ChromPolymerDB reconstructs single-cell 3D chromatin structures from bulk Hi-C data and provides a database for analyzing chromatin conformation across 50 human cell types.

Nucleic Acids Research · Nov 18, 2025Peer-reviewedBioinformatics

ZMYND11 Functions in Bimodal Regulation of Latent Genes and Brain-like Splicing to Safeguard Corticogenesis

Xuyao Chang, Wenqi Li, Satoshi Matsui, Cindy Huynh, Craig A. Erickson, Feng Guo, G. Cederquist, Lorenz Studer, Makiko Iwafuchi, Amelle Shillington, Constantinos Chronis, Jason H. Tchieu

This study investigates the role of ZMYND11 in neurodevelopment by analyzing its effects on cortical neural stem cells and splicing regulation in ASD risk factors.

Nature Communications · Oct 9, 2025Peer-reviewedNeuroscience

Platelet Factor 4 (PF4) Regulates Hematopoietic Stem Cell Aging

Sen Zhang, Charles E. Ayemoba, Anna M. Di Staulo, Kenneth Joves, Chandani M. Patel, Eva Hin Wa Leung, Maura Lima Pereira Bueno, Xiaoping Du, Mortimer Poncz, Sang‐Ging Ong, Claus Nerlov, Maria Maryanovich, Constantinos Chronis, Sandra Pinho

This study identifies PF4 as a key regulator of HSC aging, showing that PF4 deficiency accelerates aging and that PF4 supplementation can rejuvenate aged HSCs.

Blood · Sep 8, 2025Peer-reviewedCell Biology

A New Approach for Discovering Functional Links Connecting Non-Coding Regulatory Variants to Gene Targets

Hammad Farooq, Lin Du, Pourya Delafrouz, Jiang Wei, Constantinos Chronis, Jie Liang

The paper introduces an algorithm that uses 3D chromatin interactions to identify functional non-coding regulatory variants and their target genes, reducing false positives in eQTL analysis.

bioRxiv · Jun 13, 2024 · PreprintGenomics

An Xist-dependent protein assembly mediates Xist localization and gene silencing

Amy Pandya‐Jones, Yolanda Markaki, Jacques Serizay, Tsotne Chitiashvili, Walter Mancia, Andrey Damianov, Constantinos Chronis, Bernadett Papp, Chun‐Kan Chen, Robin McKee, Xiaojun Wang, Anthony C. Chau, Shan Sabri, Heinrich Leonhardt, Sika Zheng, , Kathrin Plath

The paper shows that Xist RNA forms a protein condensate with binding proteins to establish the Xi-compartment and maintain gene silencing.

Nature · Sep 9, 2020Peer-reviewedMolecular Biology

DNA methylation estimation using methylation-sensitive restriction enzyme bisulfite sequencing (MREBS)

Giancarlo Bonora, Liudmilla Rubbi, Marco Morselli, Feiyang Ma, Constantinos Chronis, Kathrin Plath, Matteo A. Pellegrini

The paper introduces MREBS, a method for DNA methylation estimation that reduces sequencing costs while improving coverage compared to existing methods.

PLoS ONE · Apr 4, 2019Peer-reviewedGenomics

Loss of MECP2 leads to induction of p53 and cell senescence

Minori Ohashi, Elena Korsakova, Denise E. Allen, Peiyee Lee, Kai Fu, Benni S. Vargas, Jessica K. Cinkornpumin, Carlos Salas, Jenny C. Park, Igal Germanguz, Justin Langerman, Constantinos Chronis, Edward Kuoy, Stephen S. Tran, Xinshu Grace Xiao, , William E. Lowry

This study shows that loss of MECP2 in neurons leads to p53 induction and cell senescence, causing dendritic defects.

Stem Cell Reports · May 1, 2018Peer-reviewedDevelopmental Biology

Comparison of reprogramming factor targets reveals both species-specific and conserved mechanisms in early iPS cells

Kai Fu, Constantinos Chronis, Abdenour Soufi, Giancarlo Bonora, Miguel Edwards, Stephen T. Smale, Kenneth S. Zaret, Kathrin Plath, Matteo A. Pellegrini

This study compares OSKM reprogramming factor binding in human and mouse fibroblasts, finding conserved mechanisms and species-specific differences in target sites and regulatory networks.

bioRxiv · Nov 27, 2017 · PreprintGenomics