RNA and protein synthesis mechanisms

This study identifies eIF4A2 as a key translation initiation factor that regulates stem cell pluripotency by controlling the translation of pluripotency factors and histone H3.3.

The paper investigates how poly-fluorophenyl-modified ligands alter the structural dynamics of Spinach2 and Broccoli aptamers, increasing ligand affinity through a slow structural rearrangement.

This study engineers efficient transcription termination sequences for T7 RNA polymerase, achieving up to 98% in vivo efficiency and demonstrating cross-polymerase functionality.

The paper introduces computational tools to analyze crosslink-ligation RNA data, revealing new RNA structures and homodimers.

The paper shows that residue A1493 in the ribosome's decoding center contributes to the stability of the second anticodon-codon base pair, establishing the genetic code's degeneracy.

This study develops PERSIST-seq and In-line-seq to optimize mRNA stability and translation, finding that in-cell stability is more critical than ribosome load for protein output.

This study optimizes in vitro transcription (IVT) for long self-amplifying RNA (saRNA) using design of experiments, identifying key factors like magnesium and NTP interactions that maximize RNA yield.

This study examines how E. coli's genetic code tolerates tRNA mutations that increase codon size, finding that while many tRNAs can be converted to quadruplet tRNAs, only nine aminoacyl tRNA synthetases tolerate quadruplet anticodons, limiting the chemical alphabet of a synthetic quadruplet code.

The paper introduces updated RNA secondary structure prediction tools and parameters for N6-methyladenosine, enabling analysis of modified RNA structures.

The paper identifies co-translational assembly domains in proteins that facilitate interactions between nascent chains and fully synthesized subunits, revealing their role in regulating complex assembly pathways.

The paper develops mito-FUNCAT-FACS to measure mitochondrial translation activity in individual cells and detects heterogeneity in cancer cells.

The paper introduces a theoretical framework to model mRNA translation with ribosome competition, showing how parameter changes affect translation dynamics across a network.

The paper develops a biophysical model to simulate transcription and translation dynamics in bacterial- and mammalian-based cell-free expression systems using experimental data.

The paper shows how the chaperone Tsr2 releases and recycles Rps26 from ribosomes during stress, enabling a reversible ribosome response without bypassing quality control.

This study identifies Xrp1 as a master regulator that triggers cell competition and translation deficits in response to ribosomal stress.

This study identifies a late-stage quality control step in human mitochondrial ribosome large subunit assembly, showing that MRM2 ablation impairs oxidative phosphorylation through defective translation and accumulation of assembly intermediates.

This paper introduces a Drosophila melanogaster model with a mistranslating tRNA variant, showing it causes developmental delays, reduced adult viability, and sexually dimorphic morphological and behavioral effects.

riboviz 2 provides a flexible and robust workflow for analyzing and visualizing Ribo-seq data with improved functionality and usability.

This paper demonstrates an RNA-based toggle switch using inhibitory RNA aptamers that can toggle between two states by sequestering RNA aptamers with DNA sequences.

This paper introduces a convolutional neural network for RNA secondary structure prediction, achieving significant accuracy improvements over existing methods.

This study analyzes the evolution of SARS-CoV-2 synonymous codon usage over time using genome sequences collected since December 2019, finding a trend toward reduced codon similarity to the human host.

PTT-quant quantifies premature transcription termination events with high sensitivity and accuracy, demonstrating improved measurement of SAM riboswitch dynamics in Bacillus subtilis.

The paper presents high-resolution structures of ribosomal complexes with chloramphenicol and specific nascent peptides, revealing how amino acids in the nascent chain modulate drug affinity and explain context-specific inhibition of translation.

The paper introduces trap-TRAP, a method to generate zebrafish transgenic lines for tissue-specific translatome analysis using TRAP combined with enhancer trap techniques.

The paper uses direct RNA sequencing to characterize engineered transcript isoforms and demonstrates how transcriptional terminators can be tuned to control read-through.

The paper identifies codon-mediated mRNA decay in zebrafish embryos, showing ribosome decoding kinetics affect mRNA stability independently of Znf598 and stall-dependent decay.

The paper introduces DART, a method to analyze ribosome targeting, revealing thousand-fold differences in 5' UTR-specific translation activity and identifying regulatory elements.

This paper develops exonuclease-deficient cell-free extracts and optimized buffers to enable robust expression from unprotected linear DNA without additional protection strategies.

This paper develops an informative RNA-base embedding using deep learning to improve RNA structural alignment and clustering, achieving better accuracy than existing methods.

The paper compares cis-acting sequence elements affecting translational efficiency in Plasmodium falciparum and humans using in vitro translation assays.