Biology subjects

Smith, J. S.

Publications and source records attributed to Smith, J. S..

At least 19 recordsLinked to original sources

bioRxiv2026

Human and Mouse Models of the Bipolar Disorder-Associated ANK3 p.W1989R Variant Display Altered Somatostatin Interneuron Connectivity and Function

Bipolar disorder (BD) is a debilitating neuropsychiatric disorder characterized by recurrent mood perturbations, cognitive and functional impairment, and increased risk of suicide. Genome-wide association studies (GWAS) have repeatedly identified the gene ANK3, which encodes the neuronal scaffolding protein ankyrin-G, as a risk locus for BD. Ankyrin-G interacts directly with the GABAA receptor-associated protein (GABARAP) to stabilize inhibitory synapses, providing a potential mechanistic link between ANK3 variation and GABAergic dysfunction observed in BD. Previously, we identified an ANK3 p.W1989R variant in a family with BD and demonstrated that this variant abolishes the ankyrin-G/GABARAP interaction, resulting in inhibitory signaling deficits in mice. Here, we investigated the effects of this variant in human induced pluripotent stem cell (hiPSC)-derived neurons generated from an affected individual heterozygous for the ANK3 p.W1989R variant. CRISPR correction of the variant increased inhibitory synapse density on both glutamatergic and GABAergic patient-derived neurons. Integrated spatial transcriptomics and calcium imaging identified cell-type-dependent changes in gene expression and calcium dynamics. ANK3 p.W1989R somatostatin (SST) positive interneurons displayed altered calcium dynamics and reduced SST expression. To determine whether the variant impacts SST interneuron-mediated inhibition of cortical circuits, we selectively stimulated prefrontal cortical SST interneurons in heterozygous Ank3 p.W1989R mice and recorded optically evoked inhibitory postsynaptic currents (oIPSCs) from cortical pyramidal neurons. SST interneuron-mediated oIPSC peak amplitude, charge transfer, and decay times were reduced in variant mice, without a significant change in the paired-pulse ratio. These findings, using complementary human and mouse models, identify novel roles for ankyrin-G in SST interneuron-mediated inhibitory signaling and demonstrate that altered inhibitory connectivity and SST interneuron function are associated with ANK3 p.W1989R. This work provides mechanistic insight into how disrupted ankyrin-G-dependent synaptic function may contribute to inhibitory signaling deficits relevant to BD.

neuroscience↗

bioRxiv2026

Integrative Nanopore and Illumina sequencing reveals age-associated tRNA modification and CCA-tail dynamics in yeast

Aging is characterized by a progressive loss of proteostasis. Transfer RNAs (tRNAs) are essential regulators of translation, yet their dynamics during aging remain poorly understood due to challenges in sequencing highly modified RNAs. Here we present a benchmarked Nanopore direct RNA sequencing (RNA004 chemistry) resource that profiles the Saccharomyces cerevisiae tRNAome during replicative aging at single-molecule resolution. Using in vitro transcribed tRNA controls, we establish modification detection thresholds and validate key findings with orthogonal Illumina sequencing. While overall tRNA abundance remains largely stable, our resource reveals age-associated terminal A cleavage at the 3' CCA tail of mature tRNAs, targeted T-loop and anticodon modification changes, and single-molecule evidence of modification co-occurrence. This dataset provides a resource for exploring tRNA regulation, translation fidelity, and longevity.

genomics↗

bioRxiv2026

Divergent activation of the RXFP1 relaxin receptor by protein and small molecule agonists

RXFP1 is an unusual G protein-coupled receptor (GPCR) that mediates physiological adaptations to pregnancy and is a therapeutic target due to its benefits in treatment of fibrosis and heart failure. Protein and small-molecule agonists are currently in mid-stage clinical trials. Here, we present three cryo-electron microscopy structures of RXFP1: ligand-free, bound to the native agonist relaxin-2, and bound to the small-molecule drug candidate AZD5462. These structures show that relaxin-2 engages the receptors ectodomain while AZD5462 binds within transmembrane domain. Together with hydrogen-deuterium exchange mass spectrometry, we show that relaxin-2 induces conformational reorganization of the linker domain into a helical secondary structure. In contrast, AZD5462 stabilizes a unique active conformation capable of inducing {beta}-arrestin recruitment. Both mechanisms are distinctive from the "push-pull" mechanism of glycoprotein hormone receptors. Altogether, our findings define divergent activation mechanisms for protein and small-molecule agonists of RXFP1 and provide structural framework for next-generation drug discovery targeting relaxin receptors and their relatives.

