transcription & RNA processing

Isoform diversity as a complementary dimension of gene expression

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.

PHYRE, a Translated uORF, is Required for Phytochrome B Translation and Photomorphogenesis in Arabidopsis

The paper identifies a uORF, PHYRE, essential for phytochrome B translation and photomorphogenesis in Arabidopsis, showing its role in translational regulation.

HOX13 factors shape cell developmental transcriptional program through multiple mechanisms that regulate chromatin accessibility.

This study shows HOX13 factors regulate chromatin accessibility through homodimerization and SWI/SNF recruitment, influencing lineage-specific transcriptional programs in iPSCs.

Long read sequencing reveals changes in measured isoform structure and abundance due to RNA processing

The paper compares RNA sequencing protocols using long-read sequencing, finding significant changes in isoform structure and abundance due to RNA processing steps.

Enhancers Silence Coupled-coding RNAs in Animals

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

Long-term dysregulation of histone acetylation, BDNF expression, and the hippocampal transcriptome in adult rats exhibiting a depressive-like phenotype following repeated chlorpyrifos exposure

This study shows that repeated chlorpyrifos exposure in rats leads to long-term epigenetic and transcriptional changes in the hippocampus, including reduced BDNF and altered neuronal plasticity pathways, associated with a depressive-like phenotype.

FoxO1 and HNF1α cooperatively remodel nucleosome architecture and mechanical stability to activate transcription

This study shows FoxO1 and HNF1α work together to change nucleosome structure and stability to activate transcription.

Genome-wide loss of chromatin accessibility coexists with selectively elevated RNA abundance in nutrient-starved U2OS cells

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.

Light induces Phytochrome B SUMOylation to recruit the immune regulator NPR1 in nuclear condensates to control immunity in plants

The paper shows light-induced SUMOylation of Phytochrome B recruits NPR1 to nuclear condensates, elevating SA levels to control plant immunity, with SA also maintaining this process in darkness.

Transient efferocytosis-induced activation of IKKβ reprograms macrophages to promote tissue resolution

This study identifies IKKβ activation as a transient upstream signal triggered by efferocytosis that promotes tissue resolution through multiple downstream pathways.

Enhanced liver regeneration via targeted mRNA delivery for partial in vivo reprogramming

The paper demonstrates that OSKM mRNA delivered via lipid nanoparticles induces liver progenitor-like cells, promoting tissue regeneration after acute liver injury.

Microbiota during early life windows orchestrates intestinal maturation and barrier formation in the offspring

This study shows that maternal and postnatal microbiota influence intestinal epithelial maturation and barrier formation through epigenetic and transcriptional mechanisms in offspring.

A naturally occurring Tat R52W variant in brain-derived HIV attenuates transcription and may contribute to reservoir persistence

This study identifies an HIV-1 Tat variant (R52W) that reduces transcriptional activity, potentially contributing to viral persistence during ART.

Maintaining transcriptome solubility constrains mRNA sequence composition

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

phyB photobodies display molecular memory, regulating light signaling transcriptional states through phase separation.

This study investigates phyB photobodies' role in light signaling memory through phase separation, showing their stability and transcriptional regulation in different light conditions.

Actuation of CRP activating region 3 by acetylation modulates V. cholerae sugar utilization and virulence

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.

Protein-driven colloid-osmotic pressure controls nuclear size, organization, and function

The paper shows that protein-driven osmotic pressure regulates nuclear size and function, affecting chromatin organization and gene expression in yeast, human, and fly cells.

Patterned alginate hydrogel spatially guides collagen fibrillogenesis, viscoelasticity and endothelial cell invasion

This paper develops 3D patterned alginate-collagen hydrogels that spatially guide endothelial cell invasion and proliferation by controlling collagen fibrillogenesis, degradation, and viscoelasticity.

Temozolomide Induces Aberrant RNA Alkylation and Widespread Translational Repression

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

Actin Depolymerization Factor (ADF) Moonlighting: Nuclear Immune Regulation by Interacting with WRKY Transcription Factors and Shaping the Transcriptome

This study shows that ADFs in Arabidopsis have a nuclear role in plant immunity by interacting with WRKY transcription factors to regulate the transcriptome during immune responses.

Small Intestinal Submucosa (SIS)-dECM Bioink with Extrusion-Induced Collagen Organization for Tympanic Membrane Tissue Engineering

This study develops a bioink using decellularized small intestinal submucosa to create a printable scaffold that promotes collagen organization for tympanic membrane regeneration.

The compartmental polarization of interphase human chromosomes within the nucleus: A mechanism for transcriptional regulation of large chromosomes

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.

Large population sizes shape genome evolution in barnacles

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

Development and validation of an SDA-500 Anopheles stephensi cell line for molecular studies

The paper develops and validates an SDA-500 Anopheles stephensi cell line for molecular studies, showing it supports efficient transgene expression and functional genomics research.

Brassinosteroid-regulated transcription factors confer epigenetic changes that repress plant immunity

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

SETD6-mediated methylation of PPARγ establishes a transcriptional feedback circuit promoting lipid accumulation in liver-derived cells

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.

Gene function predicts divergence across molecular levels

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

Dye-cycling DNA origami rotors for long-term tracking of transcription at base-pair resolution

This paper introduces dcORBIT, a method that extends DNA rotation tracking during transcription to over 10 minutes at 20 Hz with single base-pair precision.

Photoinitiator-free visible-light bioprinting: minimising radical-induced oxidative stress and DNA damage in gelatin hydrogels

This paper introduces a photoinitiator-free gelatin hydrogel system that enables visible-light-induced crosslinking, reducing oxidative stress and DNA damage in cell culture.

GSNOR-dependent nitric oxide homeostasis promotes recovery from repeated climate stress across generations in Arabidopsis thaliana

This study shows that GSNOR-dependent nitric oxide homeostasis aids recovery from repeated climate stress in Arabidopsis across generations, while its impairment leads to persistent stress responses.