Genomics and Chromatin Dynamics

The paper identifies histone modification metapeaks across diverse cell and tissue types and shows they can predict cell state using machine learning.

This paper demonstrates that CUT&Tag can achieve higher resolution epigenomic profiling in Arabidopsis than ChIP-seq, even from small tissue samples.

The paper identifies molecular regulators of centromere distribution by screening nuclear proteins and shows that mitosis influences interphase genome organization.

SnakeHichipTF decodes TF logic in enhancer-promoter wiring in human brain regions, revealing distinct regulatory programs and evolutionary elements.

This paper introduces DARSI, a deep learning model that predicts gene expression and transcription factor binding sites from DNA sequences using MPRA data.

This study shows NASP prevents H3 aggregation in the cytoplasm, indirectly protecting H3 from degradation during early Drosophila embryogenesis.

The paper uses a complete diploid human genome to study centromeric chromatin organization, revealing that DNA methylation regulates centromere structure and plasticity.

The paper determines the structure of Arabidopsis chromatin fibers with linker histone H1.3, revealing a noncanonical binding mode that scaffolds dinucleosome stacking.

The paper introduces BlueSTARR, a predictive modeling framework trained on whole-genome STARR-seq data to assess variant effects on regulatory functions, revealing purifying selection against loss-of-function and gain-of-function variants.

This study shows that transcription termination by Ppn1 is essential for maintaining quiescent chromatin structure in fission yeast, ensuring faithful cell-cycle re-entry and preventing aneuploidy.

The paper shows that humanized Traf6 promoter sequences in mice affect immune responses but not fertility, revealing distinct roles for germ and immune cells in gene regulatory evolution.

This study shows that acute RUNX1 loss reprograms enhancer activity, leading to epithelial destabilization and cancer hallmark activation in human mammary epithelial cells.

The paper shows that chromatin remodelling by NuRD enables enhancer resetting in response to ERK signalling in mouse ES cells, facilitating a rapid and precise transcriptional response.

This paper integrates single-cell Hi-C, RNA-seq, and microscopy to uncover how hypertranscription shapes lampbrush chromosome structure through transcription-dependent chromatin organization.

The paper identifies DDK-mediated phosphorylation of INO80's Arp8 subunit, which stabilizes the complex and regulates nucleosome spacing at replication origins, enhancing replication efficiency and stress response.

The paper identifies 21 human 'lonely genes' in large gene deserts, finds they are mostly cell adhesion molecules, and suggests they are structurally isolated and vulnerable in brain development.

TransBind improves TF binding site prediction by integrating DNA sequences with protein embeddings, achieving higher accuracy and generalizability for new TFs.

ECHOS enables spatial epigenome profiling at subcellular resolution by combining high-resolution imaging and high-throughput sequencing, revealing distinct gene regulatory logics and epigenetic changes in human tissues.

This study trains CNNs to predict chromatin accessibility across species but finds poor performance in predicting quantitative differences between species.

TSProm identifies tissue-specific gene regulatory elements by training specialized DNA models and using explainable AI to analyze promoter sequences in human tissues.

The paper creates a transcription-based atlas of canine regulatory elements across tissues and development, identifying promoters and enhancers and their activity patterns.

This study shows that HP1β regulates olfactory receptor choice and neuronal identity in mice by modulating H3K9me3 levels and chromatin structure, leading to changes in OR expression patterns and reduced receptor diversity.

This study shows Hat1 regulates H3K9 methylation and HMT localization in LADs, affecting heterochromatin structure and inheritance in mouse cells.

This study shows TTF2 prevents premature rRNA synthesis during mitotic exit by regulating RNA Polymerase I reactivation and nucleolar protein recruitment.

This paper introduces fCUT&Tag-Seq, an optimized method for profiling histone modifications and chromatin-binding proteins in fungi, showing improved sensitivity and applicability to difficult species.

Chiron3D predicts CTCF-mediated chromatin loops using a DNA-only model, revealing sequence determinants of loop strength and stability through interpretable deep learning.

The paper identifies distinct DAXX effector modules that separate H3.3 nucleosome assembly from ERV silencing, showing H3.3 is dispensable for repression but SUMO-dependent recruitment is required.

The paper identifies condensin-dependent loop extrusion and roadblocks in S. cerevisiae, showing their role in homology search during DNA repair.

The paper identifies tissue-specific transcriptional regulatory programs in rats undergoing endurance exercise training by integrating chromatin accessibility, DNA methylation, and gene expression data.

The paper investigates RNAPII clustering during ZGA in Drosophila embryos, showing clusters are stably associated with active genes and reflect transcriptional activity, not phase separation.