Biology subjects

Ha, T.

Publications and source records attributed to Ha, T..

At least 19 recordsLinked to original sources

bioRxiv2026

A Distributed Architectural Code Governs DNA Repair

Repair of DNA double-strand breaks (DSBs) depends on large-scale changes in nuclear shape and genome organization. How damage signaling coordinates such remodeling remains unclear. We find that the human DNA damage response (DDR) couples interdependent, temporally ordered tubulin modifications to nuclear membrane and lipid regulation, driving nuclear reshaping (nucleomorphosis) through DSB-capturing nuclear envelope tubules (dsbNETs). Tubulin detyrosination by vasohibins 1/2 (VASH1/2) and acetylation by -tubulin acetyltransferase 1 (ATAT1) promote dsbNET formation and support both homologous recombination and non-homologous end joining. Microtubule-dependent processes also promote the phosphorylation-dependent inactivation of the membrane stress-sensing lipid regulator CTP cytidylyltransferase- (CCT), which typically restrains baseline nuclear lipid droplets (nLDs) and dsbNETs while supporting ATR signaling. Damage-induced nLD formation requires diacylglycerol acyltransferases 1/2 (DGAT1/2) and supports dsbNETs. Our findings reveal a distributed architectural code spanning interconnected cytoskeletal, membrane, and lipid regulators. This code governs nucleomorphosis and its role in DNA repair and genome stability.

molecular biology↗

bioRxiv2026

A superfamily 1 helicase translocates on double-stranded DNA

Replicative and accessory helicases are essential for maintaining genome integrity during DNA replication and repair. Rep helicase belongs to superfamily 1 (SF1), the first helicase family solved at atomic resolution and a longstanding model for how helicases couple ATP hydrolysis to movement on DNA. Using optical tweezers combined with fluorescence imaging, we characterize how Rep translocates and navigates diverse nucleic acid and protein obstacles. We directly observe highly processive translocation on ssDNA (~300 nt/s over >13,000 nt) and show that this directional movement can drive single-stranded DNA-binding proteins (bacterial SSB, archaeal SSB, and eukaryotic RPA) along ssDNA without slowing. On encountering a short duplex barrier ([≤]60 bp), either a DNA duplex or an RNA/DNA hybrid, Rep frequently bypasses it, with termination and unwinding also observed. Unexpectedly, we identify a mode in which Rep transitions from ssDNA onto dsDNA and translocates directionally along the duplex with high processivity(>12,000bp) and at a much higher speed than on ssDNA (~1100 bp/s). AlphaFold3 modeling is consistent with Rep tracking a single strand while keeping the duplex intact. To our knowledge, this is the first demonstration of processive dsDNA translocation by an SF1 helicase, and it broadens models for how translocases operate on DNA during replication and repair.

biophysics↗

bioRxiv2026

Direct visualization of MCM helicase activation and replisome coupling in situ

Deciphering the spatial organization of molecular machines that copy the genome remains a fundamental challenge in biology. Essential for eukaryotic DNA replication, Mini-Chromosome Maintenance (MCM2-7) helicases are loaded during G1 as double hexamers (DHs) to license replication origins. Upon activation in S phase, each DH is thought to split into two single hexamers (SHs) that form the active CMG helicases and travel bidirectionally. However, the field has long been divided: biochemical and structural studies define CMG helicases as autonomous, independent motors, while genomic and cellular imaging assays suggest sister replisomes remain physically coupled within replication factories. Here, we use MINFLUX nanoscopy to localize individual MCM complexes down to nanometer precision in situ, directly resolving DHs in human cells and capturing their separation into SHs upon origin firing. We find that the resulting sister replisomes do not diffuse apart: they remain coupled at a characteristic distance of ~40 nm throughout S phase. Depletion experiments identify two distinct contributions to this coupling: local, protein-mediated tethering by the AND1 scaffold, and higher-order spatial confinement dependent on cohesin, which is dispensable for MCM loading in G1 but required to maintain coupling in S phase. By linking the nanometer-scale architecture of the replisome to the genome-wide topology of replication fountains, these findings provide direct spatial evidence that sister forks are coupled during DNA synthesis and define the molecular forces that organize replisomes within their native nuclear context.

