Biology subjects

Narita, H.

Publications and source records attributed to Narita, H..

8 recordsLinked to original sources

bioRxiv2026

Reactivating a schizophrenia risk gene-enriched prefrontal ensemble suppresses decision noise

Schizophrenia genetics and single-cell transcriptomics implicate prefrontal excitatory neurons and synaptic programs, but how these vulnerabilities alter circuit dynamics, behavior, and pharmacological targetability remains unclear. We identify a clozapine-responsive prefrontal ensemble enriched for schizophrenia risk genes that stabilizes value-guided choice. NMDA receptor hypofunction increased value-independent decision noise and weakened the ensembles pre-choice transient, while clozapine rescued both. Chemogenetic inhibition of the ensemble increased decision noise, demonstrating causality. By integrating receptor affinities with mouse and human single-cell transcriptomes, we designed a rational multi-receptor antagonist cocktail that reactivated the ensemble and rescued decision noise without increasing NREM sleep time or NREM delta power, in contrast to clozapine. These findings link schizophrenia genetics to cortical ensemble dynamics and establish ensemble-targeted pharmacology as a strategy for ameliorating pathological computations. One-Sentence SummaryTargeting a schizophrenia risk gene-enriched prefrontal ensemble suppresses decision noise without clozapine-like sedation.

neuroscience↗

bioRxiv2026

Decoupling Fabrication from Encoding: DNA-Addressable Template Microparticles for Large, User-Defined Optical Barcode Libraries

Optical barcodes for pooled high-throughput screening must support large libraries while remaining decodable in a single imaging step. Existing approaches often trade design control for manufacturability: deterministic barcodes often require per-code redesign of particle fabrication, whereas stochastic combinatorial barcodes are difficult to generate as predefined batches. Here we introduce a chemically programmable barcoding architecture that decouples particle fabrication from barcode assignment. Using a contact-free multilaminar flow lithography platform with all-around three-dimensional sheathing, we continuously fabricate a universal hydrogel scaffold containing five spatially segregated DNA-addressable domains at rates >106 particles/h. Chosen barcode identities are subsequently written on demand onto the same template batch by domain-selective DNA hybridization. Single-domain measurements resolved 64 candidate optical states, indicating an experimentally informed theoretical upper bound of 645 {approx} 1.1 x 109 barcodes. We further implemented a predefined 59,049-code library by split-pool labeling, achieving an 88% recovery of decoded beads at a stringent posterior threshold (>0.95). After 11 days, >7,800 beads were correctly re-identified at >0.95 accuracy in matched fields of view. This strategy provides a highly scalable, chemically programmable route to build large, user-defined optical barcode libraries with single-image optical readout and longitudinal traceability.

bioengineering↗

bioRxiv2025

Transcriptional Activation of Estrogen Receptor-alpha and Estrogen Receptor-beta from Elephant Shark (Callorhynchus milii)

Humans and other vertebrates contain two estrogen receptors (ERs), ER and ER{beta}. Among cartilaginous fish (sharks, rays, skates), which are chondrichthyans that evolved about 425 million years ago, only activation by steroids of ER{beta} orthologs has been characterized. To remedy this gap in understanding estrogen signaling in chondrichthyans, we studied estrogen activation of orthologs of human ER and ER{beta} from elephant shark (Callorhynchus milii). Unexpectedly, we found that C. milii contained three estrogen-responsive ER genes: ER1 (596 amino acids), ER2 (600 amino acids), and ER3 (599 amino acids) with strong sequence similarity to each other. We also found an estrogen-unresponsive gene, ER4 (561 amino acids), with a 39 amino acid deletion in the DNA-binding domain. An estrogen-responsive ER{beta} ortholog (580 amino acids) also was present in C. milii. The three active C. milii ERs are of similar length to human ER (595 amino acids); however, C. milii ER{beta} is longer than human ER{beta} (530 amino acids). We studied transcriptional activation of ER and ER{beta} by estradiol (E2), the main reproductive estrogen in humans. We also studied estrone (E1), the main postmenopausal estrogen, and estriol (E3), which is synthesized during pregnancy. We determined the half-maximal response (EC50) and fold-activation to E2, E1, and E3 of C. milii ER1, ER2, ER3, and ER{beta}. Among these estrogens, E2 had the lowest EC50 for all four ERs. Fold-activation by E2 and E3 was similar for ER1, ER2, ER3, and ER{beta}. Overall, estrogen activation of C. milii ER and ER{beta} was similar to that for human ER and ER{beta}, indicating substantial conservation of the vertebrate ER during the 425 million years since the divergence of cartilaginous fish and humans from a common ancestor.

evolutionary biology↗

bioRxiv2024

Priming Epigenetic Landscape at Gene Promoters through Transcriptional Activation in Mammalian Germ Cells

In mammalian germ cells, a cycle of erasing and resetting epigenetic information is crucial for sex-specific gametogenesis and early embryogenesis. Specific chromatin states at promoters allow genes to be expressed at the appropriate time during germ cell development, however, the mechanism that establishes such characteristic chromatin states remains unclear. Here, we show that, in mouse male embryonic germ cells, promoters of developmental and housekeeping genes are selectively protected from de novo DNA methylation, coinciding with their transient upregulation and genome-wide erasure of H3K27me3. Importantly, a specific level of H3K4me3 density at the promoters serves as a potent probe that distinguishes between hypo- and hyper-DNA methylation states. Subsequent restoration of H3K27me3 contributes to establishing bivalent chromatin states that prime genes for activation at later developmental stages. These findings reveal a molecular framework shaping the epigenetic landscape at promoters with long-term effects beyond germ cell development.

