Genomics and Chromatin Dynamics

This study characterizes the gene regulatory network of early human B-cell development and identifies regulatory elements linked to B-cell acute lymphoblastic leukemia.

The paper models how antagonistic histone PTMs improve epigenetic inheritance fidelity using Bayesian methods and simulations.

The paper shows that CTCF loss in mouse heart cells reorganizes enhancer activity-by-contact scores, reduces CRH numbers, increases CRH size, and increases CRH crossing TAD boundaries.

This study investigates how 3D genome organization changes during breast cancer progression using Hi-C and epigenomic data, revealing structural alterations linked to oncogenic gene activation.

This paper introduces DecoDen, a method that learns shared chromatin landscapes and de-noises histone modification assays across multiple tissues.

The paper investigates how alternative TSS usage correlates with gene expression and translation efficiency across eukaryotes, revealing its role in regulating protein production.

The paper investigates how CrebA regulates secretory capacity by analyzing gene expression and DNA binding in Drosophila embryos using scRNA-seq and identifies SPCGs as major targets.

This study shows that protamine overexpression in somatic cells causes chromatin condensation and transcription suppression without altering DNA methylation.

This study shows anthracycline drugs disrupt 3D chromatin structure by interfering with CTCF binding, altering gene regulation and clinical outcomes in AML.

The paper investigates how chromatin dynamics and gene expression change after epigenetic drug treatment, finding locus-specific chromatin remodeling and gene expression alterations.

SLUR(M)-py is a Python pipeline using SLURM for parallel processing of multi-omic epigenomic data, demonstrating improved speed and completeness over existing HPC pipelines.

The paper investigates how two chromatin remodelers, ACF and RSC, affect chromatin condensation and dynamics, revealing distinct mesoscale effects on chromatin structure and function.

The paper identifies SATB1's role in genome organization through direct binding to BURs, linking chromatin structure to cell type-specific gene expression.

The paper examines nucleosome dynamics during monocyte to macrophage differentiation, finding that nucleosome sensitivity changes dynamically while distribution remains largely static.

The paper investigates how H3K9 and H3K27 methylation regulate CTCF binding and 3D genome structure in mouse cells, showing that their loss disrupts chromatin organization and gene expression.

The paper shows that LPS stimulation causes transient nucleosome redistribution and increased MNase sensitivity in a subset of promoters, while most promoters show sensitivity changes uncoupled from gene expression.

The paper investigates how nucleosome context influences chromatin reader binding preferences using biochemical and genomic approaches, revealing that multivalent engagement often has regulatory effects beyond simple additivity.

This study identifies MAGE-A10 as a cancer-specific protein that stabilizes KAT2A and KAT2B acetyltransferases, leading to increased histone acetylation and tumorigenesis.

PTF-Vac discovers plant transcription factor binding sites using a generative deep learning model that outperforms existing methods and is independent of species and predefined motifs.

The paper introduces Histo-LCM-Hi-C to study 3D chromatin structure of rare tissue cells, showing distinct chromatin organization in liver Kupffer cells compared to whole liver and in vitro macrophages.

The paper predicts missing chromatin conformation contact maps across cell types and assays, exploring how 3D genome architecture varies.

The paper uses CRISPR-Sirius to visualize differences in large-scale chromosome conformations between osteoblasts and osteosarcoma cells, revealing regulatory mechanisms involving H3K27me3 and CTCF/cohesin.

The paper identifies an expanded HP1a-binding motif, HACs, and shows their role in heterochromatin assembly through molecular interactions and simulations.

This study identifies the role of chromatin remodelers in resetting promoter NDRs after replication in yeast, revealing a two-step mechanism involving RSC and INO80.

The paper identifies super-silencers in B cells, showing their role in development and their conversion to super-enhancers in lymphoma, with implications for carcinogenesis.

The paper investigates how condensin I and linker histone H1.8 compete to reorganize DNA loops in a sparkler structure formed in Xenopus egg extracts.

The paper develops a framework to analyze thermodynamic models of transcriptional regulation using experimental data from Drosophila embryos.

This study shows ecDNA forms nuclear condensates and reorganizes chromatin to enhance oncogenic transcription across cancer types.

The paper introduces motifDiff, a tool for variant effect prediction using biophysical TF binding models, showing it effectively scores variants and provides insights into human accelerated regions.

The paper quantifies progressive changes in chromosome shape during cell divisions and finds that an alternative loop capture model explains the observed arm length to width relationship better than the loop extrusion model.