cell biology↗

bioRxiv2026

WHaloForce enables chemigenetic imaging of molecular tension in living cells and animals

Piconewton forces borne by individual proteins within complex assemblies underlie cell adhesion, migration, and tissue morphogenesis, yet remain difficult to image in living systems. Here, we introduce WHaloForce, a chemigenetic HaloTag-based tension sensor that converts force-dependent relief of tryptophan-mediated dye quenching into a fluorescence lifetime change. Optical tweezers revealed a switch-like unquenching transition near 5 pN, and the sensor responded reversibly to force changes in cells. WHaloForce enabled quantitative tension imaging of diverse force-bearing proteins (vinculin, E-cadherin, -catenin, and laminin) in mammalian cells, mouse tissue, and C. elegans. Bright synthetic dyes made tension measurements possible at endogenous expression levels. In C. elegans, vinculin and laminin showed opposite tension patterns between tissues, revealing distinct force-transmission routes through adhesions and the extracellular matrix. During ovulation, laminin tension accumulated over repeated stretch-relaxation cycles, scaling with cumulative loading history. WHaloForce thus offers a modular platform for imaging spatiotemporal tension patterns in living systems.

cell biology↗

bioRxiv2026

Chromosome topology gates productive RecA homology search

In homologous recombination, DNA repair depends on recombinase filaments finding homologous templates on chromosomes whose topology is continually remodeled by replication and transcription. How dynamic chromosome topology affects homology search and DNA repair remains unknown. By combining live-cell imaging of RecA-mediated homology search with single-molecule assays on topologically-defined DNA substrates, we show that DNA supercoiling acts as a selectivity filter for productive homology search. In Caulobacter crescentus cells, supercoiling is dispensable for the filament movement required for homology search, but required for homology target capture and repair. In vitro, filaments transiently sample both relaxed and supercoiled DNA, yet selectively commit to capture only on negatively supercoiled targets. Mechanistically, we find an extreme kinetic preference (~100-fold) of filaments towards negatively supercoiled DNA targets; this topological preference is independent of DNA compaction, pins plectonemes at the capture site, and is conserved across diverse bacterial RecA homologs. Our findings establish that chromosome topology physically regulates homology search and DNA repair.

biophysics↗

bioRxiv2026

Cohesin activity accelerates the homology search

Homologous recombination (HR) repair preserves genome integrity in post-replicative cells by orchestrating templated repair of DNA double-strand breaks (DSBs). A critical stage of HR is the homology search, the process by which the DSB is brought in contact with a repair template, which is often the replicated locus. Using molecular dynamics simulations, we model the mammalian homology search, with focus on the role of the chromatin architecture factor cohesin. Our simulations recapitulate key experimental findings, including the distribution of genomic loci interrogated by the DSB and the chromatin interactions that accompany the homology search. We show that cohesin-mediated loop extrusion greatly accelerates the search process, and this effect is further enhanced by anchoring loop-extruding cohesin at DSB sites and recruiting a cohesive cohesin clamp that stabilizes DSB-sister chromatid interactions. We reveal that cohesins contribution to accelerating the search scales linearly with TAD size and becomes more pronounced when breaks occur in large TADs. We also show that chromatin loops along the broken and the sister chromatid play different roles in the search: the former establish initial contact between the break site and sister chromatid, whereas the latter promote scanning along the sister chromatid. Our findings indicate that coordinated activity of loop-extruding and cohesive cohesin transforms the homology search from 3D diffusion into a fast 1D scanning process.

biophysics↗

bioRxiv2026

Rapid functional classification of cardiac genetic variants directly informs precision cardiology

