Molecular Cell

Human quinone reductase 2 (QR2, NQO2) is a cytosolic flavoprotein involved in cell physiology and metabolism, and implicated in several diseases. However, the mechanisms that govern its oligomeric assembly and diverse functional outcomes remain incompletely understood. Here, we employ native mass spectrometry to directly resolve the dynamic oligomeric landscape of recombinant human QR2 expressed in Escherichia coli, preserving non-covalent interactions and enabling analysis of assembly behavior under native conditions. QR2 is predominantly observed as a dimer stabilized by multiple non-covalently bound ligands, giving rise to discrete species. Top-down native mass spectrometry reveals a single intact proteoform, excluding covalent modification or covalently bound flavins as drivers of oligomerization. Binding of flavin adenine dinucleotide (FAD) robustly stabilizes the dimer, while unexpectedly, flavin mononucleotide (FMN) also promotes dimer formation. As FMN and FAD differ structurally by the presence of an adenine dinucleotide moiety, we hypothesized that purine nucleotide binding itself may modulate QR2 assembly. Consistent with this, we identify a new concentration-dependent effect of guanosine-triphosphate (GTP) on QR2 dimerization. Functional reductase assays show that flavin-stabilized dimers exhibit the highest catalytic activity, whereas GTP-induced dimers retain reduced activity. Binding of the inhibitor YB537 abolishes activity despite promoting dimer formation. Together, these findings reveal a ligand-dependent structural plasticity in QR2 oligomerization that is decoupled from reductase function, suggesting that QR2 dimerization serves a wider regulatory role beyond simply supporting reductase catalysis.

Neuronal maturation is associated with extensive changes in gene expression and chromatin organization. However, the molecular mechanisms that control the epigenetic landscape in terminally differentiated neurons remain poorly understood. Here, we show that maturing cerebellar granule cells undergo a striking and specific increase in the levels of the repressive histone modification H3K27me3 across different genomic regions, including individual genes, broad intergenic regions, and gene clusters. The accumulation of H3K27me3 coincides with a developmental switch from EZH2 to EZH1 and colocalizes with H3K36me2 and DNA non-CpG methylation. Using mice with a conditional deletion in the catalytic domain of EZH1, we demonstrate that the maintenance of H3K27me3 in mature neurons depends on EZH1. Unexpectedly, an almost complete loss of H3K27me3 in postmitotic GCs induces minimal changes in gene expression and chromatin accessibility at 7 months of age. Using single-nucleus RNA sequencing (snRNAseq) from the mouse neocortex, we show that, similarly to GCs, the loss of EZH1-mediated H3K27me3 also has a minimal impact on cortical neuron gene expression. The amino acid composition of EZH1 suggests reduced sensitivity to H3K36 methylation, providing a potential basis for its activity in chromatin contexts that are not permissive for EZH2. Together, our results show that a postmitotic switch from EZH2 to EZH1 establishes novel chromatin domains in neurons with a minimal role in transcriptional maintenance.

Epigenetic regulation is tightly linked to cellular metabolism through chromatin-modifying enzymes that depend on central metabolites as co-substrates. Methionine is an essential amino acid that is directly converted by methionine adenosyltransferase 2A (MAT2A) into S-adenosylmethionine (SAM), the universal methyl donor required for histone and DNA methylation. Although methionine restriction/depletion can alter the chromatin methylation landscape and improve physiological outcomes in diverse biological systems, it remains unclear whether these effects arise from loss of methionine itself or from secondary depletion of SAM. Here, we show that methionine depletion induces nuclear accumulation of MAT2A together with redistribution of H3K9 methylation, derepression of transposable elements, activation of stress-response pathways, and broad transcriptional reprogramming. Surprisingly, pharmacologic inhibition reduced intracellular SAM to levels comparable to methionine depletion but failed to reproduce these major epigenetic or transcriptional responses. Furthermore, depletion of the SAM-sensor SAMTOR and inhibition of KDM4 histone demethylases did not prevent methionine-dependent chromatin remodeling, indicating that canonical SAM-sensing pathways are not required for this adaptation. Instead, methionine depletion uniquely induced innate immune and integrated stress-response programs consistent with a viral mimicry-like state. These findings demonstrate that methionine availability, rather than SAM abundance, functions as a primary metabolic signal regulating epigenetic adaptation to nutrient stress. Our data support a model in which methionine is sensed independently of SAM abundance and acts upstream of stress signaling pathways that secondarily remodel chromatin.

