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In this Tools of the Trade article, Isomursu (Ivaska lab) describes a new method for dynamic micropatterning, which enables investigation of cell adhesion and migration on substrates that mimic different extracellular matrix environments.
In mouse models of acute kidney injury, the outcome — scarless tissue repair versus fibrosis — depends on the activity of the transcription factor SOX9.
Somite formation, crucial for organization of the segmental pattern of vertebrate embryos, depends on the oscillatory expression of segmentation clock genes. Novel in vitro models of somitogenesis have provided insights into the spatiotemporal dynamics of gene expression, signalling and metabolic gradients that enable somite formation and patterning.
Gene regulation in animals depends chiefly on enhancers, yet the underlying mechanisms are poorly understood. This Review discusses enhancer–promoter interactions and transcription activation, focusing on how enhancer–promoter selectivity is achieved and on recent technical advances that may provide new insights into transcription activation.
In this Tools of the Trade article, Hugo Damstra and Josiah Passmore (Kapitein Lab) describe GelMap, which introduces a fluorescent reference grid into the workflow of expansion microscopy experiments, thus enabling a visual readout of sample deformation.
The prevailing challenge in live-cell fluorescence microscopy is capturing intra-cellular dynamics while preserving cell viability. Alongside developments of microscopy hardware, computational methods — especially those based on machine learning — are powerful tools to improve the signal-to-noise ratio, spatial resolution, temporal resolution and multi-colour capacity of live-cell imaging.
Cilia are microtubule-based cell projections that provide a unique environment with precise protein, lipid and second messenger concentrations, thereby creating specialized signalling hubs. This Review discusses recent multidisciplinary, mechanistic insights into cilia-based signalling pathways during development and homeostasis.
Ferroptosis is a non-apoptotic, iron-dependent cell death mechanism driven by plasma membrane lipid peroxidation and subsequent plasma membrane rupture. Various cellular compartments and organelles contribute to regulating susceptibility to ferroptosis. This regulation involves a plethora of mechanisms centred on iron metabolism and storage, lipid metabolism, and redox balance.
Protein S-acylation is involved in many pathophysiological processes. Here, Mesquita et al. discuss the structure, function and regulation of S-acylation and deacylation enzymes and describe how this post-transcriptional modification precisely controls protein–cell membrane interactions. Potential therapeutic applications of S-acylation are also highlighted.
In this Tools of the Trade article, Khalid Ibrahim (Radenovic and Lashuel labs) describes a tool for the artificial intelligence (AI)-driven detection of cellular aggregates that bypasses the need for fluorescent labelling.
In this Tools of the Trade article, Lei Yuan (from the Cai lab) highlights a new culture system that allows in vitro reconstitution of a dynamic miniature mammary gland.
Rapid reactivation of gene expression following mitosis-induced silencing is facilitated by a network of redundantly acting nuclear receptors that function as mitotic bookmarks.
L. Villiger, J. Joung et al. review CRISPR applications for programmable editing of the genome, epigenome and transcriptome. They discuss how CRISPR–Cas systems can be optimized to further improve editing specificity and efficiency and highlight a multitude of applications in basic biological research and for changing clinical practice.
This Review discusses the emerging roles of long non-coding RNAs (lncRNAs) in the regulation of transcription, for example by controlling the expression of transcription factors. Some lncRNA loci function in trans, but most function in cis, through their own transcription or through the lncRNA transcripts themselves.