Homeostatic control of interferon (IFN) signaling is essential, as dysregulation leads to poor outcomes. While the stimuli-dependent induction of IFNs is well understood, less is known about how IFN mRNAs are maintained at low levels basally or rapidly returned to baseline post-stimulation. We find that selective post-transcriptional control of type I and type III IFN mRNAs by the RNA-binding specificity factor tristetraprolin (TTP) and mRNA decay machinery contributes to homeostatic control by negatively regulating IFN mRNAs at steady state and post-stimulation. Loss of this pathway leads to increased poly(A) tail length, stability, and translation. This increases expression of IFNs, potently blocking severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in vitro and in vivo. A human TTP variant associated with autoimmunity shows decreased TTP levels and increased IFN signaling, further demonstrating that regulation by this pathway impacts disease. Prolonged IFN signaling driven by transient loss of mRNA decay primes cells, inducing innate memory and providing long-term antiviral protection.

In metazoans, gene expression is typically regulated by a cis-regulatory landscape (CRL) composed of a promoter and multiple enhancers. How these cis-regulatory elements (CREs) coordinate their function across large genomic distances remains unclear. For example, is the simultaneous activation of multiple enhancers required to promote transcription? Here, we combined single-molecule footprinting with long-read sequencing to quantify how often chromatin accessibility and transcription factor binding co-occur across entire CRLs in the Drosophila genome. Analysis of thousands of individual DNA molecules at each locus revealed that CREs form a specific network with shared single-molecule chromatin accessibility profiles. Co-accessibility is not limited to adjacent CREs and is frequently observed between CREs brought into proximity by chromatin looping. Co-accessible CREs exhibit strong coordination in their cell-type-specific accessibility, linking enhancer activity with transcriptional activation. Our data uncover dependencies between CREs genome-wide and suggest that coordinated enhancer activation is a widespread mechanism regulating gene expression.

DYT1 dystonia is an incurable movement disorder caused by a loss-of-function mutation in Torsin1A, an endoplasmic reticulum (ER)-resident AAA+ ATPase. Here, we use Drosophila and human cells to shed light on Torsins' mode of action. Fly germ cells lacking dTorsin arrest in development with defects in nuclear pore complex (NPC) biogenesis due to impaired nuclear envelope membrane fusion. We identify the conserved membrane protein Chloride Channel CLIC-like protein 1 (CLCC1) as a Torsin1A interaction partner whose absence phenocopies membrane fusion defects caused by Torsin deletion. CLCC1 is enriched at membrane fusion sites, and molecular dynamics (MD) simulations suggest that CLCC1 rings induce bilayer remodeling and lipid flux to initiate fusion of the outer and inner nuclear membranes. Remarkably, CLCC1 overexpression rescues defects associated with loss of Torsins, indicating that a main role of dTorsin/Torsin1A is to sustain CLCC1 functionality. Our findings inform a model of nuclear envelope membrane fusion and imply that modulating CLCC1 expression is a promising therapeutic prospect for DYT1 dystonia.

The TMEM41B scramblase and its regulatory partner CLCC1 initiate lipid flux by equilibrating newly synthesized phospholipids across the endoplasmic reticulum (ER) bilayer, a fundamental process required for diverse events ranging from membrane biogenesis to bulk lipid supply. Loss of CLCC1/TMEM41B causes ER bilayer imbalance, which induces giant ER-enclosed lipid droplets (geLDs) and drives rapid progression into severe metabolic-dysfunction-associated steatohepatitis (MASH). Combining both human cell lines and mouse models, we herein reveal CLCC1 to be the long-missing client of the luminal torsin ATPases, which selectively engage oligomerized CLCC1 at sites of ER bilayer imbalance. Mice hepatic torsinA inactivation triggers geLD formation amid disrupted lipoprotein biogenesis and severe MASH, closely phenocopying CLCC1/TMEM41B deficiency. Mechanistically, torsins act as assembly-promoting ATPases that drive CLCC1 oligomerization for its recruitment to imbalanced bilayers. Remarkably, ectopic CLCC1 expression reverses cellular and systemic lipid disorders arising from hepatic torsinA deficiency. Hence, torsin ATPases emerge as fundamental regulators that organize CLCC1 and the downstream TMEM41B scramblase to govern lipid partitioning and membrane homeostasis.