biochemistry↗

bioRxiv2025

Age-dependent topoisomerase I depletion alters recruitment of rDNA silencing complexes

Genomic instability and loss of proteostasis are two of the primary Hallmarks of Aging. Although these hallmarks are well-defined in the literature, the mechanisms that drive genomic instability and loss of proteostasis as cells age are still largely unknown. Using budding yeast replicative lifespan as a model for aging in actively dividing cells, we identified nuclear proteins that were depleted in the earliest stages of aging. We found that many age-depleted proteins were involved in ribosome biogenesis, specifically in ribosome processing, or in maintenance of chromatin stability. We focused on topoisomerase I (Top1) as a novel age-depleted nuclear protein and found that its depletion in the early stages of aging was not a result of transcriptional changes or changes in protein turnover. Despite the stark depletion of Top1 in early aging, rescue of this age-dependent depletion was actually harmful to replicative lifespan. We found that Top1, when overexpressed, disrupts the stoichiometry of the RENT complex by pulling Sir2 away from the ribosomal DNA (rDNA), a phenotype which is further enhanced when the overexpressed Top1 is catalytically dead. Loss of Sir2 from the rDNA via the overexpression of catalytically dead Top1 decreases RNA Pol II silencing of a reporter gene inside or adjacent to the rDNA, consistent with the lifespan defect. Finally, we found that the catalytic activity of Top1 plays an important role in the establishment of rDNA silencing, raising the possibility that rDNA secondary structure/DNA topology is important for RNA Pol I-dependent spreading of silent chromatin across the rDNA locus.

molecular biology↗

bioRxiv2025

β-arrestin recruitment facilitates a direct association with G proteins

G protein-coupled receptors (GPCRs) are targets for almost a third of all FDA-approved drugs. GPCRs are known to signal through both heterotrimeric G proteins and {beta}-arrestins. Traditionally these pathways were viewed as largely separable, with G proteins primarily initiating downstream signaling while {beta}-arrestins modulate receptor trafficking and desensitization in addition to regulating their own signaling events. Recent studies suggest an integrated role of G proteins and {beta}-arrestins in GPCR signaling, however the cellular and biochemical requirements for G protein: {beta}-arrestin interactions remain unclear. Here we show that G proteins and {beta}-arrestins can directly interact. Through utilization of {beta}-arrestin-biased receptors and artificially enforced {beta}-arrestin relocalization, we demonstrate that recruitment of {beta}-arrestin to the plasma membrane is sufficient to interact with the G protein Gi. Using purified proteins, we show that Gi directly interacts with {beta}-arrestin. In addition, we find that Gi family members differ in their degree of association with {beta}-arrestin, and that a large degree of this selectivity resides within the alpha helical domain of Gi. These findings delineate the cellular and biochemical conditions that drive direct interactions between G proteins and {beta}-arrestins and illuminate the molecular basis for how they work together to effect GPCR signaling.

biochemistry↗

bioRxiv2025

In silico discovery of nanobody binders to a G-protein coupled receptor using AlphaFold-Multimer

Antibodies are central mediators of the adaptive immune response, and they are powerful research tools and therapeutics. Antibody discovery requires substantial experimental effort, such as immunization campaigns or in vitro library screening. Predicting antibody-antigen binding a priori remains challenging. However, recent machine learning methods raise the possibility of in silico antibody discovery, bypassing or reducing initial experimental bottlenecks. Here, we report a virtual screen using AlphaFold-Multimer (AF-M) that prospectively identified nanobody binders to MRGPRX2, a G protein-coupled receptor (GPCR) and therapeutic target for the treatment of pseudoallergic inflammation and itch. Using previously reported nanobody-GPCR structures, we identified a set of AF-M outputs that effectively discriminate between interacting and non-interacting nanobody-GPCR pairs. We used these outputs to perform a prospective in silico screen, identified nanobodies that bind MRGPRX2 with high affinity, and confirmed activity in signaling and functional cellular assays. Our results provide a proof of concept for fully computational antibody discovery pipelines that can circumvent laboratory experiments.

