The rapidly expanding role of LC3-interacting regions in autophagy.

LC3-interacting regions (LIRs), or Atg8-interacting motifs (AIMs), are short linear motifs found in unstructured loops or intrinsically disordered regions of many autophagy-related proteins. LIRs were initially identified for their role in binding to Atg8 family proteins on autophagosomal membranes. However, emerging evidence suggests that LIRs and their surrounding residues mediate interactions with a wide array of proteins beyond Atg8s.

Structural variation in 1,019 diverse humans based on long-read sequencing.

Genomic structural variants (SVs) contribute substantially to genetic diversity and human diseases, yet remain under-characterized in population-scale cohorts. Here we conducted long-read sequencing in 1,019 humans to construct an intermediate-coverage resource covering 26 populations from the 1000 Genomes Project. Integrating linear and graph genome-based analyses, we uncover over 100,000 sequence-resolved biallelic SVs and we genotype 300,000 multiallelic variable number of tandem repeats, advancing SV characterization over short-read-based population-scale surveys.

Protocol to distinguish pre-mRNA from mRNA in RNA-protein interaction studies.

Transcriptome-wide studies on interactions between RNA-binding proteins (RBPs) and protein-coding RNAs in general preclude interpretations regarding RBP preference for binding to the more abundant mRNA over the less abundant pre-mRNA. Here, we present a protocol to determine the binding preference of the RBP tristetraprolin (TTP, Zfp36) for pre-mRNA versus mRNA. We describe steps for the identification and quantitation of intronic and exonic fragments in RNA bound to TTP.

Molecular features of TNBC govern heterogeneity in the response to radiation and autophagy inhibition.

Triple negative breast cancer (TNBC) is a heterogeneous and a highly aggressive type of breast cancer. Standard of care for TNBC patients includes surgery, radio-, chemo- and immunotherapy, depending on the stage of the disease. Immunotherapy is ineffective as monotherapy but can be enhanced with taxane chemotherapy or radiotherapy.

Nanoscale 3D DNA tracing in non-denatured cells resolves the Cohesin-dependent loop architecture of the genome in situ.

The spatial organization of the genome is essential for its functions, including gene expression and chromosome segregation. Phase separation and loop extrusion have been proposed to underlie compartments and topologically associating domains, however, whether the fold of genomic DNA inside the nucleus is consistent with such mechanisms has been difficult to establish in situ. Here, we present a 3D DNA-tracing workflow that resolves genome architecture in single structurally well-preserved cells with nanometre resolution.

Effects of base temperature, immersion medium, and EM grid material on devitrification thresholds in cryogenic optical super-resolution microscopy.

Cryogenic correlative light and electron microscopy (cryo-CLEM) is an imaging strategy that integrates specific molecular labeling and molecular resolution structural information. However, there is a resolution gap of more than two orders of magnitude between diffraction-limited fluorescence microscopy and electron microscopy (EM). Single-molecule localization microscopy (SMLM) performed at cryogenic temperatures promises to bridge this resolution gap.

Plant galls induced by insects: Coordinated developmental reprogramming and defence manipulation.

Galls, especially those induced by insects, represent one of the most dramatic examples of plant developmental reprogramming, combining complex de novo organogenesis with compromised defence. Insect-induced galls are not just a fascinating natural phenomenon but a unique system for future discoveries in developmental biology, plant defence, and evolutionary ecology. Gall development is under the control of their insect manipulators and in sync with insect growth to provide tailored nutritive and protective environments.

Foreground-aware Virtual Staining for Accurate 3D Cell Morphological Profiling.

Microscopy enables direct observation of cellular morphology in 3D, with transmitted-light methods offering low-cost, minimally invasive imaging and fluorescence microscopy providing specificity and contrast. Virtual staining combines these strengths by using machine learning to predict fluorescence images from label-free inputs. However, training of existing methods typically relies on loss functions that treat all pixels equally, thus reproducing background noise and artifacts instead of focusing on biologically meaningful signals.