Ferroptosis, a form of oxidative cell death, represents a therapeutic vulnerability for treating apoptosis-resistant cancers. Here, we identify leucine zipper transcription factor-like 1 (LZTFL1) as a key regulator of ferroptosis that rewires glutathione (GSH) metabolism. Mechanistically, LZTFL1 promotes oxidation of glucose-6-phosphate dehydrogenase (G6PD), thereby limiting NADPH production and impairing GSH regeneration. GSH depletion in turn enhances LZTFL1 translation via an AKT-mammalian target of rapamycin (mTOR)-eukaryotic initiation factor 4E (eIF4E) pathway, establishing a feedforward loop that amplifies ferroptosis. In vivo, the LZTFL1-formin homology 2 domain-containing 1 (FHOD1)-G6PD axis sensitizes multiple tumor models, including patient-derived xenografts, to ferroptosis, leading to enhanced lipid peroxidation, reduced GSH levels, suppressed tumor growth, and prolonged survival. LZTFL1 expression restores cisplatin sensitivity in resistant lung and ovarian cancer cells and predicts improved survival outcomes in patients with lung adenocarcinoma. Moreover, FDA-approved agents upregulate LZTFL1 and re-sensitize resistant tumors to cisplatin. These findings highlight LZTFL1 as a potential biomarker and a therapeutic target for enhancing ferroptosis-based cancer therapy.

Protein S-palmitoylation is a dynamic and reversible post-translational modification (PTM) that governs diverse cellular processes, yet its study remains constrained by the indirect and ensemble-averaging nature of classical biochemical assays. Here, we report a nanopore-based platform, PALM-Scan (palmitoylation analysis via label-free monitoring and signature capture on nanopore) that directly transduces physicochemical signatures of S-palmitoylated peptides into digital electrical signals. Using an engineered Mycobacterium smegmatis porin A (M2-MspA) nanopore, PALM-Scan enables sequence-independent identification of S-palmitoylation and simultaneously differentiates S-palmitoylation from other cysteine-directed PTMs, including S-nitrosylation and S-glutathionylation, without probes or enrichment. We further demonstrate its translational potential by successfully detecting and distinguishing S-palmitoylated subpopulations of disease-relevant biomarkers, including mouse beclin-1 (BECN1)- and glial fibrillary acidic protein (GFAP)-derived peptides, in complex mixtures with minimal sample input. In summary, by integrating label-free operation, single-molecule resolution, and multiplex discrimination, PALM-Scan provides a transformative tool for interrogating S-palmitoylation dynamics in both basic research and biomedical applications.

BRD4, a bromodomain and extraterminal (BET) family transcriptional regulator, is believed to be recruited to chromatin via interactions between its tandem bromodomains (BD1 and BD2) and acetylated histone tails. Although extensive studies have explained how individual BRD4 bromodomains bind to acetylated peptides and how BET inhibitors interfere with such interactions, equivalent studies of the full-length BRD4 protein with the nucleosome have been lacking. Our cryo-electron microscopy (cryo-EM) structure of the BRD4 short (BRD4-S) isoform bound to a nucleosome diacetylated on histone H4 shows how BRD4 BD1 engages both the H4 tail and nucleosomal DNA. Unlike other chromatin reader domain/nucleosome structures, BRD4 BD1 presents the acetylated histone tail for potential interactions with additional chromatin proteins. Unexpectedly, our biochemical studies indicate that BRD4 uses basic regions outside of the bromodomains to bind nucleosomes tightly even in the absence of histone acetylation. Our results further show that histone H4 acetylation influences the conformation of the BRD4/nucleosome complex.

