@article{21727,
  abstract     = {We present a comprehensive analysis of the MIRI Extremely Red Object Virgil, a Lyα emitter at zspec = 6.6379 ± 0.0035 with the photometric properties of a Little Red Dot. Leveraging new JWST/MIRI imaging from the MIDIS and PAHSPECS programs, we confirm Virgil’s extraordinary nature among galaxies in JADES/GOODS-South, exhibiting a strikingly red NIRCam-to-MIRI color (F444W–F1500W = 2.84 ± 0.04 mag). Deep NIRSpec/PRISM spectroscopy from the OASIS program offers key insights into the host galaxy, revealing properties of an average star-forming galaxy during Cosmic Reionization, such as a subsolar metallicity, low-to-moderate dust content, and a relatively high ionization parameter and electron temperature. By estimating the star formation rate of Virgil from UV and Hα, we find evidence that the galaxy is either entering or fading out of a bursty episode. Although line-ratio diagnostics employed at high z would classify Virgil as an active galactic nucleus (AGN), this classification becomes ambiguous once redshift evolution is considered. Nonetheless, Virgil occupies the same parameter space as recently confirmed AGNs at similar redshifts. The new deep MIRI data at 15 μm reinforce the AGN nature of Virgil, as inferred from multiple spectral energy distribution (SED) fitting codes. Virgil’s rising infrared SED and UV excess resemble those of Dust-Obscured Galaxies (DOGs) studied with Spitzer at Cosmic Noon, particularly blue-excess HotDOGs. Our results highlight the need for a multiwavelength approach incorporating MIRI to uncover such extreme sources at z ≳ 6 and to shed light on the interplay between galaxy evolution and early black hole growth during Cosmic Reionization.},
  author       = {Rinaldi, Pierluigi and Pérez-González, Pablo G. and Rieke, George H. and Lyu, Jianwei and D’Eugenio, Francesco and Wu, Zihao and Carniani, Stefano and Looser, Tobias J. and Shivaei, Irene and Boogaard, Leindert A. and Diaz-Santos, Tanio and Colina, Luis and Östlin, Göran and Alberts, Stacey and Álvarez-Márquez, Javier and Annuziatella, Marianna and Aravena, Manuel and Bhatawdekar, Rachana and Bunker, Andrew J. and Caputi, Karina I. and Charlot, Stéphane and Crespo Gómez, Alejandro and Curti, Mirko and Eckart, Andreas and Gillman, Steven and Hainline, Kevin and Kumari, Nimisha and Hjorth, Jens and Iani, Edoardo and Inami, Hanae and Ji, Zhiyuan and Johnson, Benjamin D. and Jones, Gareth C. and Labiano, Álvaro and Maiolino, Roberto and Melinder, Jens and Moutard, Thibaud and Peissker, Florian and Rieke, Marcia and Robertson, Brant and Scholtz, Jan and Tacchella, Sandro and Van Der Werf, Paul P. and Walter, Fabian and Williams, Christina C. and Willott, Chris and Witstok, Joris and Übler, Hannah and Zhu, Yongda},
  issn         = {1538-4357},
  journal      = {The Astrophysical Journal},
  number       = {1},
  publisher    = {IOP Publishing},
  title        = {{Deciphering the nature of Virgil: An obscured active galactic nucleus lurking within an apparently normal Lyα emitter during cosmic reionization}},
  doi          = {10.3847/1538-4357/ae089c},
  volume       = {994},
  year         = {2025},
}

@inproceedings{21885,
  abstract     = {Symbolic datatypes have proved to be central for automated reasoning about dynamical systems. In its basic form, a symbolic datatype for a class of dynamical systems supports the representation of state and transition sets, boolean operations and emptiness checks on such sets, and the transformation of a state set by a transition set. Successful examples of symbolic datatypes include BDDs and SAT for reasoning about finitestate systems, as well as polyhedra and SMT for reasoning about discrete dynamical systems over multidimensional realvalued state spaces. Most automated verification engines are based on such symbolic datatypes.},
  author       = {Henzinger, Thomas A},
  booktitle    = {Proceedings of the 27th International Symposium on Symbolic and Numeric Algorithms for Scientific Computing},
  issn         = {2470-881X},
  location     = {Timisoara, Romania},
  publisher    = {IEEE},
  title        = {{Neural Certificates}},
  doi          = {10.1109/SYNASC69064.2025.00008},
  year         = {2025},
}

