Table of Contents
Research Articles
Exploratory meta-analysis of hypoxic transcriptomes using a precise transcript reference sequence setExploratory meta-analysis of hypoxic RNA-seq data using FANTOM-CAT as a reference transcriptome facilitates the evaluation of relationship between sense–antisense transcripts from the same locus.
A dominant negative mitofusin causes mitochondrial perinuclear clusters because of aberrant tetheringOur analysis of a CMT2A-associated mitofusin variant reveals that aberrant mitochondrial tethering results in perinuclear clusters and that conformational dynamics in Hinge 2 are required to progress from membrane tethering to membrane fusion.
Low expression of EXOSC2 protects against clinical COVID-19 and impedes SARS-CoV-2 replicationGenetic evidence and in vitro experiments with live virus suggest EXOSC2 depletion can reduce SARS-CoV-2 replication without significant toxicity.
The metabolite-controlled ubiquitin conjugase Ubc8 promotes mitochondrial protein importYeast cells employ the cytosolic ubiquitin system to increase the capacity of the mitochondrial import machinery during phases of metabolic transitions.
Tandemly repeated NBPF HOR copies (Olduvai triplets): Possible impact on human brain evolutionThe human genome, unlike the genomes of other primates, contains tandemly organized higher order NBPF structures that represent a link to the development of their cognitive abilities.
A prediction model for COVID-19 liver dysfunction in patients with normal hepatic biochemical parametersThe composite model of sex and the novel protein marker ANGL3 exhibits great potential in predicting the risk of developing LD in COVID-19 patients with normal hepatic biochemical parameters on admission.
Replication-associated inversions are the dominant form of bacterial chromosome structural variationProkaryotic rearrangements symmetric to the replication origin are identified across 247 bacterial species. Large-scale inversions are found to be highly prevalent across species, and their mediating factors are examined. The full pipeline and dataset are available on GitHub at https://github.com/mdiorio371/RASR.
An inducible amphipathic α-helix mediates subcellular targeting and membrane binding of RPE65Amino acid residues 107–125 of RPE65, in concert with a palmitoyl group at C112, form a membrane-sensing amphipathic helix that targets RPE65 to smooth endoplasmic reticulum to acquire its substrate.
Dlk1-Dio3 cluster miRNAs regulate mitochondrial functions in the dystrophic muscle in Duchenne muscular dystrophyA large number of DLK1-DIO3 miRNAs are up-regulated in the muscles and the serum of Duchenne muscular dystrophy, animal models, and patients. Mitochondrial functions, and in particular oxidative phosphorylation, are targeted by these coordinately up-regulated DLK1-DIO3 miRNAs.
MDF is a conserved splicing factor and modulates cell division and stress response in ArabidopsisMDF acts like its human homolog SART1 as a splicing factor that is important for maintenance of genome stability and correct splicing and expression of genes involved in cell division and stress response.
Stepwise progression of β-selection during T cell development involves histone deacetylationT cells undergoing beta-selection differentiate via sequential expression of co-receptors CD28, CD5, and CD2, exposing new signalling controls that are disrupted by a cancer therapeutic.
Profiling subcellular localization of nuclear-encoded mitochondrial gene products in zebrafishThe vast majority (99%) of mitochondrial proteins are encoded by the nuclear genome, synthesized in the cytosol and imported into the organelle. Here we study the principles of mitochondrial import in vivo from the RNA perspective using zebrafish.
Actin-binding domain of Rng2 sparsely bound on F-actin strongly inhibits actin movement on myosin IIRng2CHD, an actin-binding domain of an IQGAP, induces cooperative conformational changes in actin filaments and inhibits movement driven by myosin II.
Miro GTPase domains regulate the assembly of the mitochondrial motor–adaptor complexRelocalizing the mitochondrial motor–adaptor protein Miro to peroxisomes and systematically manipulating each GTPase domain reveal the importance of the N-terminal GTPase domain of Miro1 for regulating mitochondrial transport.
Palmitate impairs circadian transcriptomics in muscle cells through histone modification of enhancersThe disruption of circadian rhythms because of lipid overload may lead to epigenomic changes that influence metabolism. Thus, a dietary or therapeutic modulation of lipid levels, a cornerstone in the treatment of metabolic disorders, may prevent circadian misalignment in peripheral tissues.
circEXOC5 promotes acute lung injury through the PTBP1/Skp2/Runx2 axis to activate autophagycircEXOC5 activates autophagy and promotes acute lung injury via stimulating the Skp2 decay to stabilize Runx2 by interacting with PTBP1.
In vivo probing of SECIS-dependent selenocysteine translation in ArchaeaBy turning a bacterial reporter into an archaeal selenoprotein, in vivo probing of structure–function relations during UGA recoding for selenoprotein synthesis in Archaea is greatly facilitated.
CRISPRi screening reveals regulators of tau pathology shared between exosomal and vesicle-free tauUsing a genome-wide CRISPRi screen, we identified ANKLE2, BANF1, NUSAP1, EIF1AD, and VPS18 as novel regulators of tau pathology induced by both exosome-like extracellular vesicles and free tau seeds.