Large-scale clinical genome sequencing yields vast numbers of variants of unknown significance (VUSs). The high frequency of VUSs and the paucity of platforms to characterize their functional impact pose significant challenges for clinical decision making. Here, we present an integrated end-to-end platform, REVi-SCOPE (Rapid evaluation of variants in single cells by optogenetics and prime editing), for characterization of the impact of VUSs on cardiac physiology. Our strategy consists of (1) introduction of variants directly into wild-type (WT) human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) via prime editing; (2) optogenetic assessment of calcium and membrane voltage dynamics in single hiPSC-CMs within the pool of edited and unedited cells; and (3) in situ single-cell genotyping of the phenotyped hiPSC-CMs with single-allele resolution. By optimizing and integrating each of these steps, we created a platform that enables VUS characterization in 10 days. We validated the REVi-SCOPEs capabilities by analyzing the properties of established arrhythmogenic variants. We then used REVi-SCOPE to reveal the functional impact of a VUS, TRPM4A320V, identified in a child with a conduction block. Together, our results show that REVi-SCOPE enables functional characterization of VUSs linked to cardiac arrhythmias with unprecedented throughput.

bioengineering↗

bioRxiv2026

Multivalent weak contacts shape chaperone-nascent protein interactions

Molecular chaperones interact with non-native proteins, playing crucial roles in preventing misfolding and enable efficient folding in the cellular environment. Trigger factor is a bacterial chaperone that binds to ribosomes, interacting with nascent polypeptides emerging from the ribosome and guiding their early folding steps. In contrast to the central role of the chaperone in promoting folding of newly synthesized proteins, its dynamic interactions with nascent chains emerging from the ribosome remain poorly understood. Here, we use single-molecule fluorescence and optical tweezers approaches to directly observe and characterize trigger factor interactions with a ribosome-bound client protein at increasing chain lengths. We find that trigger factor binding to nascent proteins is best described by a combination of multiple weak, dynamic interactions that are established after the chaperone docks onto the ribosome and evolve during polypeptide elongation. Application of mechanical force perturbs trigger factor binding, supporting a multivalent interaction model. This binding mode may help to stabilize nascent proteins against misfolding while allowing them to dynamically sample conformational space in search of their native structures.

biophysics↗

bioRxiv2026

A Modular Framework for Automated Segmentation and Analysis of AFM Imaging of Chromatin Organization

Chromatin organization underlies essential genome functions, but its nanoscale organization remains challenging to capture and quantify with precision. Atomic force microscopy (AFM) offers direct structural readouts of DNA and chromatin, yet translating these rich images into reproducible biological metrics has been limited by the lack of standardized, scalable analysis tools. Here we present DNAsight, an automated analysis framework that integrates machine learning (ML)-based segmentation with modular, base-pair-calibrated quantification of DNA spatial organization, looping, nucleosome spacing, and protein clustering. Applied across diverse chromatin-associated proteins, DNAsight reveals protein-specific organizational signatures, including topology-dependent compaction by integration host factor (IHF), condition-dependent changes in loop-like DNA structures in cohesin-CTCF-precocious dissociation of sisters 5A (PDS5A) reactions, and promoter-driven multimerization of GAGA factor (GAF) clusters. The framework further enables direct extraction of nucleosome spacing distributions from raw AFM images, providing a label-free route to investigate chromatin fiber architecture. Together, these advances establish DNAsight as a generalizable and scalable approach for converting AFM measurements into quantitative insights into the physical principles of chromatin organization. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=79 SRC="FIGDIR/small/708946v2_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@1225883org.highwire.dtl.DTLVardef@1e1041dorg.highwire.dtl.DTLVardef@1d53d18org.highwire.dtl.DTLVardef@9e0a2a_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2025

