The rockefeller university

The regulation of gene expression is crucial for the functional integration of evolutionarily young genes, particularly those that emerge de novo. However, the regulatory programmes governing the expression of de novo genes remain unknown. To address this, we applied computational methods to single-cell RNA sequencing data, identifying key transcription factors probably instrumental in regulating de novo genes. We found that transcription factors do not have the same propensity for regulating de novo genes; some transcription factors regulate more de novo genes than others. Leveraging genetic and genomic tools in Drosophila, we further examined the role of two key transcription factors, achintya and vismay, and the regulatory architecture of new genes. Our findings identify key transcription factors associated with the expression of de novo genes and highlight how transcription factors, and possibly their duplications, are linked to the expressional regulation of de novo genes.

A primary goal in the development of an AIDS vaccine is the elicitation of broadly neutralizing antibodies (bNAbs) that protect against diverse HIV-1 strains. To this aim, germline-targeting immunogens have been developed to activate bNAb precursors and initiate the induction of bNAbs. While most preclinical germline-targeting HIV-1 vaccine candidates only include a single bNAb precursor epitope, an effective HIV-1 vaccine will likely require bNAbs that target multiple epitopes on Env. Here, we report a newly designed germline-targeting Env SOSIP trimer, named 3nv.2, that presents three bNAb epitopes on Env: the CD4bs, V3, and V2 epitopes. 3nv.2 forms a stable trimeric Env and binds to bNAb precursors from each of the desired epitopes. Immunization experiments in rhesus macaques and mice demonstrate 3nv.2 elicits the combined effects of its parent immunogens. Our results provide proof of concept for using a germline-targeting immunogen presenting three or more bNAb epitopes and a framework to develop improved next-generation HIV-1 vaccine candidates.

Heightened activity in the orbitofrontal cortex (OFC), a brain region that contributes to motivation, emotion, and reward-related decision-making, is a key clinical feature of major depressive disorder (MDD). However, the cellular and molecular substrates underlying this dysfunction remain unclear. Here, we performed cell-type-specific profiling of human OFC and unexpectedly mapped MDD-linked epigenomic features (including genetic risk variants) to non-neuronal cells, revealing significant glial dysregulation in this region. Characterization of MDD-specific chromatin loci further identified ZBTB7A-a transcriptional regulator of astrocyte reactivity-as an important mediator of MDD-related alterations. In rodent models, we found that Zbtb7a induction in astrocytes is both necessary and sufficient to drive stress-mediated behavioral deficits, cell-type-specific transcriptional/epigenomic signatures, and aberrant OFC astrocyte-neuronal communication in male mice-an established MDD risk factor. These findings thus highlight essential roles for astrocytes in OFC-mediated stress susceptibility and identify ZBTB7A as a critical and therapeutically relevant regulator of MDD-related OFC dysfunction.

Congenital anomalies of the kidneys and urinary tract (CAKUT) are developmental disorders that commonly cause pediatric chronic kidney disease and mortality. We examine here rare coding variants in 248 CAKUT trios and 1742 singleton CAKUT cases and compare them to 22,258 controls. Diagnostic and candidate diagnostic variants are detected in 14.1% of cases. We find a significant enrichment of rare damaging variants in constrained genes expressed during kidney development and in genes associated with other developmental disorders, suggesting phenotype expansion. Consistent with these data, 18% of CAKUT patients with diagnostic variants have neurodevelopmental or cardiac phenotypes. We identify 40 candidate genes, including CELSR1, SSBP2, XPO1, NR6A1, and ARID3A. Two are confirmed as CAKUT genes: ARID3A and NR6A1. This study suggests that many yet-unidentified syndromes would be discoverable with larger cohorts and cross-phenotype analysis, leading to clarification of the genetic and phenotypic spectrum of developmental disorders.

Lipids are essential components of cancer cells due to their structural and signalling roles1. To meet metabolic demands, many cancers take up extracellular lipids2, 3, 4-5; however, how these lipids contribute to cancer growth and progression remains poorly understood. Here, using functional genetic screens, we identify uptake of lipoproteins-the primary mechanism for lipid transport in circulation-as a key determinant of ferroptosis sensitivity in cancer. Lipoprotein supplementation robustly inhibits ferroptosis across diverse cancer types, primarily through the delivery of alpha-tocopherol (alpha-toc), the most abundant form of vitamin E in human lipoproteins. Mechanistically, cancer cells take up lipoproteins through a pathway dependent on sulfated glycosaminoglycans (GAGs) linked to cell-surface proteoglycans. Disrupting GAG biosynthesis or acutely degrading surface GAGs reduces lipoprotein uptake, sensitizes cancer cells to ferroptosis and impairs tumour growth in mice. Notably, human clear cell renal cell carcinomas-a lipid-rich malignancy-exhibit elevated levels of chondroitin sulfate and increased lipoprotein-derived alpha-toc compared with normal kidney tissue. Together, our study establishes lipoprotein uptake as a critical anti-ferroptotic mechanism in cancer and implicates GAG biosynthesis as a therapeutic target.

Retrons are a retroelement class found in diverse prokaryotes that can be adapted to augment CRISPR-Cas9 genome engineering technology to efficiently rewrite short stretches of genetic information in bacteria and yeast. However, efficiency in human cells has been limited by unknown factors. We identified non-coding RNA (ncRNA) instability and impaired Cas9 activity due to 5 ' sgRNA extension as key contributors to low retron editor efficiency in human cells. We re-engineered the Eco1 ncRNA to incorporate an exoribonuclease-resistant RNA pseudoknot from the Zika virus 3 ' UTR and devised an RNA processing strategy using Csy4 ribonuclease to minimize 5 ' sgRNA extension. This strategy increased steady-state ncRNA levels and rescued sgRNA activity, leading to increased templated repair. This work reveals a previously unappreciated role for ncRNA stability in retron editor efficiency in human cells and presents an enhanced Eco1 retron editor capable of precise genome editing in human cells from a single integrated lentivirus and, in the context of the nCas9 H840A nickase, without creating double-strand breaks.

