chromatin & epigenetic regulation

The paper shows how COOLAIR co-transcriptional dynamics integrate temperature fluctuations to repress FLC through chromatin regulation.

This paper identifies a SOX9 C-terminal module that recruits cBAF to enhancers, controlling cell state by remodeling chromatin.

This study identifies SUMOylation and non-proteolytic ubiquitination as mechanisms regulating IRF2BP2 nuclear localization and stability through a SUMO1-NLS-importin-β pathway.

This study shows increasing PCAF-1 in C. elegans extends lifespan, preserves healthspan, and enhances stress responses by reprogramming transcription and improving proteostasis.

The paper introduces scTPPM, a single-cell multi-omics approach that co-profiles transcriptomes, proteomes, eight PTMs, and metabolomes, revealing dynamic crosstalk during mouse oocyte meiosis.

The paper identifies latitudinal clines in gene variants related to defence and reproductive pathways in Norway spruce, suggesting local adaptation to climate conditions.

This study identifies a shared paleopolyploid event and its role in the C3-to-C4 photosynthetic transition in Heliantheae alliance species through genome analysis and phylogenetic association mapping.

This study shows that SAM supply regulates DNA methylation turnover in synovial sarcoma, with SAM depletion causing methylation redistribution rather than global hypomethylation.

This study shows that cortical ER-PM contact sites maintain nuclear envelope integrity and proper mitotic nuclear segregation by preventing membrane damage and supporting nuclear dynamics.

This paper introduces a jump-diffusion model to explain cohesin extrusion and CTCF barrier function by integrating active and passive motion mechanisms.

The paper identifies molecular and physiological differences between asymptomatic Alzheimer's disease brains and Alzheimer's disease brains that correlate with cognitive resilience.

The paper analyzes somatic mutations and gene expression in TP53/PTEN DKO murine glioblastoma cell lines using WES and RNA-seq to reveal early genomic instability and later replication-driven mutations associated with malignancy and TMZ resistance.

The paper uses long-read sequencing to analyze human 5S rDNA arrays, revealing zoned methylation patterns linked to chromatin structure.

This study identifies cRps6kb1 as a hyperglycemia-responsive circRNA that drives diabetic neuropathic pain by competing with PUM2 for Nt3 3-UTR binding, increasing proNT3/CCL2 expression and nociceptive hypersensitivity.

This study shows that GSNOR-dependent nitric oxide homeostasis affects methylome persistence in Arabidopsis after multi-generational environmental stress exposure.

The paper investigates how B chromosomes in maize affect chromatin accessibility and gene expression in pollen nuclei using ATAC-seq and RNA-seq.

This study shows that NEDD4 in neural crest cells regulates HA synthesis in cardiac outflow tract valves, affecting valve development and ECM composition.

The paper maps gene expression, chromatin accessibility, and DNA methylation in developing human brain cells to understand regulatory interactions and their role in disease.

The paper examines the structural relationships between SLC12 cotransporter C-terminal domains, universal stress proteins, and adenylating enzymes, identifying potential sites for protein adenylation.

This study generates a transcriptomic atlas of Bostrychia moritziana to investigate the regulatory architecture and evolution of its triphasic life cycle, revealing modular gene regulation and evolutionary integration of developmental programs.

The paper shows that SMARCB1 loss disrupts TF-dependent chromatin priming, revealing lineage-specific regulatory output of BAF complexes is constrained by TF repertoire in ATRT tumors.

The paper shows that simple thresholding on 3D distance measurements from live-cell microscopy leads to inaccurate estimates of chromatin looping parameters, and proposes noise-aware methods for better accuracy.

This study uses molecular dynamics simulations and experiments to show that lipid interactions modulate RhoA conformational dynamics and signaling.

This study uses whole-genome sequencing data from 26 Finnish golden eagles over 136 years to show drastic genetic erosion post-bottleneck despite population recovery.

The paper examines genomic variation across nine co-occurring plant species in an Australian mountain range, finding shared spatial patterns but differing associations with geographic and environmental factors.

This study shows non-coding RNA disrupts enhancer-promoter interactions when increased, and stabilizes them when decreased, independent of transcription initiation.

This study investigates why transcription factors use simple, uncorrelated binding motifs despite potential benefits of correlated ones, finding that simpler strategies are more robust to mutations.

The paper analyzes whole genome data from Plasmodium falciparum isolates in Ethiopia to identify adaptive trajectories of antimalarial resistance evolution.

The paper develops a computational model to show that Hsp70 chaperones only delay, not prevent, protein aggregation, depending on client-specific kinetic and thermodynamic properties.

This paper uses Hi-C data to infer 3D genome structure and chromatin dynamics in budding yeast without prior assumptions about nuclear organization.