biochemistry↗

bioRxiv2024

Small Molecule Modulators of Beta-arrestins

{beta}-arrestins are multifunctional regulators of G protein-coupled receptor (GPCR) signaling, orchestrating diverse downstream signaling events and physiological responses across the vast GPCR superfamily. While GPCR pharmacology has advanced to target orthosteric and allosteric sites, as well as G proteins and GRKs, comparable chemical tools to study {beta}-arrestins remain lacking. Here, we report the discovery of small-molecule inhibitors that selectively target {beta}-arrestins and delineate their mechanism of action through integrated pharmacological, biochemical, biophysical, and structural analyses. These inhibitors disrupt {beta}-arrestin-engagement with agonist-activated GPCRs, impairing desensitization, internalization, and {beta}-arrestin-dependent functions while sparing G protein-receptor coupling. Cryo-EM, MD simulations, and structure-guided mutagenesis reveal that one modulator, Cmpd-5, engages a cryptic pocket formed by the middle, C-, and lariat loops of {beta}-arrestin1--a critical receptor-binding interface--stabilizing a distinct conformation incompatible with GPCR engagement. Together, these findings provide a mechanistic framework for {beta}-arrestin modulation, introducing transducer-targeted strategies to fine-tune GPCR signaling and guide the development of pathway-specific therapeutics.

biochemistry↗

bioRxiv2024

SuperWater: Predicting Water Molecule Positions on Protein Structures by Generative AI

Water molecules play a significant role in maintaining protein structural stability and facilitating molecular interactions. Accurate prediction of water molecule positions around protein structures is essential for understanding their biological roles and has significant implications for protein engineering and drug discovery. Here, we introduce SuperWater, a novel generative AI framework that integrates a score-based diffusion model with equivariant graph neural networks to predict water molecule placements around proteins with high accuracy. SuperWater surpasses existing methods, delivering state-of-the-art performance in both crystal water coverage and prediction precision, achieving water localization within 0.3 {+/-} 0.06 {degrees}A of experimentally validated positions. We demonstrate the capabilities of SuperWater through case studies involving protein hydration, protein-ligand binding, and protein-protein binding sites. This framework can be adapted for various applications, including structural biology, binding site prediction, multi-body docking, and water-mediated drug design.

bioinformatics↗

bioRxiv2023

Phosphorylation barcodes direct biased chemokine signaling at CXCR3

G protein-coupled receptor (GPCR) biased agonism, the activation of some signaling pathways over others, is thought to largely be due to differential receptor phosphorylation, or "phosphorylation barcodes." At chemokine receptors, ligands act as "biased agonists" with complex signaling profiles, which contributes to the limited success in pharmacologically targeting these receptors. Here, mass spectrometry-based global phosphoproteomics revealed that CXCR3 chemokines generate different phosphorylation barcodes associated with differential transducer activation. Chemokine stimulation resulted in distinct changes throughout the kinome in global phosphoproteomic studies. Mutation of CXCR3 phosphosites altered {beta}-arrestin conformation in cellular assays and was confirmed by molecular dynamics simulations. T cells expressing phosphorylation-deficient CXCR3 mutants resulted in agonist- and receptor-specific chemotactic profiles. Our results demonstrate that CXCR3 chemokines are non-redundant and act as biased agonists through differential encoding of phosphorylation barcodes and lead to distinct physiological processes.

biochemistry↗

bioRxiv2022

Control of neuronal terminal differentiation through cell context-dependent CFI-1/ARID3 functions

ARID3 transcription factors are expressed in the nervous system, but their functions and mechanisms of action are largely unknown. Here, we generated in vivo a genome-wide binding map for CFI-1, the sole C. elegans ARID3 ortholog. We identified 6,396 protein-coding genes as putative direct targets of CFI-1, most of which (77%) are expressed in post-mitotic neurons and encode terminal differentiation markers (e.g., neurotransmitter receptors, ion channels, neuropeptides). To gain mechanistic insights, we focused on two neuron types. In sensory neurons (IL2 class), CFI-1 exerts a dual role: it acts directly to activate, and indirectly to repress, distinct terminal differentiation genes. In motor neurons, however, CFI-1 acts directly as a repressor, continuously antagonizing three transcriptional activators (UNC-3/Ebf, LIN-39/Hox4-5, MAB-5/Hox6-8). By focusing on a glutamate receptor gene (glr-4/GRIK1), we found CFI-1 exerts its repressive activity through proximal binding to the glr-4 locus. Further, the core DNA binding domain of CFI-1 is partially required for glr-4 repression in motor neurons. Altogether, this study uncovers cell context-dependent mechanisms through which a single ARID3 protein controls the terminal differentiation of distinct neuron types.