YnaI is a member of the family of bacterial MscS (mechanosensitive channel of small conductance)-like channels. Channel gating upon hypoosmotic stress and the role of lipids in this process have been extensively studied for MscS, but are less well understood for YnaI, which features two additional transmembrane helices. Here, we combined cryogenic electron microscopy, molecular dynamics simulations and patch-clamp electrophysiology to advance our understanding of YnaI. The two additional helices move the lipid-filled hydrophobic pockets in YnaI further away from the lipid bilayer and change the function of the pocket lipids from being a critical gating element in MscS to being more of a structural element in YnaI. Unlike MscS, YnaI shows pronounced gating hysteresis and remains open to a substantially lower membrane tension than is needed to initially open the channel. Thus, at near-lytic membrane tension, both MscL and YnaI will open, but while MscL has a large pore and must close quickly to minimize loss of essential metabolites, YnaI only conducts ions and can thus remain open for longer to continue to facilitate pressure equilibration across the membrane.

The Nidovirus RdRp-associated nucleotidyltransferase (NiRAN) domain initiates mRNA capping in coronaviruses through a GDP-polyribonucleotidyltransferase reaction, with RNA covalently linked to nsp9. GDP is the preferred substrate for this reaction, but the NiRAN domain can also utilize GTP to produce an authentic 5 ' RNA cap structure, though the GTP-mediated mechanism is unclear. Yan and colleagues claimed to have delineated the reaction mechanism from the analysis of a cryoelectron microscopy (cryo-EM) structure of a trapped catalytic intermediate of the SARS-CoV-2 NiRAN domain with a beta-gamma-non-hydrolyzable GTP analog (GMPPNP) and RNA-nsp9 (PDB: 8GWE). We show that the cryo-EM data used to derive PDB: 8GWE do not support the presence of GMPPNP in the NiRAN active site, and the resulting atomic model is incompatible with fundamental chemical principles. We conclude that Yan and colleagues' conclusions are not experimentally supported and the mechanism for GTP-mediated RNA capping by the SARS-CoV-2 NiRAN domain remains unresolved. This Matters Arising paper is in response to Yan et al. (2022), published in Cell. See also the response by Huang et al. (2025), published in this issue.

Spatial refugia offered by structurally complex habitats mitigate high rates of predation for many aquatic and terrestrial prey species. These refuges are particularly important for small juvenile marine invertebrates, for which predation often represents the greatest cause of mortality. When the availability or quality of habitat landscapes and refugia are diminished by natural or anthropogenic forces, prey populations face further risk. In this study, we examined the utilization of alternative types of submerged aquatic vegetation (SAV) by juvenile bay scallops, Argopecten irradians, in a system where their historical habitat of eelgrass, Zostera marina, has largely disappeared. We found that scallops settled on and remained attached, above the bottom, to 9 species of macroalgae, 6 of which were fine filamentous or fleshy red algae. Macroalgae thus serve as suitable substrates for scallop larval settlement and early juvenile life, clearly important to successful population rebuilding that occurred following commencement of our restoration efforts. However, the much smaller maximum observed size (2-9 mm) and calculated duration of attachment (5-27 days) of scallops in the canopy of red macroalgae were considerably lower than those previously reported for eelgrass and the green macroalgae Codium fragile. With scallops dropping sooner to the bottom from red macroalgae, at smaller sizes, they are accessible to greater numbers of predator species/sizes and higher rates of predation (as shown in supporting laboratory experiments). Furthermore, this transition occurs well before scallops have undergone an ontogenetic shift to evasive swimming or have grown to reach a refuge in larger size. Fine filamentous red macroalgae, in which juvenile scallops demonstrated the highest frequency of attachment in this study and among the shortest duration in the canopy, now predominate in many areas of the Peconic Bays, New York, where eelgrass was formerly widespread. This apparent habitat degradation/replacement is thus acting to compress the length of time scallops are able to utilize a spatial refuge from predation at a critical life history stage, with potential cascading ontogenetic impacts on the use of a subsequent behavioral refuge and possible negative demographic consequences. Few prior studies have revealed such clear impacts of this kind resulting from habitat loss.

The Christchurch mutation (R136S) in the APOE3 (E3S/S) gene is associated with attenuated tau load and cognitive decline despite the presence of a causal PSEN1 mutation and high amyloid burden in the carrier. However, the molecular mechanisms enabling the E3S/S mutation to mitigate tau-induced neurodegeneration remain unclear. Here, we replaced mouse Apoe with wild-type human APOE3 or APOE3S/S on a tauopathy background. The R136S mutation decreased tau load and protected against tau-induced synaptic loss, myelin loss, and reduction in hippocampal theta and gamma power. Additionally, the R136S mutation reduced interferon responses to tau pathology in both mouse and human microglia, suppressing cGAS-STING pathway activation. Treating E3 tauopathy mice with a cGAS inhibitor protected against tau-induced synaptic loss and induced transcriptomic alterations similar to the R136S mutation across brain cell types. Thus, suppression of the microglial cGAS-STING-interferon (IFN) pathway plays a central role in mediating the protective effects of R136S against tauopathy.