Rong Hu

Integrative analysis of the 3D genome and epigenome in mouse embryonic tissues

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

A chromosome-level genome assembly of the cabbage aphid Brevicoryne brassicae

This study presents a high-quality, chromosome-level genome assembly of the cabbage aphid Brevicoryne brassicae using PacBio and Hi-C data, enabling comprehensive genomic analysis.

Genome-wide analysis of the interplay between chromatin-associated RNA and 3D genome organization in human cells

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.

Parallel Characterization of cis-Regulatory Elements for Multiple Genes Using CRISPRpath

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

Topologically Associating Domain Boundaries are Commonly Required for Normal Genome Function

This study shows that deleting TAD boundaries in mice often causes molecular or developmental phenotypes, highlighting their importance for genome function.

Preservation of Chromatin Organization after Acute Loss of CTCF in Mouse Embryonic Stem Cells

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.

CTCF Mediates Dosage and Sequence-context-dependent Transcriptional Insulation through Formation of Local Chromatin Domains

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.

CTCF Promotes Long-range Enhancer-promoter Interactions and Lineage-specific Gene Expression in Mammalian Cells

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.

Cell type-specific enhancer-promoter connectivity maps in the human brain and disease risk association

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.

3D Chromatin Architecture Remodeling during Human Cardiomyocyte Differentiation Reveals A Role Of HERV-H In Demarcating Chromatin Domains

The paper investigates chromatin architecture changes during human cardiomyocyte differentiation and identifies HERV-H retrotransposons as key regulators of TAD boundaries and gene regulation.