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Intrinsic and acquired resistance to poly(ADP-ribose) polymerase (PARP) inhibitors (PARPi) remains a major barrier in treating homologous recombination (HR) repair-deficient tumors, including those with germline or somatic <i>BRCA1/2</i> mutations. Although PARPi are FDA approved for …
Read PDFAlternative polyadenylation (APA) is a widespread post-transcriptional regulatory mechanism in eukaryotes, which contributes greatly in shaping transcriptome complexity and proteome diversity. The advancement of 3' tag-based single-cell RNA sequencing (scRNA-seq) technology has facilitated the emergence …
Read PDF<h4>Background</h4>Dysregulated interferon-alpha/beta-receptor 1 (IFNAR1) signaling was recently identified to contribute to the development of sporadic Parkinson's disease (PD) into PD with Dementia (PDD). The molecular, cellular, and phenotypic impacts of brain IFNAR1 loss in aging …
Read PDFAs integral parts of the transcription super elongation complex, the ENL and AF9 proteins are two master regulators of gene expression involved in the development and homeostasis of various tissues. They are encoded by MLLT1 …
Read PDFN4-acetylcytidine (ac<sup>4</sup>C), which is an evolutionarily conserved RNA modification in eukaryotes, functions as a critical epitranscriptomic regulator that enhances mRNA stability and translation efficiency. In Arabidopsis thaliana and Oryza sativa, ac<sup>4</sup>C has been characterized as …
Read PDFIntegrative analysis of RNA-seq datasets faces critical challenges in disentangling biologically meaningful signals from implicit confounders, such as unmeasured technical variability and nonlinear interactions between biological and technical variables. Traditional methods like Surrogate Variable Analysis …
Read PDFCollective behavior emerges from socially interacting individuals. Across species, the social behavior of healthy adults is often not present in immature animals, in socially isolated animals, or in animals with certain genetic perturbations, including models …
Read PDFWildfire smoke (WFS) exposures are becoming more common, and firefighters and community members are often exposed to WFS for days to weeks. Controlled studies assessing the effects of repeated exposure to WFS and woodsmoke (WS; …
Read PDFLeprosy is a debilitating disease that requires early detection for effective control, yet diagnosis still relies on clinical signs. Previous RNA-Seq analysis of coding genes from leprosy patients' household contacts (HHC) who developed leprosy (progressors) …
Read PDFUpstream open reading frames (uORFs) in the 5' leader of bacterial mRNAs can modulate gene expression, yet genome-wide identification remains limited. We combined bioinformatic prediction of ribosome-binding sites (RBSs)-a Shine-Dalgarno sequence and a start codon-with …
Read PDFMALAT1 is a long non-coding RNA (lncRNA) with altered expression in many cancers but poorly studied in B-cell neoplasms like mantle cell lymphoma (MCL), a very aggressive B-cell lymphoma. To elucidate the role of MALAT1 …
Read PDFA model plant, Nicotiana benthamiana, was examined as a host for persistent fungal viruses capable of crossing organismal kingdoms. Protoplasts of N. benthamiana were transfected with a mixture of virions of a betapartitivirus, Rosellinia necatrix …
Read PDFAged normal tissues harbour cancer mutations predisposing to transformation. However, how different pro-oncogenic events in the human colon compare in frequency, behaviour and subsequent transformation risk remains unclear. Here, we analyse mutation hotspot regions in …
Read PDF<h4>Introduction</h4>Early-life exposure to general anesthetics has been associated with increased neurodevelopmental vulnerability, but the cell type-resolved mechanisms remain incompletely understood. Here, we investigated whether isoflurane-induced neonatal neurotoxicity is associated with a glia-linked ferroptotic susceptibility state …
Read PDFBulk RNA sequencing (RNA-seq) produces high-dimensional gene expression data where the number of measured features greatly exceeds the number of available samples, which challenges artificial intelligence (AI)-based modeling. In this setting, models are highly susceptible …
Read PDFThe content of unsaturated fatty acids (UFAs) is significantly associated with the flavor, taste, and nutritional value of beef. Adipose tissue (AT) develops in multiple depots, and the UFA content of AT varies among different …
Read PDFThe intestinal mucosa is a complex functional layer which is formed from a diverse range of cell types that include epithelial cells (within crypts and villi) and an array of mesenchymal cells. Many intestinal diseases …
Read PDFDevelopmental plasticity allows organisms to adapt to environmental stressors and improve fitness. Caenorhabditis elegans can enter an alternative larval stage, the dauer, marked by developmental quiescence and complete transcriptomic remodeling. The energy modulator AMPK is …
Read PDFThe NAD<sup>+</sup> cap has been discovered in RNAs across prokaryotes and eukaryotes, suggesting a possible role of NAD capping in gene regulation. Current NAD-capped RNA (NAD-RNA) profiling methods lack precision in 5'-end mapping or bias …
Read PDFCircular RNAs (circRNAs) are closed-loop, single-stranded RNAs particularly enriched in the brain. Despite this enrichment, and evidence showing that synaptic development and plasticity alter their expression <i>in vitro</i>, circRNA regulation by and function in experience-dependent …
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