A comprehensive atlas of full-length Arabidopsis eccDNA populations identifies their genomic origins and epigenetic regulation.

Extrachromosomal circular DNA (eccDNA) has been described in several eukaryotic species and has been shown to impact phenomena as diverse as cancer and herbicide tolerance. EccDNA is thought to arise mainly through transposable element (TE) mobilization. Because studies based on short-read sequencing cannot efficiently identify full-length eccDNA forms generated from TEs, we employed the CIDER-Seq pipeline based on long-read sequencing, to obtain full-length eccDNAs from Arabidopsis.

A lyophilized open-source RT-LAMP assay for molecular diagnostics in resource-limited settings.

A critical bottleneck for equitable access to population-scale molecular diagnostics is the limited availability of rapid, inexpensive point-of-care tests, especially in low- and middle-income countries. Here, we developed an open-source reverse transcription loop-mediated isothermal amplification (RT-LAMP) molecular assay for pathogen detection. It is based on nonproprietary enzymes, namely, HIV-1 reverse transcriptase, LF DNA polymerase, and UDG BMTU thermolabile uracil-DNA glycosylase.

White-Brown switching controls phenotypic plasticity and virulence of Candida auris.

The skin-tropic human fungal pathogen Candida auris can cause life-threatening infections of high mortality in healthcare settings. Clinical isolates display a pronounced heterogeneity in virulence traits, such as antifungal susceptibility, stress adaptation, and growth fitness. However, the mechanistic bases underlying intraspecies variations remain enigmatic.

Coping with uncertainty: Challenges for robust pattern formation in dynamical tissues.

An outstanding question in biology is how tissue patterning emerges during development. The concept of positional information, which posits that gradients of morphogens instruct cell fate in a concentration-dependent manner, has been an influential framework to understand pattern formation. Recent studies, however, highlight that developing tissues are highly dynamic, with cellular movements, arising from local mechanical fluctuations or global morphogenetic forces, that often coincide with morphogen signaling and cell fate specification.

Photocatalytic Diselenide Contraction as a Tool for Site-Selective Isosteric Ubiquitylation.

Ubiquitylation is a highly conserved post-translational modification (PTM) in eukaryotes, which serves as a critical regulatory mechanism for protein homeostasis, cellular transport, signal transduction pathways, and numerous other functions. The biological function of ubiquitylation is dictated predominantly by the topology of its linkage. Deciphering ubiquitin's complex biochemistry necessitates novel synthetic methods that deliver well-defined, biosimilar ubiquitylation.

A tighter grip on gene expression.

A previously unknown cofactor function stabilizes transcription factor binding across the genome.

Vacuolar signaling, biogenesis, and quality control in plants.

The plant vacuole, traditionally viewed as a static storage organelle, has recently emerged as a dynamic hub orchestrating signaling, metabolic integration, and stress responses. This review synthesizes recent advances that position the vacuole as a pivotal regulator of plant development and environmental adaptation. We discuss the vacuole's multifaceted roles in ion sequestration, lipid trafficking, mechanosensing, and signal transduction, highlighting its central role in preserving cellular homeostasis.

Phytochrome A is required for light-inhibited germination of Aethionema arabicum seed.

The germination of most seeds is influenced by the duration, intensity, and quality of light. The seeds of the model plant Arabidopsis are positive photoblastic and require light to germinate. The germination of negative photoblastic seeds is inhibited by white light.

The dynamic genomes of Hydra and the anciently active repeat complement of animal chromosomes.

Background: Many metazoan genomes are characterized by highly conserved chromosomal homologies that predate the ancient origin of this clade. This conservation has been tested by expansions of selfish DNA elements, in particular transposable elements (TEs). While comparative genomics studies have highlighted their diversity across animal genomes, common principles underlying their evolution along deeply conserved chromosomes have been elusive.