Ultrafast CTCF dynamics control cohesin barrier function

Genomes are organized into chromatin loops through cohesin-mediated extrusion, with CTCF acting as a polar boundary element. As cohesin approaches CTCF at kilobase-per-second speeds, it must rapidly choose whether to stall or bypass. How CTCF encodes this probabilistic decision within a brief encounter window has remained unclear. Here we show that CTCF governs this probabilistic outcome by rapidly sampling a dynamic ensemble of conformations generated by spontaneous rearrangements of its DNA-binding zinc fingers. This ensemble is tuned by DNA sequence, CpG methylation, nearby nucleosomes, and the cohesin regulator PDS5A before cohesin engagement. Upon cohesin binding, PDS5A enhances loop-anchor mechanical stability, reinforcing orientation-dependent boundaries. These findings establish conformational ensemble tuning, rather than static occupancy, as a regulatory principle linking base pair-scale motions to megabase-scale genome organization. One sentence summaryChromatin boundary function is governed not by CTCF occupancy alone, but by a tunable ensemble of DNA-bound conformations that probabilistically gates cohesin capture.

biophysics↗

bioRxiv2025

Nuclear Localization Signals Enable the Cellular Delivery of an Anti-CRISPR Protein to Control Genome Editing

Precise regulation of Cas9 activity is essential to minimize off-target effects, mosaicism, chromosomal alterations, immunogenicity, and genotoxicity in genome editing. Although type II anti-CRISPR proteins (Acrs) can inhibit and regulate Cas9, their size and anionic charge generally prevent them from crossing the cell membrane. Existing Acr delivery methods employing vectors or electroporation are either slow and persistent or require external equipment, limiting their therapeutic utility. To address these challenges, we developed a cell-permeable Acr (6xNLS-Acr), which uses nuclear localization signals (NLSs) to cross the cell membrane. We conjugated 6xNLS-Acr to a fluorescent dye to elucidate its cellular entry mechanism and directly visualized its binding to a fluorescent Cas9{middle dot}gRNA complex to study its inhibitory mechanism. 6xNLS-Acr (IC50 = 0.47 {micro}M) directly transduces human cells, including immortalized cell lines, embryonic stem cells, and 3D cell cultures, within 5 min, inhibiting up to 99% of Cas9 activity and increasing genome-editing specificity by nearly 100%. We further compared 6xNLS-Acr with our anthrax-derived Acr delivery platform. Our results demonstrate that 6xNLS-Acr is the most efficacious cell-permeable CRISPR-Cas inhibitor, significantly enhancing the precision and therapeutic potential of CRISPR-based genome editing.

genomics↗

bioRxiv2025

Bringing the Genetically Minimal Cell to Life on a Computer in 4D

We present a whole-cell spatial and kinetic model for the 100 minute cell cycle of the genetically minimal bacterium, JCVI-syn3A. This is the first simulation of a complete cell cycle in 4D including all genetic information processes, metabolic networks, growth, and cell division. Integrating hybrid computational methods, dynamics of the morphological transformations were achieved. Growth is driven by synthesis of lipids and membrane proteins and constrained by new fluorescence imaging data. Chromosome replication and segregation is controlled by essential SMC and topoisomerase proteins in Brownian dynamics simulations with replication rates responding to dNTP pools from metabolism. The model captures the origin to terminus ratio measured in our DNA sequencing and recovers other experimental measurements like doubling time, mRNA half-lives, protein distributions, and ribosome counts. Because of stochasticity, each replicate cell is unique. Not only do we predict average behavior for partitioning to daughter cells, we predict the heterogeneity among them.

biophysics↗

bioRxiv2025

Mechanistic insights into direct DNA and RNA strand transfer and dynamic protein exchange of SSB and RPA

