transcription & RNA processing

This study identifies the molecular mechanism by which eRNAs stimulate Pol II pause release by interacting with NELF through unpaired guanosines.

The paper examines how ammonium nutrition alters the epitranscriptome in maritime pine roots, showing m6A modifications regulate translation and proteome responses.

This paper develops fibrous hydrogel assemblies that contract when encapsulated with mesenchymal stromal cells, enabling programmed shape changes for biofabrication and tissue engineering.

The paper uses RNA imaging in live Arabidopsis plants to study single-cell transcriptional dynamics, finding rapid transcriptional repression in response to phosphate and high intrinsic noise.

The paper investigates how RNA-binding proteins (RBPs) influence RNA polymerase II activity through phase separation, showing that RBPs like PSPC1 enhance polymerase engagement and transcription.

The paper shows that G1 cyclin-Cdk phosphorylates RNA Polymerase II at SBF-regulated promoters to activate transcription and promote cell cycle entry.

This study identifies NPR1 and EDS1 as interacting coactivators that synergistically activate PR genes and plant defenses through Mediator complex recruitment and mutual stabilization.

This study shows that type I and type II interferons induce similar epigenomic and transcriptional changes in macrophages, including 3D chromatin rearrangements and increased DNA accessibility at ISG loci.

This study uses evolve and resequence to identify genetic changes in Toxoplasma gondii during lab-adaptation, revealing transcriptional reprogramming and lipid metabolism shifts.

The paper identifies sulphate-TOR signalling as a key pathway for transcriptional reprogramming during shoot apex activation in Arabidopsis, revealing its role in growth and stress responses.

The paper identifies widespread alternative transcription initiation and rapid transcription factor activation in PAMP-triggered immunity in plants.

The paper shows that multisite phosphorylation of Ndd1 by Cdk1 initiates delayed negative feedback, controlling mitotic transcription through a pulse of gene expression.

This study shows O-GlcNAc modification of MTA1 enhances its chromatin binding and transcriptional activity, aiding breast cancer cells in adapting to genotoxic stress.

This paper develops a cell-free, densified collagen tubular graft that is mechanically strong, customizable, and supports cell incorporation for tissue replacement and disease modeling.

This study models Wilms tumor initiation in human kidney organoids by showing WT1 loss halts progenitor cell differentiation and recapitulates tumor-like transcriptional changes.

The paper shows that multivalent interactions enhance transcription activation by stabilizing chromatin binding and recruiting co-activators, independent of phase separation.

This study shows HIV-1 infects resting memory T cells without prior activation, inducing a tissue-resident memory-like phenotype driven by Vpr.

This study shows that nuclear cholesterol is required for BASP1-mediated transcriptional repression by facilitating chromatin remodelling and gene-specific repression.

The paper reconstructs genomes of freshwater nitrifiers in the Laurentian Great Lakes to explore their metabolism, ecology, and functional diversity, revealing new species and adaptations like proteorhodopsin.

This study identifies two distinct mechanisms by which Hox a3 and a11 TIE elements inhibit cap-dependent translation using uORFs.

This study examines transcriptional and translational changes in E. coli over 22 years of adaptation, finding that mRNA abundance increases with cell size and that gene expression patterns are similar across replicate populations despite few shared mutations.

This study identifies Batf's role in regulating effector CD8+ T cell differentiation through transcriptional and epigenetic mechanisms using genome-scale profiling.

The paper shows that Agaricus bisporus uses synchronized hyphal activity and cyclic gene expression to degrade lignocellulose and uptake nutrients from litter.

This study examines SARS-CoV-2 transcriptional and epi-transcriptional dynamics using long-read sequencing in human and primate infection models, revealing distinct patterns of sgRNA regulation and modification.

This study identifies signaling pathways involved in temperature-induced translatome reprogramming and cell wall masking in C. neoformans using glucan unmasking as a readout.

This study investigates Fxr signaling and microbial bile salt metabolism in zebrafish intestines, revealing conserved pathways and Fxr roles in transcriptional programs.

CDKL5 is a DNA damage-sensing kinase that modulates transcriptional activity near DNA breaks.

This study analyzes SARS-CoV-2 superspreading events in Austria using genomic and epidemiological data to understand viral transmission and mutation dynamics.

This paper introduces a bioprinting method that controls cellular orientation through stretching, enabling aligned myofiber formation and effective tissue repair in vivo.

The paper investigates how transcription factor residence time affects transcriptional burst frequency and develops a model of gene transcription based on quantitative measurements.