@unpublished{21920,
  abstract     = {Vertebrates display remarkable diversity of sensorimotor behaviors, each adapted to distinct ecological and survival demands. This diversity raises fundamental questions about the evolutionary origin of motor control: do conserved spinal circuits underlie these behaviors, and how have they diverged across species. Recent studies detail spinal cell-type architecture in mammals but comparable, high-resolution atlases of the non-mammalian spinal cord are lacking. Here, we compare spinal cord cell types between fish, frogs, mice and humans, spanning ∼450 million years of evolution. Across species, we define highly conserved programs of cell type specification that segregate spinal neurons into nearly identical cardinal classes during development. This contrasts with adult stages, when spinal cell-type composition selectively diverges for excitatory neuron subpopulations. Using spatial transcriptomics, we localize this species divergence to the superficial, dorsal spinal cord, where variant neuropeptide expression defines mammalian-specific cell types. The most dorsal spinal cord thus emerges as a recently evolved hub for sensory integration in mammals, a neospinal cord analogous to the neocortex.</jats:p>},
  author       = {Ignatyev, Yuri and Papadopoulos, Stavros and Soretić, Mateja and Yeung, Jake and Lin, Tzi-Yang and Tanaka, Elly M and Peshkin, Leonid and Levine, Ariel J and Gabitto, Mariano I and Sweeney, Lora Beatrice Jaeger},
  booktitle    = {bioRxiv},
  title        = {{Innovations in spinal cord cell type heterogeneity across vertebrate evolution}},
  doi          = {10.1101/2025.10.09.680955},
  year         = {2025},
}

@article{14647,
  abstract     = {In the developing vertebrate central nervous system, neurons and glia typically arise
sequentially from common progenitors. Here, we report that the transcription factor Forkhead
Box G1 (Foxg1) regulates gliogenesis in the mouse neocortex via distinct cell-autonomous roles in progenitors and postmitotic neurons that regulate different aspects of the gliogenic FGF signalling pathway. We demonstrate that loss of Foxg1 in cortical progenitors at neurogenic stages causes premature astrogliogenesis. We identify a novel FOXG1 target, the pro-gliogenic FGF pathway component Fgfr3, which is suppressed by FOXG1 cell-autonomously to maintain neurogenesis. Furthermore, FOXG1 can also suppress premature astrogliogenesis triggered by the augmentation of FGF signalling. We identify a second novel function of FOXG1 in regulating the expression of gliogenic cues in newborn neocortical upper-layer neurons. Loss of FOXG1 in postmitotic neurons non-autonomously enhances gliogenesis in the progenitors via FGF signalling. These results fit well with the model that newborn neurons secrete cues that trigger progenitors to produce the next wave of cell types, astrocytes. If FGF signalling is attenuated in Foxg1 null progenitors, they progress to oligodendrocyte production. Therefore, loss of FOXG1 transitions the progenitor to a gliogenic state, producing either astrocytes or oligodendrocytes depending on FGF signalling levels. Our results uncover how FOXG1 integrates extrinsic signalling via the FGF pathway to regulate the sequential generation of neurons, astrocytes, and oligodendrocytes in the cerebral cortex. },
  author       = {Bose, Mahima and Suresh, Varun and Mishra, Urvi and Talwar, Ishita and Yadav, Anuradha and Biswas, Shiona and Hippenmeyer, Simon and Tole, Shubha},
  issn         = {2050-084X},
  journal      = {eLife},
  publisher    = {eLife Sciences Publications},
  title        = {{Dual role of FOXG1 in regulating gliogenesis in the developing neocortex via the FGF signalling pathway}},
  doi          = {10.7554/elife.101851.3},
  volume       = {13},
  year         = {2025},
}

@article{15128,
  abstract     = {We prove a universal mesoscopic central limit theorem for linear eigenvalue statistics of a Wigner-type matrix inside the bulk of the spectrum with compactly supported twice continuously differentiable test functions. The main novel ingredient is an optimal local law for the two-point function $T(z,\zeta)$  and a general class of related quantities involving two resolvents at nearby spectral parameters.},
  author       = {Riabov, Volodymyr},
  issn         = {0246-0203},
  journal      = {Annales de l'institut Henri Poincare (B) Probability and Statistics},
  number       = {1},
  pages        = {129--154},
  publisher    = {Institute of Mathematical Statistics},
  title        = {{Mesoscopic eigenvalue statistics for Wigner-type matrices}},
  doi          = {10.1214/23-AIHP1438},
  volume       = {61},
  year         = {2025},
}