Tanshinone functions as a coenzyme that confers gain of function of NQO1 to suppress ferroptosisNQO1 catalyzes the reduction of tanshinones to detoxify lipid peroxyl radicals and inhibit ferroptosis both in vitro and in vivo, providing a molecular mechanism for the therapeutic effects of tanshinones, such as cardiac protection.
The potential of a universal influenza virus-like particle vaccine expressing a chimeric cytokineHerein, a virus-like particle vaccine with chimeric cytokine shows the protective efficacy against different strains of influenza virus, laying the foundation for designing a universal influenza vaccine.
Lack of peroxisomal catalase affects heat shock response in Caenorhabditis elegansThe authors present a previously unknown crosstalk between peroxisomes and the heat shock response, whereby the peroxisomal catalase is vital for cellular capacity to survive heat stress and undergo heat-induced lifespan extension.
C-to-U RNA deamination is the driving force accelerating SARS-CoV-2 evolutionThe authors propose that the host-mediated C-to-U RNA editing event, which is also affected by the RNA structure, is the driving force that accelerates SARS-CoV-2 mutation and evolution.
LACTB exerts tumor suppressor properties in epithelial ovarian cancer through regulation of SlugWe show the ability of LACTB to function as a tumor suppressor in ovarian cancer through down-regulation of Slug and induction of differentiation.
Lipid saturation induces degradation of squalene epoxidase for sterol homeostasis and cell survivalThe authors describe the ER-associated degradation of Erg1 under increased membrane lipid saturation and show its importance in balancing sterol levels for membrane integrity in budding yeast.
Loss of autism-candidate CHD8 perturbs neural crest development and intestinal homeostatic balanceA combination of zebrafish and transcriptomic analyses revealed the role of the autism-candidate chd8 in the development of the enteric nervous system, serotonin metabolism, and intestinal integrity.
Discovery of RUF6 ncRNA–interacting proteins involved in P. falciparum immune evasionAn RNA-directed proteomic discovery (ChIRP-MS) protocol is used to identify in vivo RUF6 ncRNA–protein interactions that sustain virulence genes in the human malaria parasite, Plasmodium falciparum.
SMA-linked SMN mutants prevent phase separation properties and SMN interactions with FMRP family membersThe survival motor neuron (SMN) protein associates with translation regulators and phase-separates into RNA-stabilized droplets that are likely candidates for the formation of nuclear and cytoplasmic membraneless organelles.
Endoplasmic reticulum membranes are continuously required to maintain mitotic spindle size and forcesUsing microinjection approaches in Drosophila embryos, Araújo et al reveal that acute disruption of the ER at centrosome-proximal sites perturbs the architecture of the mitotic spindle, with a direct impact on nuclear positioning.
ZBTB18 inhibits SREBP-dependent lipid synthesis by halting CTBPs and LSD1 activity in glioblastomaThis study identifies a new mechanism of fatty acid synthesis regulation in glioblastoma that involves ZBTB18, CTBP, and LSD1. The transcriptional repressor ZBTB18 interacts with CTBP and inhibits LSD1 demethylase activity.
GPER1 links estrogens to centrosome amplification and chromosomal instability in human colon cellsThis study reveals a causal link between (xeno)estrogen-activated GPER1, centriole-positive numerical centrosome amplification, and genomic instability in normal colon and colorectal cancer cells.
Hepatic DKK1-driven steatosis is CD36 dependentIncreased DKK1 in hepatic steatosis contributes CD36-mediated fatty acid uptake and insulin resistance.
Resources
Myeloma immunoglobulin rearrangement and translocation detection through targeted capture sequencingTargeted capture sequencing (CapIG-seq) is a novel, efficient, and effective approach to examine multiple genomic alterations in ctDNA and bone marrow aspirates of patients with multiple myeloma.
Protein and RNA ADP-ribosylation detection is influenced by sample preparation and reagents usedMono(ADP-ribosyl)ation is an emerging modification, for which recently detection reagents were generated. We cross-validated all reagents and observe remarkable differences in efficiency, depending on the substrate investigated and on the methods that are used.
Concordance of MERFISH spatial transcriptomics with bulk and single-cell RNA sequencingSingle-cell RNA-seq is an important technology for capturing gene expression in individual cells. It has limitations as spatial context and accurate representation of cell types in the tissue are lost. Here, we show that MERFISH is comparable to scRNA-seq.
Methods
A high-content endogenous GLUT4 trafficking assay reveals new aspects of adipocyte biologyThe authors describe a high-throughput method for measuring endogenous GLUT4 and transferrin receptor translocation in adipocytes. They reveal that this method has advantages over studying GLUT4 trafficking using overexpressed GLUT4 reporters, which are commonly used in the field.
Genome-wide profiling of histone modifications in Plasmodium falciparum using CUT&RUNWe present a detailed step-wise protocol for reliable genome-wide profiling of histone modifications using CUT&RUN that requires only low numbers of Plasmodium falciparum blood stages.
