Jie Xiao

Disentangling polymer confinement from specific-folding interactions reveals the drivers of E. coli chromosome organization

The paper develops a polymer simulation framework to distinguish specific-folding interactions from polymer compaction in E. coli, revealing SFIs shape chromosome organization and gene expression.

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.

Substrate binding and activation mechanism of the essential bacterial septal cell wall synthase FtsW

This study defines the substrate binding and activation mechanism of FtsW using simulations, mutagenesis, and assays, revealing conserved residues and structural constraints involved in lipid II binding and catalysis.

Chromosomal Topological Domain Formation Modulates Transcription and the Coupling of Neighboring Genes in Escherichia coli

This study shows that chromosomal topological domains in E. coli repress transcription, reduce orientation effects, and modulate gene coupling through supercoiling changes.

Differential effect of supercoiling on bacterial transcription in topological domains

This paper develops a computational model to quantify how DNA supercoiling and topoisomerases regulate bacterial transcription, showing distinct roles for topoisomerase I and gyrase in gene expression.

A novel peptidoglycan deacetylase modulates daughter cell separation in E. coli

This paper identifies SddA, a periplasmic deacetylase that modulates daughter cell separation in E. coli by modifying denuded peptidoglycan strands, and links its function to amidase activation.

E. coli FtsN coordinates synthesis and degradation of septal peptidoglycan by partitioning between a synthesis track and a denuded glycan track

Light-dependent modulation of protein localization and function in living bacteria cells

This study shows that the CRY2/CIB1 system can be used to precisely control protein localization in E. coli, enabling manipulation of cellular functions like cytokinesis.

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.

Gene regulation network inference using k-nearest neighbor-based mutual information estimation- Revisiting an old DREAM

This paper improves gene regulatory network reconstruction by combining a new algorithm with a k-nearest neighbor mutual information estimator, achieving better precision-recall performance on synthetic datasets.

Unidirectional fork movement coupled with strand-specific histone incorporation ensures asymmetric histone inheritance

The paper shows that histone H4 is asymmetrically inherited in Drosophila male germline stem cells during asymmetric division, while H2A and H2B are symmetrically inherited.

Phage-encoded cationic antimicrobial peptide used for outer membrane disruption in lysis

This study identifies a phage-encoded cationic antimicrobial peptide, Gp28, that disrupts bacterial outer membranes during lysis, functioning similarly to human antimicrobial peptides like LL-37.

RNA polymerase organizes into distinct spatial clusters independent of ribosomal RNA transcription in E. coli

This study shows that RNA polymerase forms distinct spatial clusters in E. coli independent of rRNA transcription, with cluster organization influenced by nucleoid structure.

Improved single-molecule localization precision in astigmatism-based 3D superresolution imaging using weighted likelihood estimation

The paper improves 3D superresolution imaging by using weighted likelihood estimation to enhance z-axis localization precision, especially when PSFs deviate from standard models.

GTPase activity-coupled treadmilling of the bacterial tubulin FtsZ organizes septal cell-wall synthesis

The bacterial tubulin FtsZ uses GTP hydrolysis to power treadmilling, driving processive synthesis of the septal cell wall.