@article{18478,
  abstract     = {For a given graph G=(V,E), we define its \emph{nth subdivision} as the graph obtained from G by replacing every edge by a path of length n. We also define the \emph{mth power} of G as the graph on vertex set V where we connect every pair of vertices at distance at most m in G. In this paper, we study the chromatic number of powers of subdivisions of graphs and resolve the case m=n asymptotically. In particular, our result confirms a conjecture of Mozafari-Nia and Iradmusa in the case m=n=3 in a strong sense.},
  author       = {Anastos, Michael and Boyadzhiyska, Simona and Rathke, Silas and Rué, Juanjo},
  issn         = {0166-218X},
  journal      = {Discrete Applied Mathematics},
  pages        = {506--511},
  publisher    = {Elsevier},
  title        = {{On the chromatic number of powers of subdivisions of graphs}},
  doi          = {10.1016/j.dam.2024.10.002},
  volume       = {360},
  year         = {2025},
}

@article{18529,
  abstract     = {Temporal networks are obtained from time-dependent interactions among individuals, whereas the interactions can be emails, phone calls, face-to-face meetings, or work collaboration. In this article, a temporal game framework is established, in which interactions among rational individuals are embedded into two-player games in a time-dependent manner. This allows studying the time-dependent complexity and variability of interactions, and the way they affect prosocial behaviors. Based on this simple mathematical model, it is found that the level of cooperation is promoted when the time of collaboration is equally limited for every individual. This observation is confirmed by a series of systematic human experiments on over 1,400 subjects, forming a foundation for comprehensively describing human temporal interactions in collaboration. The research results reveal an important incentive for human cooperation, leading to a better understanding of a fascinating aspect of human nature in society.},
  author       = {Zhang, Yichao and Wang, Jiasheng and Wen, Guanghui and Guan, Jihong and Zhou, Shuigeng and Chen, Guanrong and Chatterjee, Krishnendu and Perc, Matjaz},
  issn         = {2327-4697},
  journal      = {IEEE Transactions on Network Science and Engineering},
  number       = {1},
  pages        = {4--12},
  publisher    = {IEEE},
  title        = {{Limitation of time promotes cooperation in structured collaboration systems}},
  doi          = {10.1109/TNSE.2024.3481434},
  volume       = {12},
  year         = {2025},
}

@article{18580,
  abstract     = {Motivated by the study of recurrent orbits and dynamics within a Morse set of a Morse decomposition we introduce the concept of Morse predecomposition of an isolated invariant set within the setting of both combinatorial and classical dynamical systems. While Morse decomposition summarizes solely the gradient part of a dynamical system, the developed generalization extends to the recurrent component as well. In particular, a chain recurrent set, which is indecomposable in terms of Morse decomposition, can be represented more finely in the Morse predecomposition framework. This generalization is achieved by forgoing the poset structure inherent to Morse decomposition and relaxing the notion of connection between Morse sets (elements of Morse decomposition) in favor of what we term ’links’. We prove that a Morse decomposition is a special case of Morse predecomposition indexed by a poset. Additionally, we show how a Morse predecomposition may be condensed back to retrieve a Morse decomposition.},
  author       = {Lipiński, Michał and Mischaikow, Konstantin and Mrozek, Marian},
  issn         = {1662-3592},
  journal      = {Qualitative Theory of Dynamical Systems},
  number       = {1},
  publisher    = {Springer Nature},
  title        = {{Morse predecomposition of an invariant set}},
  doi          = {10.1007/s12346-024-01144-3},
  volume       = {24},
  year         = {2025},
}

@article{18626,
  abstract     = {The local angle property of the (order-1) Delaunay triangulations of a generic set in R2
 asserts that the sum of two angles opposite a common edge is less than π. This paper extends this property to higher order and uses it to generalize two classic properties from order-1 to order-2: (1) among the complete level-2 hypertriangulations of a generic point set in R2, the order-2 Delaunay triangulation lexicographically maximizes the sorted angle vector; (2) among the maximal level-2 hypertriangulations of a generic point set in R2, the order-2 Delaunay triangulation is the only one that has the local angle property. We also use our method of establishing (2) to give a new short proof of the angle vector optimality for the (order-1) Delaunay triangulation. For order-1, both properties have been instrumental in numerous applications of Delaunay triangulations, and we expect that their generalization will make order-2 Delaunay triangulations more attractive to applications as well.},
  author       = {Edelsbrunner, Herbert and Garber, Alexey and Saghafian, Morteza},
  issn         = {1090-2082},
  journal      = {Advances in Mathematics},
  publisher    = {Elsevier},
  title        = {{Order-2 Delaunay triangulations optimize angles}},
  doi          = {10.1016/j.aim.2024.110055},
  volume       = {461},
  year         = {2025},
}