Dbl2 interacts with helicases and an endonuclease to maintain the integrity of repetitive regions.

Helicases and endonucleases play crucial roles in genome maintenance by unwinding or cleaving various forms of DNA and RNA structures in order to facilitate essential biological processes, such as DNA replication and recombination. Here, we identified fission yeast Dbl2 as a potential interactor of several complexes that exhibit either helicase or endonuclease activity, namely Fml1-MHF, SCF, Rqh1-Top3-Rmi1, and Mus81-Eme1. In vitro, Dbl2 binds to DNA, with a preference for branched molecules, such as D-loops, mobile Holliday junctions, and fork structures, making it a good candidate to play a central role in modulating the activity of helicases and endonucleases during replication and recombination repair.

ERH regulates type II interferon immune signaling through post-transcriptional regulation of JAK2 mRNA.

Type II interferon (IFNγ) signaling is essential for innate immunity and critical for effective immunological checkpoint blockade in cancer immunotherapy. Genetic screen identification of post-transcriptional regulators of this pathway has been challenging since such factors are often essential for cell viability. Here, we utilize our inducible CRISPR/Cas9 approach to screen for key post-transcriptional regulators of IFNγ signaling, and in this way, we identify ERH and the ERH-associated splicing and RNA export factors MAGOH, SRSF1, and ALYREF.

A Roadmap for Improving Reliability and Data Sharing in Crosslinking Mass Spectrometry.

Crosslinking mass spectrometry (MS) can uncover protein-protein interactions and provide structural information on proteins in their native cellular environments. Despite its promise, the field remains hampered by inconsistent data formats, variable approaches to error control, and insufficient interoperability with global data repositories. Recent advances, especially in false discovery rate models and pipeline benchmarking, show that crosslinking MS data can reach a reliability that matches the demand of integrative structural biology.

Regulation of somatic hypermutation by higher-order chromatin structure.

The generation of protective antibodies by somatic hypermutation (SHM) is essential for antibody maturation and adaptive immunity. SHM involves co-transcriptional mutagenesis of immunoglobulin variable (V) regions regulated by enhancers located hundreds of kilobases away. How 3D chromatin topology affects SHM is poorly understood.

Developing a new cleavable crosslinker reagent for in-cell crosslinking.

Crosslinking mass spectrometry (XL-MS) is a powerful technology that recently emerged as an essential complementary tool for elucidating protein structures and mapping interactions within a protein network. Crosslinkers which are amenable to post-linking backbone cleavage simplify peptide identification, aid in 3D structure determination and enable system-wide studies of protein-protein interactions (PPIs) in cellular environments. However, state-of-the-art cleavable linkers are fraught with practical limitations, including extensive evaluation of fragmentation energies and fragmentation behavior of the crosslinker backbone.

k-mer-based GWAS in a wheat collection reveals novel and diverse sources of powdery mildew resistance.

Wheat genetic resources hold the diversity required to mitigate agricultural challenges from climate change and reduced inputs. Using DArTseq, we genotype 461 wheat landraces and cultivars and evaluate them for powdery mildew resistance. By developing a k-mer-based GWAS approach with fully assembled genomes of Triticum aestivum and its progenitors, we uncover 25% more resistance-associated k-mers than single-reference methods, outperforming SNP-based GWAS in both loci detection and mapping precision.

Specific origin selection and excess functional MCM2-7 loading in ORC-deficient cells.

The six-subunit origin recognition complex (ORC) loads excess MCM2-7 on chromosomes to promote initiation of DNA replication and is believed to be important for origin specification. Mapping of origins in cancer cell lines engineered to delete three of the subunits, ORC1, ORC2, or ORC5, shows that specific origins are still used and are mostly at the same sites in the genome as in wild-type cells. The few thousand origins that were upregulated in the absence of ORC suggest that GC/TA skewness and simple repeat sequences facilitate, but are not essential for, origin selection in the absence of the six-subunit ORC.