RAF kinases interpret signals from the three major RAS isoforms to initiate MAPK pathway activation, yet the molecular logic that governs isoform-specific RAS recruitment and the early events that relieve RAF autoinhibition are not yet fully understood. In particular, how the modular N-terminal regulatory architecture of CRAF and ARAF, anchored by the multifunctional cysteine-rich domain (CRD), discriminates among HRAS, KRAS, and NRAS has remained a central unresolved question. Here, we combine quantitative biophysical measurements with structural and dynamic analyses to define how RAS isoform identity and CRD engagement shape the earliest steps of RAF activation. These studies reveal unexpectedly divergent modes of RAS recognition between CRAF and ARAF and expose previously unappreciated functions of the CRD in modulating RAS affinity and intramolecular regulatory contacts. We further identify a direct link between RAS binding and destabilization of RAF autoinhibition, providing mechanistic insight into how RAS initiates the transition from an inactive monomer to an activation-competent assembly. Finally, we show that emerging KRAS inhibitors variably perturb KRAS-CRAF interactions, offering insight into how these therapeutics influence early RAS-RAF signaling events. Together, this work uncovers distinct biophysical principles that govern RAS-RAF selectivity and reveals a regulatory role for the CRD that reframes our understanding of RAF activation and its dysregulation in RAS-driven cancers. SignificanceProteins in the RAS-RAF signaling pathway control cell growth and are frequently mutated in cancer. Despite their importance, how different RAS proteins selectively recruit RAF kinases has remained incompletely understood. This study reveals that the cysteine-rich regulatory region of RAF plays a central role in distinguishing RAS isoforms and controlling RAF activation. These insights clarify early steps in MAPK signaling and may guide the development of improved therapies targeting RAS-driven cancers.

The electron shuttle and coenzyme nicotinamide adenine nucleotide (NAD) is essential for cellular metabolism and homeostasis. NAD levels significantly fluctuate in cells, whilst several age-related diseases are associated with depletion of this metabolite. However, how NAD changes are monitored by nutrient/energy sensing signalling pathways remains poorly understood. We found that at physiological concentrations NAD controls the activity of the AMP-activated protein kinase (AMPK) in vitro and in human cells. Mechanistically, NAD binds gamma subunit of AMPK, and mutagenesis of the putative binding site renders the holoenzyme insensitive to NAD inhibition. Hyperactivation of AMPK in response to NAD depletion suppresses metabolic pathways including mammalian Target of Rapamycin Complex I (mTORC1) and autophagy. These results demonstrate that in addition to monitoring cellular energy levels AMPK functions as a NAD sensor, providing novel insight into how cells and tissues detect and respond to metabolic fluctuations with implications for stress resistance and ageing.

Post-translational modifications (PTMs) of chromatin remodelers are abundant but functionally understudied. Here we investigate the role of asymmetric dimethylation of arginine 1064 (BAF155me2a) on the SWI/SNF core subunit BAF155, a mark deposited by CARM1/PRMT4 that has been linked to tumor progression but whose molecular function remains unclear. Using immunoprecipitation-mass spectrometry with a dimethyl-specific antibody, we found that R1064me2 selectively enhances BAF155 interactions with RNA processing factors, including the anti-termination protein SCAF4, splicing factors, and the transcription factor RFX5. CUT&RUN profiling showed that BAF155me2a, SCAF4, and RFX5 co-occupy promoter regions, and reciprocal immunoprecipitations confirmed that the SCAF4-BAF155 interaction depends on R1064 methylation. To test the functional consequences of this modification, we generated cells expressing either wild-type BAF155 or a methylation-deficient BAF155-R1064K mutant. Loss of methylation did not alter chromatin accessibility, BAF155 genomic occupancy, or SCAF4 recruitment. However, nascent transcription measured by TT-seq revealed a coordinated reduction in 5' sense transcripts and upstream antisense transcripts (PROMPTs) at BAF155-bound promoters, with a quantitatively larger decrease in PROMPTs at SCAF4 co-bound sites. The effect was restricted to the promoter-proximal region and resolved toward the gene end, consistent with a defect in productive elongation downstream of RNA polymerase II recruitment. These data support a model in which BAF155 dimethylation provides a co-transcriptional interface coupling SWI/SNF to RNA processing machinery, and identify regulation of nascent transcription as a non-canonical function of SWI/SNF PTMs.