@article{18632,
  abstract     = {For an arbitrary dimension (Formula presented.), we study: the polyharmonic Gaussian field (Formula presented.) on the discrete torus (Formula presented.), that is the random field whose law on (Formula presented.) given by (Formula presented.) where (Formula presented.) is the Lebesgue measure and (Formula presented.) is the discrete Laplacian; the associated discrete Liouville quantum gravity (LQG) measure associated with it, that is, the random measure on (Formula presented.) (Formula presented.) where (Formula presented.) is a regularity parameter. As (Formula presented.), we prove convergence of the fields (Formula presented.) to the polyharmonic Gaussian field (Formula presented.) on the continuous torus (Formula presented.), as well as convergence of the random measures (Formula presented.) to the LQG measure (Formula presented.) on (Formula presented.), for all (Formula presented.). },
  author       = {Dello Schiavo, Lorenzo and Herry, Ronan and Kopfer, Eva and Sturm, Karl Theodor},
  issn         = {1522-2616},
  journal      = {Mathematische Nachrichten},
  number       = {1},
  pages        = {244--281},
  publisher    = {Wiley},
  title        = {{Polyharmonic fields and Liouville quantum gravity measures on tori of arbitrary dimension: From discrete to continuous}},
  doi          = {10.1002/mana.202400169},
  volume       = {298},
  year         = {2025},
}

@misc{18697,
  abstract     = {The information-processing capability of the brain’s cellular network depends on the physical wiring pattern between neurons and their molecular and functional characteristics. Mapping neurons and resolving their individual synaptic connections can be achieved by volumetric imaging at nanoscale resolution with dense cellular labelling. Light microscopy is uniquely positioned to visualize specific molecules but dense, synapse-level circuit reconstruction by light microscopy has been out of reach due to limitations in resolution, contrast, and volumetric imaging capability. Here we developed light-microscopy based connectomics (LICONN). We integrated specifically engineered hydrogel embedding and expansion with comprehensive deep-learning based segmentation and analysis of connectivity, thus directly incorporating molecular information in synapse-level brain tissue reconstructions. LICONN will allow synapse-level brain tissue phenotyping in biological experiments in a readily adoptable manner.},
  author       = {Danzl, Johann G and Lyudchik, Julia and Kreuzinger, Caroline},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Light-microscopy based connectomic reconstruction of mammalian brain tissue}},
  doi          = {10.15479/AT:ISTA:18697},
  year         = {2025},
}

@misc{18712,
  abstract     = {This file contains the code associated with the manuscript 'Effect of assortative mating and sexual selection on polygenic barriers to gene flow'. },
  author       = {Surendranadh, Parvathy and Sachdeva, Himani},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Mathematica notebook and Fortran code for 'Effect of assortative mating and sexual selection on polygenic barriers to gene flow'}},
  doi          = {10.15479/AT:ISTA:17344},
  year         = {2025},
}

@inbook{18765,
  abstract     = {Mosaic Analysis with Double Markers (MADM) represents a mouse genetic approach coupling differential fluorescent labeling to genetic manipulations in dividing cells and their lineages. MADM uniquely enables the generation and visualization of individual control or homozygous mutant cells in a heterozygous genetic environment. Among its diverse applications, MADM has been used to dissect cell-autonomous gene functions important for cortical development and neural development in general. The high cellular resolution offered by MADM also permits the analysis of transcriptomic changes of individual cells upon genetic manipulations. In this chapter, we describe an experimental protocol combining the generation and isolation of MADM-labeled cells with downstream single-cell RNA-sequencing technologies to probe cell-type specific phenotypes due to genetic mutations at single-cell resolution.},
  author       = {Cheung, Giselle T and Pauler, Florian and Hippenmeyer, Simon},
  booktitle    = {Lineage Tracing},
  editor       = {Garcia-Marques, Jorge and Lee, Tzumin},
  isbn         = {9781071643099},
  issn         = {1940-6029},
  pages        = {139--151},
  publisher    = {Springer Nature},
  title        = {{Probing Cell-Type Specificity of Mutant Phenotype at Transcriptomic Level Using Mosaic Analysis with Double Markers (MADM)}},
  doi          = {10.1007/978-1-0716-4310-5_7},
  volume       = {2886},
  year         = {2025},
}