developmental biology↗

bioRxiv2022

Fob1-dependent condensin recruitment and loop extrusion on yeast chromosome III

Despite recent advances in single-molecule and structural analysis of condensin activity in vitro, mechanisms of functional condensin loading and loop extrusion that lead to specific chromosomal organization remain unclear. In Saccharomyces cerevisiae, the most prominent condensin loading site is the rDNA locus on chromosome XII, but its repetitiveness deters rigorous analysis of individual genes. An equally prominent non-rDNA condensin site is located on chromosome III (chrIII). It lies in the promoter of a putative non-coding RNA gene called RDT1, which is in a segment of the recombination enhancer (RE) that dictates MATa-specific chrIII organization. Here, we unexpectedly find that condensin is recruited to RDT1 through interactions with Fob1, Tof2, and cohibin (Lrs4/Csm1), a set of nucleolar factors that also recruit condensin to the rDNA. Using Micro-C XL, we uncover evidence for condensin-driven loop extrusion anchored by Fob1 and cohibin at RDT1 that extends toward MATa on the right arm of chrIII, supporting donor preference during mating-type switching. S. cerevisiae chrIII therefore provides a new platform for the study of programmed condensin-mediated chromosome conformation.

molecular biology↗

bioRxiv2021

Isonicotinamide extends yeast chronological lifespan through a mechanism that diminishes nucleotides

Isonicotinamide (INAM) is an isomer of the NAD+ precursor nicotinamide (NAM) that stimulates the enzymatic activity of Sir2, an NAD+-dependent histone deacetylase from the budding yeast, Saccharomyces cerevisiae. Supplementing INAM into growth media promotes the replicative lifespan (RLS) of this single cell organism by maintaining intracellular NAD+ homeostasis. INAM also extends yeast chronological lifespan (CLS), but the underlying mechanisms remain largely uncharacterized. To identify interacting genes, a chemical genomics screen of the yeast knockout (YKO) collection was performed for mutants sensitized to growth inhibition by INAM. Significant Gene Ontology (GO) terms included transcription elongation factors, metabolic pathways converging on one-carbon metabolism, and de novo purine biosynthesis, collectively suggesting that INAM may perturb nucleotide metabolism. Indeed, INAM caused dose-dependent depletion of intracellular cytidine, uridine and guanosine, ribonucleosides derived from the breakdown of nucleotide monophosphates by a set of nucleotidases (Phm8, Sdt1, Isn1) or the alkaline phosphatase Pho8. Direct inhibition of recombinant Sdt1 and Phm8 nucleotidase activity by INAM was confirmed in vitro, as was inhibition of alkaline phosphatase activity. Each of these enzymes can also convert nicotinamide mononucleotide (NMN) to nicotinamide riboside (NR), consistent with an accumulation of NMN and NAD+ upon inhibition by INAM. Taken together, the findings suggest a model whereby partial impairment of nucleotide salvage pathways can trigger a hormetic stress response that supports enhanced quiescence during chronological aging.

biochemistry↗

bioRxiv2020

A cell non-autonomous mechanism of yeast chronological aging regulated by caloric restriction and one-carbon metabolism

Caloric restriction (CR) improves healthspan and lifespan of organisms ranging from yeast to mammals. Understanding the mechanisms involved will uncover future interventions for aging associated diseases. In budding yeast, Saccharomyces cerevisiae, CR is commonly defined by reduced glucose in the growth medium, which extends both replicative and chronological lifespan (CLS). We found that conditioned media collected from stationary phase CR cultures extended CLS when supplemented into non-restricted (NR) cultures, suggesting a potential cell non-autonomous mechanism of CR-induced lifespan regulation. Chromatography and untargeted metabolomics of the conditioned media, as well as transcriptional responses associated with the longevity effect, pointed to specific amino acids enriched in the CR conditioned media (CRCM) as functional molecules, with L-serine being a particularly strong candidate. Indeed, supplementing L-serine into NR cultures extended CLS through a mechanism dependent on the one-carbon metabolism pathway, thus implicating this conserved and central metabolic hub in lifespan regulation.

cell biology↗

bioRxiv2020

Biased agonists of the chemokine receptor CXCR3 differentially drive formation of Gαi:β-arrestin complexes