In Schizosaccharomyces pombe, the conserved CHD remodeler Mit1 function within the SHREC remodeler-deacetylase complex (a homolog of the metazoan Mi-2/NuRD complex), which is essential for H3K9 methylation-dependent heterochromatin establishment. However, the mechanism by which remodeler activity promotes silencing is unknown. Current models posit a hierarchical relationship between histone modifications and remodeler activity, with Mit1 acting exclusively downstream of H3K9 methylation. Here, we challenge this model by showing that tethering Mit1 at an ectopic site within euchromatin is sufficient to initiate heterochromatin assembly and generate extended domains of de novo H3K9 methylation. This process requires the Mit1 catalytic activity but does not involve direct physical interaction with Clr4, suggesting Mit1-mediated nucleosome remodeling creates a chromatin context that enhances Clr4 function. Using a genome-wide deletion screen, we determined that Mit1-initiated silencing requires all core heterochromatin factors and is critically dependent on Clr4 dosage. Furthermore, Mit1 activity facilitates heterochromatin spreading at subtelomeric regions and promotes H3K9 methylation at novel genomic sites implicated in cellular adaptation. Together, our findings support a model in which remodeler-writer pairs, analogous to reader-writer pairs, constitute conserved regulatory modules through which nucleosome organization directs the establishment of heritable epigenetic states.

Although MTBP is essential for replication origin firing, we show here that strong depletion of MTBP can have minor effects on DNA replication rates. This suggests an adaptive process in the DNA replication program, so we examined mechanisms underlying this plasticity. Using an auxin-inducible degron to deplete MTBP, we found that acute suppression of MTBP blocked DNA replication, but that replication rates recovered over time. The timing of this recovery paralleled S phase expression of Cyclin B1, and inhibition of CDK1-Cyclin B1 prevented the recovery. Recovery did not involve restoration of origin firing; instead, replication recovered through accelerated fork progression. Consistent with CDK1 driving this acceleration, ATR inhibition, which activates CDK1, stimulated DNA replication in MTBP-depleted cells through CDK1-dependent increased fork progression rather than increased origin firing. Knockdown of RIF1, a known CDK1 target, phenocopied this effect. Although RIF1 is best known for opposing DDK-dependent MCM phosphorylation at origins, we find that RIF1 knockdown stimulates replication even when DDK is inhibited. Furthermore, RIF1 loss increased replication by accelerating fork progression rather than increasing origin firing. Together, these findings reveal a CDK1-RIF1-dependent mechanism that promotes fork speed during S phase and defines a form of replication plasticity in which fork rate compensates for reduced origin firing. SIGNIFICANCE STATEMENTAccurate genome duplication requires thousands of replication origins to fire and replication forks to complete DNA synthesis on schedule. When origin firing is compromised, it is unclear how cells avoid replication failure. We show that cells adapt to persistent loss of the origin-firing factor MTBP by accelerating replication fork progression through a CDK1-RIF1-dependent mechanism, partially compensating for reduced initiation. This adaptive response defines a form of replication plasticity in which cells rebalance origin usage and fork speed to sustain DNA synthesis. This mechanism may be especially relevant in cancer cells or other contexts where replication initiation is chronically stressed.

