transcription & RNA processing

The paper analyzes splicing evolution across human, chimpanzee, and macaque lineages, finding that changes in exon inclusion frequency are more functionally relevant than constitutive-to-alternative transitions.

This study shows that some GATA3 mutations in breast cancer cause both loss and gain of function, altering the transcriptional network.

This paper reviews molecular evolution in diffuse gliomas over time and introduces the Glioma Longitudinal Analysis Consortium to systematically study longitudinal changes in gliomas.

This study identifies two distinct mechanisms by which GIGYF2 mediates mRNA repression: one through m4EHP-dependent translation repression and another through CCR4/NOT complex-mediated deadenylation.

This study uses molecular dynamics simulations to show how chromosome conformation affects transcription factor traffic, revealing that low-density contacts enhance traffic while high-density contacts reduce it through volume exclusion.

This study shows IRF5 promotes mRNA translation of ATF4 during amino acid deprivation by interacting with the translation initiation complex without eIF4E.

The paper identifies intrasplicing events in the human transcriptome and shows their regulatory impact on intron removal and gene expression.

This study identifies an evolutionary hourglass pattern in herbivore-induced transcriptomic responses in Nicotiana attenuata, showing conserved gene activation in the middle stage and rapid evolution of early and late genes.

This study identifies a lanthanide-dependent PQQ-ADH (PedH) in Pseudomonas putida KT2440, showing its role in catalytic activity and transcriptional regulation of pedE/pedH, and highlights its ecological relevance in volatile alcohol metabolism.

This study introduces BLInCR, a tool for real-time observation of light-controlled transcription in living cells, showing rapid RNA production and biphasic activation kinetics.

This paper develops a method to capture in vivo RNA transcriptional dynamics in Plasmodium falciparum by engineering parasites to salvage pyrimidines and label nascent mRNAs, revealing transcriptional reprogramming during gametocyte stage transition.

The paper develops a method to produce a multilayer cell mass from olfactory stem cells without scaffolds, showing viability and potential for nerve tissue regeneration.

RapMap introduces a quasi-mapping approach to efficiently align RNA-seq reads to transcriptomes, improving speed and accuracy over existing tools.

Strawberry provides a fast and accurate method for transcript reconstruction and quantification from RNA-seq data, outperforming existing tools in speed and accuracy.

The paper compares gene expression patterns between gametophytes and sporophytes in three plant species, finding that gametophytes have a higher proportion of rapidly evolving and young genes.

This study maps transcription start sites in Plasmodium falciparum using high-throughput sequencing, revealing TSS selection constraints and stage-specific isoform production.

The paper improves ribosome-footprint and mRNA measurements in yeast, revealing new insights into translation dynamics and regulation.

The paper uses nanopore sequencing to identify full-length isoforms from four Drosophila genes, demonstrating its ability to resolve exon connectivity in complex mRNAs.

limma couples gene-wise linear models with empirical Bayes variance moderation and weights; voom extends it to RNA-seq, and added functions test differential splicing and gene sets.

The paper introduces Mix2, a model that improves RNA-Seq transcript quantification by accounting for positional fragment bias, leading to more accurate abundance estimates and better differential expression detection.

The paper investigates cross-stress responses in Escherichia coli by analyzing genetic and transcriptional changes under multiple abiotic stresses, identifying cases of protection and vulnerability.

The paper introduces RSEM-EVAL, a model-based score to evaluate de novo RNA-Seq assemblies, and demonstrates its effectiveness using axolotl limb regeneration data.

The paper identifies 196 zero nucleotide exon ratchet points in 115 Drosophila genes using RNA-Seq data, revealing recursive splicing as a common and conserved mechanism.

This paper develops a Bayesian method to reconstruct disease outbreaks from genomic data, finding that even with high substitution rates, uncertainty remains in transmission inference.

The paper uses polysomal ribo-Seq to assess smORF translation, finding they are translated at similar levels and conserved across species as canonical proteins.