genomics↗

bioRxiv2023

Morc1 re-establishes heterochromatin on activated transposons and shapes the host transcriptome in gonocytes

Following reprogramming of DNA methylation, numerous transposable elements (TEs) are transiently activated in male prenatal gonocytes. Persistent expression of such TEs to adulthood leads to arrest of germ cell development. However, how these TEs are re-silenced has been unexplored. Here, we found that DNA-binding protein Morc1 re-established H3K9me3-marked heterochromatin on activated TEs, which involved methyltransferase SetDB1. Although Morc1 also triggered DNA methylation, the types of Morc1-targeted TEs for each epigenetic modification were different, suggesting that these two mechanisms were largely independent of each other. Significant overlap between TEs targeted by Morc1 and those by Miwi2, a nuclear PIWI protein, indicated that piRNA-loaded Miwi2 conferred target specificity to Morc1. Activated TEs drove transcription of adjacent genes by acting as ectopic cis-regulatory elements. Such a disrupting effect of TEs on the transcriptome was compensated by Morc1. Thus, Morc1 ensures proper interactions of TEs with host genes through re-establishment of heterochromatin in gonocytes.

bioinformatics↗

bioRxiv2022

N-terminal region of Drosophila melanogaster Argonaute2 forms amyloid-like aggregates

Argonaute proteins play a central role in RNA silencing by forming protein-small RNA complexes responsible for the silencing process. While most Argonaute proteins have a short N-terminal region, Argonaute2 in Drosophila melanogaster (DmAgo2) harbors a long and unique N-terminal region. Previous in vitro biochemical studies have shown that the loss of this region does not impair the RNA silencing activity of the complex. However, an N-terminal mutant of Drosophila melanogaster has demonstrated abnormal RNA silencing activity. To explore the causes of this discrepancy between in vitro and in vivo studies, we investigated the biophysical properties of the region. Because the N-terminal region is highly rich in glutamine and glycine residues, which is a well-known property for prion-like domains (PrLD), the possibility of the N-terminal region functioning as a PrLD was tested. Our biochemical assays demonstrated that the N-terminal region can form aggregates that are not dissociated even in the presence of SDS. Also, the aggregates enhanced the fluorescence intensity of thioflavin-T, an amyloid detection reagent. The kinetics of the aggregation followed that of typical amyloid formation exhibiting the self-propagating activity. Further, we directly visualized the aggregation process of the N-terminal region under fluorescence microscopy and found that the aggregations took fractal or fibril shapes. Together, the results indicate that the N-terminal region is a PrLD. Many other PrLDs have been reported to modulate the function of proteins through their aggregation. Therefore, our results raise the possibility that aggregation of the N-terminal region regulates the RNA silencing activity of DmAgo2.

biochemistry↗

bioRxiv2021

An intramolecular scrambling path controlled by a gatekeeper in Xkr8 phospholipid scramblase

Xkr8-Basigin is a phospholipid scramblase at plasma membranes that is activated by kinase or caspase. We investigated its structure at a resolution of 3.8[A]. Its membrane-spanning region had a cuboid-like structure stabilized by salt bridges between hydrophilic residues in helices in the lipid layer. The molecule carried phosphatidylcholine in a cleft on the surface that may function as an entry site for phospholipids. Five charged residues placed from top to bottom inside the molecule were essential for providing a path for scrambling phospholipids. A tryptophan residue was present at the extracellular end of the pathway and its mutation made the Xkr8-Basigin complex constitutively active, indicating its function as a gatekeeper. The structure of Xkr8-Basigin provides novel insights into the molecular mechanisms underlying phospholipid scrambling.

biochemistry↗

bioRxiv2020

Implementation of single molecule FRET for visualizing intramolecular movement in CRISPR-Cas9

SHORT ABSTRACTThis paper summarizes how to visualize the flexible inter-domain movements of CRISPR-associated protein Cas9 using single molecule FRET LONG ABSTRACTThe CRISPR-associated protein Cas9 is widely used as a genome editing tool because of its ability to be programmed to cleave any DNA sequence that is followed by a protospacer adjacent motif. The continuing expansion of Cas9 technologies has stimulated studies regarding the molecular basis of the Cas9 catalytic process. Here we summarize methods for single molecule FRET (smFRET) to visualize the inter-domain movements of Cas9 protein. Our measurements and analysis demonstrate flexible and reversible movements of the Cas9 domains. Such flexible movements allow Cas9 to adopt transient conformations beyond those solved by crystal structures and play important roles in the Cas9 catalytic process. In addition to the smFRET measurement itself, to obtain precise results, it is necessary to validate Cas9 catalytic activity. Also, fluorescence anisotropy data are required to interpret smFRET data properly. Thus, in this paper, we describe the details of these important additional experiments for smFRET measurements.

biophysics↗