Single-stranded DNA-binding proteins (SSBs) are essential for genome stability, facilitating replication, repair, and recombination by binding ssDNA, recruiting other proteins, and dynamically relocating in response to cellular demands. Using single-molecule fluorescence resonance energy transfer (smFRET) assays, we elucidated the mechanisms underlying direct strand transfer from one locale to another, protein exchange, and RNA interactions at high resolution. Both bacterial SSB and eukaryotic replication protein A (RPA) exhibited direct strand transfer to competing ssDNA, with rates strongly influenced by ssDNA length. Strand transfer proceeded through multiple failed attempts before a successful transfer, forming a ternary intermediate complex with transient interactions, supporting a direct transfer mechanism. Both proteins efficiently exchanged DNA-bound counterparts with freely diffusing molecules, while hetero-protein exchange revealed that SSB and RPA could replace each other on ssDNA in a length-dependent manner, indicating that protein exchange does not require specific protein-protein interactions. Additionally, both proteins bound RNA and underwent strand transfer to competing RNA, with RPA demonstrating faster RNA transfer kinetics. Competitive binding assays confirmed a strong preference for DNA over RNA. These findings provide critical insights into the dynamic behavior of SSB and RPA in nucleic acid interactions, advancing our understanding of their essential roles in genome stability, regulating RNA metabolism, and orchestrating nucleic acid processes.

molecular biology↗

bioRxiv2025

Cohesin drives chromatin scanning during the RAD51-mediated homology search.

Cohesin folds genomes into chromatin loops, whose roles are under debate. We report that double strand breaks (DSB) induce de novo formation of chromatin loops, with the break positioned at the loop base. These loops form only in S/G2 phases and occur during repair via homologous recombination (HR), concomitant with DNA end resection and RAD51 assembly. RAD51 showed two-tiered accumulation around DSBs, with a broad (~Mb) domain arising from the homology search. This domain is regulated by cohesin unloader, is constrained by TAD boundaries, and it overlaps with chromatin regions reeled through the break-anchored loop, suggesting that loop extrusion regulates the homology search. Indeed, depletion of NIPBL results in reduced HR, and this effect is more pronounced when the HR donor is far (~100 kb) from the break. Our data indicates that loop-extruding cohesin promotes the mammalian homology search by facilitating break-chromatin interactions within the damaged TAD. One-Sentence SummaryHigh spatiotemporal resolution analysis of double strand beak repair in 3D genome revealed the role of cohesin-driven loop extrusion in the homology search.

cell biology↗

bioRxiv2025

Searching for Sequence Features that Control DNA Cyclizability

The mechanical properties of DNA molecules are crucial in many biological processes, from DNA packaging to transcription regulation. While the mechanics of long DNA typically follow the worm-like chain polymer model, multiple studies have shown that the mechanics of short DNA - at the length scale of DNA-protein interactions - depend strongly on its sequence content. Motivated by recent high-throughput measurements of sequence-dependent DNA cyclizability - the DNAs tendency to mechanically bend and form a loop, we developed a statistical mechanics approach to systematically explore how cyclizability depends on interactions between individual nucleotides in the sequence. By applying this method to datasets of randomly generated and biologically derived sequences, we identified characteristic sequence features that control DNA cyclizability and extracted the most and least cyclizable sequences, the behavior of which we validated through all-atom molecular dynamics simulations. We found that while highly cyclizable sequences share the same periodic features across datasets, distinct sequence patterns can result in low cyclizability. This work contributes to our understanding of the sequence dependence of DNA mechanics and its role in various biological processes, and has implications for the growing field of DNA nanofabrication.

biophysics↗

bioRxiv2024

Probing mechanical selection in diverse eukaryotic genomes through accurate prediction of 3D DNA mechanics