G-protein-coupled receptors (GPCRs), the largest family of cell surface receptors, signal through the proximal effectors G proteins and {beta}-arrestins to influence nearly every biological process. Classically, the G protein and {beta}-arrestin signaling pathways have largely been considered separable. Recently, direct interactions between G protein and {beta}-arrestin have been described and suggest a distinct GPCR signaling pathway. Within these newly described G:{beta}-arrestin complexes, Gi/o, but not other G protein subtypes, have been appreciated to directly interact with {beta}-arrestin, regardless of canonical GPCR G protein subtype coupling. However it is unclear how biased agonists differentially regulate this newly described Gi:{beta}-arrestin interaction, if at all. Here we report that endogenous ligands (chemokines) of the GPCR CXCR3, CXCL9, CXCL10, and CXCL11, along with two small molecule biased CXCR3 agonists, differentially promote the formation of Gi:{beta}-arrestin complexes. The ability of CXCR3 agonists to form Gi:{beta}-arrestin complexes does not correlate well with either G protein signaling or {beta}-arrestin recruitment. Conformational biosensors demonstrate that ligands that promoted Gi:{beta}-arrestin complex formation generated similar {beta}-arrestin conformations. We find these Gi:{beta}-arrestin complexes can associate with CXCR3, but not with ERK. These findings further support that Gi:{beta}-arrestin complex formation is a distinct GPCR signaling pathway and enhance our understanding of biased agonism.

biochemistry↗

bioRxiv2019

Noncanonical scaffolding of Gαi and β-arrestin by G protein-coupled receptors

G-protein-coupled receptors (GPCRs) enable cells to sense and respond appropriately to hormonal and environmental signals, and are a target of ~30% of all FDA-approved medications. Canonically, each GPCR couples to distinct G proteins, such as Gs, Gi, Gq or G12/13, as well as {beta}-arrestins. These transducer proteins translate and integrate extracellular stimuli sensed by GPCRs into intracellular signals through what are broadly considered separable signalling pathways. However, the ability of G proteins to directly interact with {beta}-arrestins to integrate signalling has not previously been appreciated. Here we show a novel interaction between Gi protein family members and {beta}-arrestin. Gi:{beta}-arrestin complexes were formed by all GPCRs tested, regardless of their canonical G protein isoform coupling, and could bind both GPCRs as well as the extracellular signal-regulated kinase (ERK). This novel paradigm of Gi:{beta}-arrestin scaffolds enhances our understanding of GPCR signalling.

cell biology↗

bioRxiv2019

A Novel, Versatile Speculum-free Callascope for Clinical Examination and Self-Visualization of the Cervix

BackgroundInvasive cervical cancer is preventable, yet affects 500,000 women worldwide each year, and over half these women die. Barriers to cervical cancer screening include lack of awareness of cervical cancer and the cervix, fear of the speculum, and lack of women-centric technologies. We developed a low-cost ([~]$50), cervix-imaging device called the Callascope, which comprises an imaging component, camera and inserter that eliminates the need for a speculum and enables self-insertion. We sought to assess the quality of physicians images of the cervix using the Callascope versus the speculum in live patients and study womens willingness to independently use the Callascope to image their cervix.\n\nMethodsWe conducted two main studies: (1) a clinical study in which a physician imaged the cervix of patients using both the speculum and Callascope in a 2x2 crossover design; and (2) home-based self-cervix imaging with the Callascope.\n\nResultsParticipants of the clinical study (n=28) and home study (n=12) all indicated greater comfort and an overall preference for the Callascope over the speculum. The clinical study data indicated that the Callascope enabled similar visualization compared to the speculum while significantly improving patient experience. With physician insertion and manipulation, the Callascope enabled cervix visualization for 82% of participants. In the home-study, 83% of participants were able to visualize their cervix with the Callascope on the first try and 100% after multiple attempts.\n\nConclusionThe Callascope is more comfortable and provides similar visualization to the speculum. The Callascope can be used by medical providers for clinical exams while also enabling home self-screening for cervical cancer and promoting a better understanding of ones cervix to increase awareness of cervical screening needs. The Callascope may increase cervical cancer screening rates through reducing barriers including cost, discomfort, lack of awareness and stigma.

