Table of Contents
Reviews
Toward an understanding of glucose metabolism in radial glial biology and brain developmentWe review the literature exploring the role of glycolysis and glucose metabolism in cortical development and discuss recent advances and future directions to better understand metabolic disease and neurodevelopment disorders.
Exploring the basis of heterogeneity of cancer aggressiveness among the mutated POLE variantsMechanisms and consequences of POLE mutations in human cancers.
Interconnections between m6A RNA modification, RNA structure, and protein–RNA complex assemblyThis review summarizes current knowledge and future directions on the mechanisms that govern the interplay between m6A RNA modification, RNA folding, and protein–RNA interactions, focusing on the mechanisms and available quantitative information.
Corrections
- Correction: Expansion microscopy reveals subdomains in C. elegans germ granules
Correction to Materials and Methods.
Correction: Dispersal of PRC1 condensates disrupts polycomb chromatin domains and loopsEndogenous PRC1–mediated chromatin compaction and clustering of polycomb target loci are reversibly perturbed in mESCs by the addition of 1,6 hexandiol.
Research Articles
Determinants of cytoplasmic microtubule depolymerization during ciliogenesis in ChlamydomonasChemically induced deciliation previously shown to induce cytoplasmic microtubule depolymerization occurs independently of ciliary loss. Furthermore, immediate ciliogenesis can occur in the presence of polymerized cytoplasmic microtubules.
Structural insights into the complex of oncogenic KRas4BG12V and Rgl2, a RalA/B activatorThe work reports the KRas4BG12V oncogenic mutation alters the binding kinetics with Rgl2, a RalA/B activator, and the V12 resides at the KRas4B(G12V)•Rgl2 complex interface in the crystal structure.
Passive diffusion accounts for the majority of intracellular nanovesicle transportIn contrast to large vesicles and organelles that are moved by motors inside cells, a detailed analysis of intracellular vesicle mobility reveals that passive diffusion is the main mode of small vesicle transport.
NRF2 connects Src tyrosine kinase to ferroptosis resistance in glioblastomaThe hyperactivation of Src tyrosine kinase in glioblastoma leads to the constitutive stabilization and activation of NRF2, thus causing resistance to ionizing radiation-induced ferroptosis.
APR-246 increases tumor antigenicity independent of p53Michels, Venkatesh et al demonstrate that APR-246, a small molecule Michael acceptor, enhances tumor immunogenicity. Combination of APR-246 with immune modulation enhances antitumor responses. APR-246, initially described as a P53 stabilizer, induces immunogenicity irrespective of the tumor’s p53 status.
Biogenesis, inheritance, and 3D ultrastructure of the microsporidian mitosomeQuantitative electron and light microscopy combined with bioinformatics reveal that microsporidian mitosomes grow and divide incrementally and are inherited at the microsporidian centrosome (spindle pole body), whereas mitochondrial dynamins participate in mitosome division.
Synergistic roles of tristetraprolin family members in myeloid cells in the control of inflammationSimultaneous deficiency of three tristetraprolin family members in myeloid cells resulted in severe inflammation in mice, suggesting that these three proteins act together to prevent inflammation.
Cell cycle-dependent gene networks for cell proliferation activated by nuclear CK2α complexesFunctional connection between activation of nuclear CK2α by phosphorylation which leads to association of CK2α with transcriptional start sites, and activation of histone genes, growth-related genes, and rDNA for cell proliferation.
Polycomb regulates circadian rhythms in Drosophila in clock neuronsThis study demonstrated that Pc regulates the circadian rhythm. The targeted DamID analysis identified the Pc-binding profiles in different clock neuron clusters, indicating Pc regulates circadian rhythms by specific clock genes.
Suppressed transcript diversity and immune response in COVID-19 ICU patients: a longitudinal studyThis integrative longitudinal clinico-genomic study delves deep into the gene and transcript expression pattern dynamics in severe COVID-19 patients with ARDS admitted to the ICU.
Meta-analysis of dispensable essential genes and their interactions with bypass suppressorsThis work compiles data from several studies on dispensable essential genes in S. cerevisiae to comprehensively characterize these genes and to explore how their interactions with bypass suppressor genes reflect evolution in natural populations.
Characterization of Na+ currents regulating intrinsic excitability of optic tectal neuronsThis study examines how developing optic tectal neurons adapt their intrinsic excitability. Changes in Nav 1.1 and 1.6 expressions correlate with changes in intrinsic excitability, whereas dynamic regulation of Nav1.6 is central for intrinsic plasticity and normal sensory circuit development.
