transcription & RNA processing

The paper shows isoform diversity is a distinct dimension of gene expression, complementary to gene-level abundance, and changes with age and tissue-specific processes.

The paper identifies regulatory non-coding genes marked by nucleosome arginine methylation and regulated by JMJD5, showing their coupling with coding genes in animals.

This study shows that during nutrient starvation, chromatin accessibility decreases genome-wide, but RNA abundance increases selectively in stress-adaptive genes, indicating limited predictive power of ATAC-seq for transcript abundance.

The paper shows that mRNA sequences have evolved to minimize self-association, maintaining transcriptome solubility through stable folding and reduced intermolecular contacts.

This study investigates phyB photobodies, showing they form molecular memory through phase separation, influencing light signaling and transcriptional states in plant cells.

This study shows that acetylation of CRP K52 activates AR3, leading to changes in gene expression that affect sugar utilization and virulence in V. cholerae.

This study shows temozolomide causes RNA alkylation and widespread translational repression in glioblastoma cells by targeting guanine-rich transcripts.

The paper uses simulations and imaging data to show that lamina-associated chromosomes have polarized compartmentalization and enhanced euchromatin contacts, potentially improving transcription for large chromosomes.

This study examines genome evolution in the Pacific acorn barnacle, showing high polymorphism and evidence of positive selection in large populations.

This study shows brassinosteroids repress plant immunity by inducing DNA methylation and altering splicing of immune receptor genes through bHLH transcription factors.

The paper identifies a feedback loop between SETD6-mediated methylation of PPARγ and lipid metabolism gene expression in liver-derived cells, linking it to lipid accumulation and disease.

The paper develops a framework to compare evolutionary divergence across molecular levels and finds that divergence patterns vary by gene function and taxon.

This study shows elevated CO2 improves tomato tolerance to Botrytis cinerea by reprogramming transcriptional and metabolic defenses across multiple cultivars.

This paper identifies senescence-induced CTCF clusters (SICCs) and shows they sustain the senescence splicing program by repurposing nuclear speckle components.

This study investigates the relationship between TP53 dysfunction, LINE-1 retrotransposon activity, and transcriptomic changes in CLL, finding that retrotransposons influence RNA splicing rather than causing DNA damage.

This study uses long-read multi-omics sequencing to analyze DNA-to-RNA remodeling in recurrent astrocytoma, identifying patient-specific genetic and epigenetic changes and their impact on RNA isoforms and protein fate.

This study identifies a conserved chromatin-driven maturation checkpoint in macrophages that occurs independently of tissue specialization and enhances innate immune responsiveness.

This study uses multi-omics to analyze pepper fruit development and ripening, revealing epigenetic and transcriptional changes and their roles in regulating key metabolic pathways.

The paper identifies IGF2BP3 as a regulator of MYC that contributes to growth heterogeneity in colorectal adenoma cells through both transcriptional and translational mechanisms.

This study compares gene expression and network architecture in diploid, synthetic, and natural autotetraploid Arabidopsis arenosa under stress, showing synthetic tetraploids have higher expression variation and network plasticity.

This study uses high-resolution transcriptomics to reveal complex transcriptional architecture in the archaeal virus SSV1, including new transcription start and termination sites and antisense RNAs.

The paper shows TEAD1 forms transcriptionally inactive condensates in cancer cell pericentromeric heterochromatin, acting as storage sites and influencing YAP/TEAD target gene expression.

This study investigates how Lamin A/C disruption affects nuclear mechanics, chromatin architecture, and transcription in skeletal muscle in vivo, finding that it alters chromatin organization and gene expression in mechanically stiff tissues.

The paper analyzes RNAseq data from yeast species to study how regulatory networks controlling gene expression plasticity evolve in response to environmental changes.

The paper investigates how H3K27me3 and H2A.Z chromatin modifications influence cold response in Arabidopsis by analyzing their effects on gene regulation and transcriptional activity.

This study shows FOXA1 maintains cell polarity and limits lysosome biogenesis in lung adenocarcinoma by regulating transcriptional circuits and interacting with TFE3.

The paper identifies MANCR isoforms' roles in epigenomic and P53-responsive transcriptional control in TNBC through computational and experimental methods.

This study examines how photoperiod affects gene expression in tomato by analyzing RNA-seq time-course data across different light regimes, revealing distinct transcriptional responses in morning and evening transcripts.

This study identifies a distinct transcriptional program in mast cells during desensitization, showing it involves active reprogramming rather than passive hyporesponsiveness.

The paper develops a new chemical dynamics model to quantify adaptive gene expression in E. coli, revealing a quadratic relationship between mean and variance of activation times.