clinical trials↗

bioRxiv2019

Pathogen-encoded evasion of CXCL10 and T cell responses

Clearance of intracellular pathogens, such as Leishmania (L.) major, depends on a well-regulated adaptive T cell response. Here we describe a pathogen-encoded mechanism to alter T cell recruitment by suppressing CXCL10, a chemokine that recruits CD4+ and CD8+ T cells by signaling through the CXCR3 receptor. L. major suppresses CXCL10 through the virulence factor and protease, glycoprotein-63 (gp63). GP63 cleaves CXCL10 after amino acid A81, impairing T-cell chemotaxis in vitro. GP63 from either extracellular promastigotes or intracellular amastigotes is capable of cleaving CXCL10. Consistent with CXCL10 cleavage during infection, we observed GP63-mediated impairment of activated CD8+ T-cells in the draining lymph nodes of C57BL/6JWT mice. Correspondingly, in C57BL/6JWT mice, gp63 deletion resulted in slower lesion development and a smaller maximum lesion size. However, infection in C57BL/6Jcxcr3-/- mice revealed the delay to lesion development required CXCR3 signaling. Finally, Salmonella enterica and Chlamydia trachomatis infection also suppress CXCL10, demonstrating convergent evolution of this immune evasion strategy in diverse intracellular pathogens. Understanding mechanisms of CXCL10 evasion may facilitate the development of novel therapeutic strategies to treat intracellular pathogens. Author SummaryLeishmaniasis is an infectious disease that affects over one million people annually. It is caused by intracellular parasites that have evolved to evade the hosts attempts to eliminate the parasite. The most common form of disease, cutaneous leishmaniasis, causes disfiguring skin lesions if the host immune system does not appropriately respond to the infection. A family of molecules called chemokines are critical for the recruitment of specific subsets of immune cells required to eliminate infection. Here, we demonstrate a novel mechanism that the parasite Leishmania (L.) major employs to disrupt the immune response by interfering with chemokine signaling. By this strategy, L. major uses a protease to cleave chemokines known to recruit T-cells required for fighting off infection. We show that L. major cleavage of these immune signals changes the recruitment of CD8+ T-cells and alters disease progression in mice. Finally, we observe that multiple common human intracellular pathogens, including Chlamydia trachomatis and Salmonella enterica, interfere with the same chemokines, suggesting a strong selective pressure to avoid this component of the immune response. Our study provides new insights into how intracellular pathogens interact with the host immune response to enhance pathogen survival and exacerbate disease outcomes.

microbiology↗

bioRxiv2019

A Sir2-regulated locus control region in the recombination enhancer of Saccharomyces cerevisiae specifies chromosome III structure

The NAD+-dependent histone deacetylase Sir2 was originally identified in Saccharomyces cerevisiae as a silencing factor for HML and HMR, the heterochromatic cassettes utilized as donor templates during mating-type switching. MATa cells preferentially switch to MAT using HML as the donor, which is driven by an adjacent cis-acting element called the recombination enhancer (RE). In this study we demonstrate that Sir2 and the condensin complex are recruited to the RE exclusively in MATa cells, specifically to the promoter of a small gene within the right half of the RE known as RDT1. We go on to demonstrate that the RDT1 promoter functions as a locus control region (LCR) that regulates both transcription and long-range chromatin interactions. Sir2 represses the transcription of RDT1 until it is redistributed to a dsDNA break at the MAT locus induced by the HO endonuclease during mating-type switching. Condensin is also recruited to the RDT1 promoter and is displaced upon HO induction, but does not significantly repress RDT1 transcription. Instead condensin appears to promote mating-type switching efficiency and donor preference by maintaining proper chromosome III architecture, which is defined by the interaction of HML with the right arm of chromosome III, including MATa and HMR. Remarkably, eliminating Sir2 and condensin recruitment to the RDT1 promoter disrupts this structure and reveals an aberrant interaction between MATa and HMR, consistent with the partially defective donor preference for this mutant. Global condensin subunit depletion also impairs mating type switching efficiency and donor preference, suggesting that modulation of chromosome architecture plays a significant role in controlling mating type switching, thus providing a novel model for dissecting condensin function in vivo. Author summarySir2 is a highly conserved NAD+-dependent protein deacetylase and defining member of the sirtuin protein family. It was identified about 40 years ago in the budding yeast, Saccharomyces cerevisiae, as a gene required for silencing of the cryptic mating-type loci, HML and HMR. These heterochromatic cassettes are utilized as templates for mating-type switching, whereby a programmed DNA double-strand break at the MATa or MAT locus is repaired by gene conversion to the opposite mating type. The preference for switching to the opposite mating type is called donor preference, and in MATa cells, is driven by a cis-acting DNA element called the recombination enhancer (RE). It was believed that the only role for Sir2 in mating-type switching was silencing HML and HMR. However, in this study we show that Sir2 also regulates expression of a small gene (RDT1) in the RE that is activated during mating-type switching. The promoter of this gene is also bound by the condensin complex, and deleting this region of the RE drastically changes chromosome III structure and alters donor preference. The RE therefore appears to function as a complex locus control region (LCR) that links transcriptional control to chromatin architecture, and thus provides a new model for investigating the underlying mechanistic principles of programmed chromosome architectural dynamics.

molecular biology↗