Connections between the mechanical properties of DNA and biological functions have been speculative due to the lack of methods to measure or predict DNA mechanics at scale. Recently, a proxy for DNA mechanics, cyclizability, was measured by loop-seq and enabled genome-scale investigation of DNA mechanics. Here, we use this dataset to build a computational model predicting bias-corrected intrinsic cyclizability, with near-perfect accuracy, solely based on DNA sequence. Further, the model predicts intrinsic bending direction in 3D space. Using this tool, we aimed to probe mechanical selection - that is, the evolutionary selection of DNA sequence based on its mechanical properties - in diverse circumstances. First, we found that the intrinsic bend direction of DNA sequences correlated with the observed bending in known protein-DNA complex structures, suggesting that many proteins co-evolved with their DNA partners to capture DNA in its intrinsically preferred bent conformation. We then applied our model to large-scale yeast population genetics data and showed that centromere DNA element II, whose consensus sequence is unknown, leaving its sequence-specific role unclear, is under mechanical selection to increase the stability of inner-kinetochore structure and to facilitate centromeric histone recruitment. Finally, in silico evolution under strong mechanical selection discovered hallucinated sequences with cyclizability values so extreme that they required experimental validation, yet, found in nature in the densely packed mitochondrial(mt) DNA of Namystynia karyoxenos, an ocean-dwelling protist with extreme mitochondrial gene fragmentation. The need to transmit an extraordinarily large amount of mtDNA, estimated to be > 600 Mb, in combination with the absence of mtDNA compaction proteins may have pushed mechanical selection to the extreme. Similarly extreme DNA mechanics are observed in bird microchromosomes, although the functional consequence is not yet clear. The discovery of eccentric DNA mechanics in unrelated unicellular and multicellular eukaryotes suggests that we can predict extreme natural biology which can arise through strong selection. Our methods offer a way to study the biological functions of DNA mechanics in any genome and to engineer DNA sequences with desired mechanical properties.

biophysics↗

bioRxiv2024

The human RAD52 complex undergoes phase separation and facilitates bundling and end-to-end tethering of RAD51 presynaptic filaments

Human RAD52 is a prime target for synthetical lethality approaches to treat cancers with deficiency in homologous recombination. Among multiple cellular roles of RAD52, its functions in homologous recombination repair and protection of stalled replication forks appear to substitute those of the tumor suppressor protein BRCA2. However, the mechanistic details of how RAD52 can substitute BRCA2 functions are only beginning to emerge. RAD52 forms an undecameric ring that is enveloped by eleven [~]200 residue-long disordered regions, making it a highly multivalent and branched protein complex that potentiates supramolecular assembly. Here, we show that RAD52 exhibits homotypic phase separation capacity, and its condensates recruit key players in homologous recombination such as single-stranded (ss)DNA, RPA, and the RAD51 recombinase. Moreover, we show that RAD52 phase separation is regulated by its interaction partners such as ssDNA and RPA. Using fluorescence microscopy, we show that RAD52 can induce the formation of RAD51-ssDNA fibrillar structures. To probe the fine structure of these fibrils, we utilized single-molecule super-resolution imaging via DNA-PAINT and atomic force microscopy and showed that RAD51 fibrils are bundles of individual RAD51 nucleoprotein filaments. We further show that RAD52 induces end-to-end tethering of RAD51 nucleoprotein filaments. Overall, we demonstrate unique macromolecular organizational features of RAD52 that may underlie its various functions in the cell.

biophysics↗

bioRxiv2024

Ultrastable and Versatile FoxP3 Ensembles on Microsatellites

Microsatellites are essential genomic components increasingly linked to transcriptional regulation. FoxP3, a transcription factor critical for regulatory T cell (Treg) development, recognizes TTTG repeat microsatellites by forming multimers along DNA. However, FoxP3 also binds a broader range of TnG repeats (n=2-5), often at the edges of accessible chromatin regions. This raises questions about how FoxP3 adapts to sequence variability and the potential role of nucleosomes. Using cryo-electron microscopy and single-molecule analyses, we show that FoxP3 assembles into distinct supramolecular structures depending on DNA sequence. This structural plasticity enables FoxP3 to bridge 2-4 DNA duplexes, forming ultrastable structures that coordinate multiple genomic loci. Nucleosomes further facilitate FoxP3 assembly by inducing local DNA bending, creating a nucleus that recruits distal DNA elements through multiway bridging. Our findings thus reveal FoxP3s unusual ability to shapeshift to accommodate evolutionarily dynamic microsatellites and its potential to reinforce chromatin boundaries and three-dimensional genomic architecture.

biochemistry↗