Approximately 10%-15% of human cancers maintain their telomeres through alternative lengthening of telomeres (ALT), a recombination-based pathway that exploits chronic telomeric replication stress to drive telomere elongation. Although initiated in S phase, ALT-associated telomere synthesis is prominent in G2 phase and can extend into mitosis through mitotic DNA synthesis (MiDAS) and even into G1 phase of the next cell generation through post-mitotic DNA synthesis (post-MiDAS). Here, we review recent advances in the mechanistic understanding of ALT across the cell cycle. We emphasize how persistent replication stress and elevated DNA damage at telomeres drive ALT activity but must be tightly controlled to preserve telomere integrity and cell viability. We further highlight how MiDAS and post-MiDAS may act as last-resort pathways to preserve genome integrity when under-replicated telomeres bypass cell cycle checkpoints. Finally, we discuss how these mechanistic insights could be leveraged to develop novel therapeutic strategies specifically targeting ALT-dependent cancers.

Cells owe a lot to their mitochondria-to their many mitochondria. Recent discoveries and emerging technologies point to functional distinctions within that population. We asked a group of researchers about what mitochondrial heterogeneity means for understanding cellular and organismal physiology.

In a recent Cell paper, Maurais et al.1 show that genomic instability drives human cells to transfer fragmented chromosomes to neighbors via tunneling nanotubes (TNTs), with heritable functional consequences, raising fundamental questions about intercellular communication, genome surveillance, and cancer evolution.

In this issue of Molecular Cell, Smalinskaitė et al.[1] reveal that transmembrane domain pairs (TMD-pairs), the fundamental biosynthetic units of multipass membrane proteins, are inserted into the endoplasmic reticulum membrane by Oxa1-family insertases through largely Sec61-independent mechanisms.

In this issue of Molecular Cell, Lee et al.[1] address a central structural biology challenge: capturing low-affinity protein interactions in cells and integrating the resulting restraints with cryoelectron microscopy and AlphaFold to localize dynamic interactors on native human proteasomes.

In this issue of Molecular Cell, Cuneo et al.1 propose an equilibrium between two quaternary states of SPOP that can become dysregulated in cancer. SPOP oligomers form inactive double donuts or active linear filaments, as seen in gain-of-function cancer mutations.

Tandemly repeated satellite DNAs provide the building blocks for centromeres, but whether and how their transcripts regulate chromosome segregation remain poorly defined. Here, we show that human α-satellite RNAs (α-SatRNAs) are required for maintaining centromeric cohesion during mitosis. α-SatRNAs localize to centromeres and physically associate with α-satellite chromatin to form R-loops both in cis and in trans. Disruption of these R-loops by RNase H1 overexpression causes centromeric cohesion defects, phenocopying α-SatRNA knockdown, which can be rescued by the expression of an α-satellite consensus sequence, supporting a major role for α-SatRNA-formed R-loops in centromeric cohesion. Furthermore, ectopic targeting of the cohesion protector Shugoshin (Sgo)1 to centromeric α-SatDNAs largely rescues centromeric cohesion defects caused by α-SatRNA knockdown or RNase H1 overexpression. Our findings reveal a critical pathway comprising α-SatRNAs, R-loops, and Sgo1 in regulating centromeric cohesion, thus providing an important mechanism to explain how satellite transcripts regulate chromosomal stability.

TnpB is a compact RNA-guided endonuclease and an evolutionary ancestor of CRISPR-Cas12 that offers a promising platform for genome engineering. However, the genome-editing activity of TnpBs remains limited, and its underlying determinants are poorly understood. Here, we used biochemical and single-molecule assays to examine the DNA-unwinding mechanism of Youngiibacter multivorans TnpB (Ymu1 TnpB). DNA unwinding proceeds through a discrete, long-lived, partially unwound intermediate state before reaching a fully unwound open state. The open state forms inefficiently and collapses readily in the absence of negative supercoiling. An optimized variant, H4W-L304F-V305R (Ymu1-WFR), stabilizes formation of both the intermediate and open states, resulting in enhanced DNA cleavage in vitro and increased genome editing in plants. These findings identify the physical basis for the observed minimal activities of natural TnpBs, revealing how stabilizing specific unwinding states enables efficient DNA targeting.