@article{18778,
  abstract     = {Transcription by RNA polymerase II (Pol II) can be repressed by noncoding RNA, including the human RNA Alu. However, the mechanism by which endogenous RNAs repress transcription remains unclear. Here we present cryogenic-electron microscopy structures of Pol II bound to Alu RNA, which reveal that Alu RNA mimics how DNA and RNA bind to Pol II during transcription elongation. Further, we show how distinct domains of the general transcription factor TFIIF control repressive activity. Together, we reveal how a noncoding RNA can regulate mammalian gene expression.},
  author       = {Tluckova, Katarina and Kaczmarek, Beata M and Testa Salmazo, Anita P and Bernecky, Carrie A},
  issn         = {1545-9985},
  journal      = {Nature Structural & Molecular Biology},
  pages        = {607--612},
  publisher    = {Springer Nature},
  title        = {{Mechanism of mammalian transcriptional repression by noncoding RNA}},
  doi          = {10.1038/s41594-024-01448-7},
  volume       = {32},
  year         = {2025},
}

@article{18821,
  abstract     = {Even though the one-dimensional contact interaction requires no regularization, renormalization methods have been shown to improve the convergence of numerical calculations considerably. In this work, we compare and contrast these methods: “the running coupling constant” where the two-body ground-state energy is used as a renormalization condition, and two effective interaction approaches that include information about the ground as well as excited states. In particular, we calculate the energies and densities of few-fermion systems in a harmonic oscillator with the configuration-interaction method and compare the results based upon renormalized and bare interactions. We find that the use of the running coupling constant instead of the bare interaction improves convergence significantly. A comparison with an effective interaction, which is designed to reproduce the relative part of the energy spectrum of two particles, showed a similar improvement. The effective interaction provides an additional improvement if the center-of-mass excitations are included in the construction. Finally, we discuss the transformation of observables alongside the renormalization of the potential, and demonstrate that this might be an essential ingredient for accurate numerical calculations.},
  author       = {Brauneis, Fabian and Hammer, Hans Werner and Reimann, Stephanie M. and Volosniev, Artem},
  issn         = {2469-9934},
  journal      = {Physical Review A},
  number       = {1},
  publisher    = {American Physical Society},
  title        = {{Comparison of renormalized interactions using one-dimensional few-body systems as a testbed}},
  doi          = {10.1103/PhysRevA.111.013303},
  volume       = {111},
  year         = {2025},
}

@article{18823,
  author       = {Cao, Dechang and De Jaeger-Braet, Joke G},
  issn         = {1532-2548},
  journal      = {Plant Physiology},
  number       = {1},
  publisher    = {Oxford University Press},
  title        = {{Memory of maternal temperatures: DNA methylation alterations across generations}},
  doi          = {10.1093/plphys/kiae651},
  volume       = {197},
  year         = {2025},
}

@misc{18837,
  abstract     = {Super-resolution methods provide far better spatial resolution than the optical diffraction limit of about half the wavelength of light (∼200-300 nm). Nevertheless, they have yet to attain widespread use in plants, largely due to plants’ challenging optical properties. Expansion microscopy improves effective resolution by isotropically increasing the physical distances between sample structures while preserving relative spatial arrangements and clearing the sample. However, its application to plants has been hindered by the rigid, mechanically cohesive structure of plant tissues. Here, we report on whole-mount expansion microscopy of thale cress (Arabidopsis thaliana) root tissues (PlantEx), achieving a four-fold resolution increase over conventional microscopy. Our results highlight the microtubule cytoskeleton organization and interaction between molecularly defined cellular constituents. Combining PlantEx with stimulated emission depletion (STED) microscopy, we increase nanoscale resolution and visualize the complex organization of subcellular organelles from intact tissues by example of the densely packed COPI-coated vesicles associated with the Golgi apparatus and put these into a cellular structural context. Our results show that expansion microscopy can be applied to increase effective imaging resolution in Arabidopsis root specimens.},
  author       = {Danzl, Johann G and Kreuzinger, Caroline},
  publisher    = {Institute of Science and Technology Austria},
  title        = {{Research Data for the publication "Super-resolution expansion microscopy in plant roots"}},
  doi          = {10.15479/AT:ISTA:18837},
  year         = {2025},
}