Evolutionary insights into 3D genome organization and epigenetic landscape of Vigna mungoBy integrating SMRT long read, Hi-C, and Illumina pair-end sequencing technologies, we report a nearly complete, chromosomal-level assembly of V. mungo and characterize its 3D genome architecture.
Clathrin light chains CLCa and CLCb have non-redundant roles in epithelial lumen formationDeletion of genes encoding vertebrate clathrin light chain isoforms reveals a role for both in epithelial lumen formation and dominance of CLCa function in vivo during uterine epithelium development.
Integrins regulate hERG1 dynamics by girdin-dependent Gαi3: signaling and modeling in cancer cellsWe combine experimental data and mathematical modeling to offer a coherent explanation of the dynamics of hERG1 interaction with integrins, which governs f-actin organization and migration in cancer cells.
Enucleation of the C. elegans embryo revealed dynein-dependent spacing between microtubule astersUsing a genetic trick to produce enucleated C. elegans embryos, the authors revealed how the microtubule asters take space between each other inside the cell.
Immunosuppressive low-density neutrophils in the blood of cancer patients display a mature phenotypeLow-density neutrophils (LDN) in cancer patient’s blood are heterogeneous: CD45high LDN are mature and suppress T-cell proliferation, whereas CD45low LDN are immature and non-suppressive.
ESYT1 tethers the ER to mitochondria and is required for mitochondrial lipid and calcium homeostasisA protein complex composed of the outer mitochondrial membrane protein SYNJ2BP and the endoplasmic reticulum protein ESYT1 tethers the two organelles to facilitate calcium and lipid transfer.
Spt5 interacts genetically with Myc and is limiting for brain tumor growth in DrosophilaKnockdown of Spt5 in Drosophila affects various Myc-dependent phenotypes and delays the growth of a Myc-dependent brain tumor, thereby significantly extending the longevity of tumorous animals.
FAT10 is phosphorylated by IKKβ to inhibit the antiviral type-I interferon responseIKKβ-mediated phosphorylation of FAT10 dampens the antiviral type I interferon response by stabilizing OTUB1.
DCAF14 regulates CDT2 to promote SET8-dependent replication fork protectionDCAF14 modulates CRL4CDT2-dependent turnover during DNA replication. Loss of DCAF14 causes nascent strand degradation due to excessive proteasomal turnover of SET8 by aberrant CDT2 activity.
Methods
Assessing MAPPs assay as a tool to predict the immunogenicity potential of protein therapeuticsThis work highlights the use of streptavidin magnetic beads as a valuable approach for the immunoaffinity purification of mass spectrometry MHCII-eluted ligands (MAPPs) and their practical application in assessing the drug-induced immunogenicity risk of novel biotherapeutics.
High-resolution analysis of bound Ca2+ in neurons and synapsesThe amount of bound Ca2+ in neurons correlates significantly to the intensity of markers for GABAergic pre-synapse and glutamatergic post-synapses, and negatively to pre-synaptic activity.
Pathway-driven analysis of synthetic lethal interactions in cancer using perturbation screensThis study introduces a signaling pathway-informed computational approach to identify synthetic lethal (SL) interactions in various cancer types, uncovering potential targeted therapies for specific genetic alterations.
Automated staging of zebrafish embryos with deep learningIntroducing KimmelNet: A deep learning model that accurately stages populations of zebrafish embryos from 2D brightfield images, offering a rapid and objective alternative to manual observations.
CRISPR/Cas9 bioluminescence-based assay for monitoring CFTR trafficking to the plasma membraneA novel CRISPR/Cas9-based bioluminescence system to assess total and live-cell plasma membrane WT-CFTR levels offers a versatile platform for new screening systems in CFTR modulator discovery.
Resources
MICA: a multi-omics method to predict gene regulatory networks in early human embryosOur comparative analysis of gene regulatory network predictions defines a pipeline to infer transcription factor–target gene regulatory interactions in early human embryos. Mutual information refined by chromatin accessibility allowed us to construct the first network during early human development.
Performance and robustness analysis reveals phenotypic trade-offs in yeastThis study combines phenotypic data from yeast cultivations with quantification of robustness over a defined perturbation space, revealing trade-offs between performance and robustness.
