiatric disorders.

MAPS processes PLAC-seq and HiChIP data to identify long-range chromatin interactions by removing biases and analyzing contact frequencies.

The paper shows MeCP2 binds to mCG and mCAC sequences in mouse brain, with binding density correlating with transcriptional regulation of neuronal genes.

The paper introduces a method combining proximity ligation with chromatin immunoprecipitation and sequencing to map long-range chromatin interactions in eukaryotic cells, showing improved sensitivity and accuracy in mouse embryonic stem cells.

This study shows that bacterial infection rapidly alters DNA methylation in human dendritic cells, affecting enhancer elements and gene expression related to immune responses.