@article{18848,
  abstract     = {Type II CRISPR endonucleases are widely used programmable genome editing tools. Recently, CRISPR-Cas systems with highly compact nucleases have been discovered, including Cas9d (a type II-D nuclease). Here, we report the cryo-EM structures of a Cas9d nuclease (747 amino acids in length) in multiple functional states, revealing a stepwise process of DNA targeting involving a conformational switch in a REC2 domain insertion. Our structures provide insights into the intricately folded guide RNA which acts as a structural scaffold to anchor small, flexible protein domains for DNA recognition. The sgRNA can be truncated by up to ~25% yet still retain activity in vivo. Using ancestral sequence reconstruction, we generated compact nucleases capable of efficient genome editing in mammalian cells. Collectively, our results provide mechanistic insights into the evolution and DNA targeting of diverse type II CRISPR-Cas systems, providing a blueprint for future re-engineering of minimal RNA-guided DNA endonucleases.},
  author       = {Ocampo, Rodrigo Fregoso and Bravo, Jack Peter Kelly and Dangerfield, Tyler L. and Nocedal, Isabel and Jirde, Samatar A. and Alexander, Lisa M. and Thomas, Nicole C. and Das, Anjali and Nielson, Sarah and Johnson, Kenneth A. and Brown, Christopher T. and Butterfield, Cristina N. and Goltsman, Daniela S.A. and Taylor, David W.},
  issn         = {2041-1723},
  journal      = {Nature Communications},
  publisher    = {Springer Nature},
  title        = {{DNA targeting by compact Cas9d and its resurrected ancestor}},
  doi          = {10.1038/s41467-024-55573-4},
  volume       = {16},
  year         = {2025},
}

@article{18849,
  abstract     = {Many biological systems operate near the physical limits to their performance, suggesting that aspects of their behavior and underlying mechanisms could be derived from optimization principles. However, such principles have often been applied only in simplified models. Here, we explore a detailed mechanistic model of the gap gene network in the Drosophila embryo, optimizing its 50+ parameters to maximize the information that gene expression levels provide about nuclear positions. This optimization is conducted under realistic constraints, such as limits on the number of available molecules. Remarkably, the optimal networks we derive closely match the architecture and spatial gene expression profiles observed in the real organism. Our framework quantifies the tradeoffs involved in maximizing functional performance and allows for the exploration of alternative network configurations, addressing the question of which features are necessary and which are contingent. Our results suggest that multiple solutions to the optimization problem might exist across closely related organisms, offering insights into the evolution of gene regulatory networks.},
  author       = {Sokolowski, Thomas R and Gregor, Thomas and Bialek, William and Tkačik, Gašper},
  issn         = {1091-6490},
  journal      = {Proceedings of the National Academy of Sciences},
  number       = {1},
  publisher    = {National Academy of Sciences},
  title        = {{Deriving a genetic regulatory network from an optimization principle}},
  doi          = {10.1073/pnas.2402925121},
  volume       = {122},
  year         = {2025},
}

@article{18850,
  abstract     = {Biophysical constraints limit the specificity with which transcription factors (TFs) can target regulatory DNA. While individual nontarget binding events may be low affinity, the sheer number of such interactions could present a challenge for gene regulation by degrading its precision or possibly leading to an erroneous induction state. Chromatin can prevent nontarget binding by rendering DNA physically inaccessible to TFs, at the cost of energy-consuming remodeling orchestrated by pioneer factors (PFs). Under what conditions and by how much can chromatin reduce regulatory errors on a global scale? We use a theoretical approach to compare two scenarios for gene regulation: one that relies on TF binding to free DNA alone and one that uses a combination of TFs and chromatin-regulating PFs to achieve desired gene expression patterns. We find, first, that chromatin effectively silences groups of genes that should be simultaneously OFF, thereby allowing more accurate graded control of expression for the remaining ON genes. Second, chromatin buffers the deleterious consequences of nontarget binding as the number of OFF genes grows, permitting a substantial expansion in regulatory complexity. Third, chromatin-based regulation productively co-opts nontarget TF binding for ON genes in order to establish a “leaky” baseline expression level, which targeted activator or repressor binding subsequently up- or down-modulates. Thus, on a global scale, using chromatin simultaneously alleviates pressure for high specificity of regulatory interactions and enables an increase in genome size with minimal impact on global expression error.},
  author       = {Perkins, Mindy Liu and Crocker, Justin and Tkačik, Gašper},
  issn         = {1091-6490},
  journal      = {Proceedings of the National Academy of Sciences},
  number       = {1},
  publisher    = {National Academy of Sciences},
  title        = {{Chromatin enables precise and scalable gene regulation with factors of limited specificity}},
  doi          = {10.1073/pnas.2411887121},
  volume       = {122},
  year         = {2025},
}

