Weiqiang Zhou

Repetitive extragenic palindrome (REP) elements are local, context-dependent, dual 3'UTR regulators in Escherichia coli

This study identifies REP elements as dual regulators of 3'UTR function in E. coli, controlling transcription termination and mRNA stability in a context-dependent manner.

DNA methylation stochasticity is linked to transcriptional variability and identifies convergent epigenetic disruption across genetically-defined subtypes of AML

The paper analyzes DNA methylation stochasticity in AML subtypes, identifying high-entropy subtypes and linking methylation entropy to transcriptional variability and leukemogenesis.

Global Mapping of Combinatorial Chromatin Regulatory Events Using Hi-Plex CUT&Tag

The paper introduces Hi-Plex CUT&Tag, a method to detect co-localization of over 600 CRF pairs, enabling comprehensive analysis of chromatin regulatory interactions in a single experiment.

DNA methylation memory of pancreatic acinar-ductal metaplasia transition state altering Kras-downstream PI3K and Rho GTPase signaling in the absence of Kras mutation

The paper investigates DNA methylation changes during pancreatic acinar-ductal metaplasia (ADM) and their persistence without Kras mutation, linking epigenetic memory to signaling pathway alterations and cancer cell plasticity.

Quantifying Functional Conservation of Human and Mouse Regulatory Elements via FUNCODE

The paper introduces FUNCODE, a framework to quantify functional conservation between human and mouse regulatory elements using in silico sample matching, identifying 3.3 million conserved element pairs and demonstrating its applications in annotation and cross-species data integration.

Differential Roles of positive and negative supercoiling in organizing the E. coli genome

This study investigates how positive and negative supercoiling influence 3D genome organization in E. coli using Hi-C and ChIP-seq data, finding positive supercoiling enhances spatial contacts more than negative supercoiling.

BAF chromatin complexes do not mediate GLI transcriptional repression of Hedgehog target genes

The paper shows SMARCC1 does not mediate GLI3 repression of Hedgehog target genes, as it maintains chromatin accessibility at GLI-regulated enhancers independently of GLI3.

DNA methylation entropy is associated with DNA sequence featuresand developmental epigenetic divergence

The paper analyzes DNA methylation entropy in human and mouse datasets, finding associations with sequence features, developmental patterns, and gene expression variability.

Hedgehog regulation of epithelial cell state and morphogenesis in the larynx

This study shows that Sonic hedgehog (SHH) signaling is critical for maintaining epithelial integrity in the larynx and anterior foregut, with SHH loss causing abnormal epithelial to mesenchymal transition and replacement by Pax-1 expressing cells.

Identification of regulatory elements in primary sensory neurons involved in neuropathic pain

The paper identifies cis-regulatory elements in dorsal root ganglion neurons that show differential chromatin accessibility and TF binding after nerve injury, linking them to chronic pain.

GLI transcriptional repression is inert prior to Hedgehog pathway activation

The paper shows GLI3 repression does not prevent precocious activation of HH target genes or regulate anterior-posterior limb polarity.

Edaravone activates the GDNF/RET neurotrophic signaling pathway and protects mRNA-induced motor neurons from iPS cells.

This paper shows edaravone protects mRNA-induced motor neurons from neurotoxicity by activating the GDNF/RET signaling pathway and can replace neurotrophic factors for neuron survival.

Dynamics of global gene expression and chromatin accessibility of the peripheral nervous system in animal models of persistent pain

The paper identifies transcriptomic and epigenetic changes in rat dorsal root ganglia under two chronic pain models, revealing shared and distinct chromatin accessibility alterations.

Single-cell ATAC-seq Signal Extraction and Enhancement with SCATE

SCATE improves the accuracy of estimating cis-regulatory element activities in single-cell ATAC-seq data by integrating co-activated elements, similar cells, and regulome data.

GLI transcriptional repression regulates tissue-specific enhancer activity in response to Hedgehog signaling

The paper identifies HH-responsive enhancers that lose acetylation in the absence of Hedgehog signaling and are regulated by GLI repression rather than Polycomb complexes.

Sex differences in gene regulation in the dorsal root ganglion after nerve injury

The paper identifies sex-related gene expression differences in the dorsal root ganglion of male and female rats after nerve injury using RNA-seq.