transcription & RNA processing

The paper describes an evolutionary pathway in fungi where a new transcriptional circuit evolved through coding changes in a master regulator followed by cis-regulatory changes in its target genes.

This study evaluates the effectiveness of whole-genomic sequencing in predicting drug resistance in tuberculosis isolates from Mexico, showing high sensitivity and specificity for first-line drugs and identifying multidrug-resistant cases.

The paper shows that YAP-dependent transcription is activated by cycles of rapid nuclear-cytoplasmic shuttling, not just nuclear enrichment, and identifies factors that induce these cycles.

This study decellularizes pancreases to create scaffolds, reseeds them with mesenchymal stem cells, and transplants them into diabetic mice, restoring histomorphology and function within 20 days.

This paper establishes the mayfly Cloeon dipterum as a new model system for studying insect evolution through continuous culture and -omics resources.

The paper shows that H1 depletion in Arabidopsis thaliana vegetative cells allows DNA demethylation and transposon activation through DEMETER access.

The paper identifies novel nuclear actin binding partners and functional roles in chromatin remodeling, transcription, and RNA splicing using mass spectrometry techniques.

The paper assesses RNA folding specificity in mRNA and noncoding RNA, finding that specific folding is more evolutionarily adaptive and functionally significant.

This study identifies transcription start sites and RNA cleavage sites in Mycobacterium smegmatis under aerobic growth and hypoxia, revealing regulatory mechanisms shared with Mycobacterium tuberculosis.

This paper describes a method using silk proteins to create 3D fibrillar networks that integrate mammalian cells, promoting proliferation and tissue-like morphology.

This study shows RBM7 activates P-TEFb to promote cell survival during genotoxic stress by enhancing Pol II elongation and transcription of DDR genes.

The paper compares diurnal gene expression across nine Archaeplastida species, finding conserved transcriptional programs despite evolutionary divergence and lifestyle differences.

This study shows that mechanical loading enhances bone regeneration through engineered mesenchymal condensations, mimicking endochondral ossification without heterotopic bone formation.

This study develops a microsampling protocol for rodent malaria parasites that reduces animal usage and enables time-series transcriptomics with high correlation to traditional methods.

This study identifies the transcriptional stages of germination in Rhizopus delemar, revealing key molecular processes involved in spore-to-hyphae transition and disease progression.

This study uses single-molecule long-read sequencing to analyze red clover transcriptome, identifying novel splice isoforms, alternative splicing events, and non-coding RNAs.

This study uses live-cell single-molecule imaging to show that TF low-complexity domains form dynamic, selective interaction hubs that stabilize DNA binding and activate transcription.

This study identifies topovectorial mechanisms that control Nrf1 proteolytic processing to generate mature CNC-bZIP transcription factor isoforms through ER-associated degradation.

This study investigates how miR-305 and P-bodies regulate bicoid mRNA translational repression during Drosophila oogenesis.

The paper shows mTORC1 inhibits GSK3β nuclear localization and function, linking metabolic signals to transcriptional control of biomass production.

This paper develops a synthetic 3D bone marrow hydrogel with marrow-specific peptides that enhance stem cell differentiation and proliferation compared to generic hydrogels.

This study uses 4-TU labeling to track real-time transcription dynamics of Plasmodium falciparum during its blood-stage development, revealing transcription timing and stabilization patterns across the IDC.

The paper develops a model to study how mechanical properties of transcription affect gene expression and DNA structure in multi-gene systems.

This study identifies YeaG as a kinase that regulates methionine biosynthesis in E. coli under sustained nitrogen starvation by modulating the activity of the transcriptional repressor MetJ.

This study shows that Elongator regulates SHORT ROOT transcription in Arabidopsis roots, essential for stem cell maintenance and radial patterning.

This study shows miR-92a targets NF2 3UTR, reducing its expression and promoting tumor-like traits in cancer cells.

This study characterizes the cooperative and antagonistic roles of H2A.Z and BRAHMA in transcriptional regulation and chromatin dynamics in Arabidopsis.

The paper uses PRISMA to map C/EBPβ's PTM-dependent interactome, revealing interaction footprints and functional links to chromatin and RNA processing.

The paper shows that cytoplasmic mRNA processing amplifies transcriptional bursts, contributing to most cellular noise in both human and mouse cells.

This paper develops a theoretical framework showing how nucleosomes affect transcription factor diffusion and binding, finding that nucleosomes hinder 1D diffusion when between TFs and their sites but can enhance search when between nucleosomes and TFBS.