Error-free genome duplication is critical for cellular homeostasis and genome maintenance. Stalled forks undergo remodeling during replication stress, and unprotected forks undergo degradation by nucleases. RAD51 paralogs are evolutionarily conserved essential proteins for genome maintenance with diverse roles ranging from homologous recombination (HR) to replication stress responses. However, the mechanisms underlying their participation in fork maintenance remain unclear. Here, we demonstrate that the RAD51 paralogs do not participate in the canonical SMARCAL1-BRCA2 axis of fork protection. Instead, RAD51D-XRCC2 (DX2) and RAD51C-XRCC3 (CX3) complexes protect forks remodeled by the FBH1 helicase, whereas the RAD51B-RAD51C (BC) subcomplex but not BRCA2 safeguards forks remodeled by the FANCM translocase, revealing a new FANCM-mediated pathway of fork remodeling which is protected by the BC sub-complex. Mechanistically, we show that FANCM-mediated fork reversal is RAD51-dependent and generates substrates for MRE11-, EXO1-, and DNA2-mediated degradation in the absence of RAD51B/C. Our findings establish the participation of the RAD51 paralogs in multiple fork protection pathways in a fork-remodeler-specific manner, highlighting the existence of several independent fork remodeling and protection mechanisms for maintaining genomic stability under replication stress.

Hypoxia-inducible factor 2 (HIF-2) is a central regulator of cellular homeostasis and a known oncogenic driver in multiple cancers. Although HIF-2 is canonically defined as a nuclear transcription factor, its cytoplasmic presence and non-canonical functions remain poorly understood. Here, we performed a structural survey of HIF-2 to determine the mechanisms underlying subcellular localization, protein abundance, and activity using a deletion-construct library, transcriptional assays, and in vivo xenograft models. We found that the oxygen-dependent degradation domain (ODD), the N-terminal intrinsically disordered region (n-IDR) and the N-terminal transactivation domain (NTAD) promote cytoplasmic localization, whereas the C-terminal IDR drives nuclear accumulation. Surprisingly, we found that HIF-2 nuclear localization occurs also in the absence of PAS A and B, the domains required for ARNT (HIF-1{beta}) dimerization, resolving the long-standing question in the field. These data suggest a dominant role for non-canonical cytoplasmic mechanisms in HIF-2-driven tumorigenesis. Strikingly, neither NTAD nor the C-terminal CTAD was required for tumor growth in vivo, in coherence with our transcriptional assays indicating that CTAD is dispensable for transactivation and NTAD functions as a suppressor rather than an activator of transcription. Proteomic analyses reveal HIF-2 interactions with regulators of mitochondrial function, translation initiation, RNA splicing, vesicular transport, and DNA replication. Together, these findings uncover previously unrecognized structural and functional complexity of HIF-2 compartmentalization and expand its role beyond canonical transcriptional regulation.

Histone H4 lysine 20 trimethylation (H4K20me3) is a histone modification that is critical in maintaining genome integrity. Dysregulation of H4K20me3 and KMT5C, the major methyltransferase for H4K20me3, occurs commonly in multiple types of cancer but the mechanisms surrounding how they contribute to shaping the epigenomic landscape remains unclear. Here, we show that KMT5C is involved in non-canonical deposition of H4K20me3, independent of H3K9me3, which was previously recognized as a prerequisite for H4K20me3. This novel subtype of H4K20me3 lacks canonical repressive epigenetic signatures and instead overlaps with multiple activating marks. These activating modifications likely contribute to the dynamic changes in transcript levels upon loss of H4K20me3. The mechanism involved in recruiting KMT5C to these loci is independent of HP1, the factor reported to be involved in recruitment of KMT5C to heterochromatin marked with H3K9me3. Instead, biochemical analyses revealed ZNF280C to be a novel interacting partner of KMT5C, with ZNF280C localizing specifically at H3K9me3-/H4K20me3+ sites. Together, these results suggest a novel, non-canonical function of KMT5C-H4K20me3 that protects vulnerable regions of the genome from uncontrolled expression.

Activation of the CMG (CDC45-MCM-GINS) helicase by MCM10 is a central unresolved step in DNA replication. DNA is melted within a dimeric CMG complex and one strand is expelled from each topologically closed MCM ring. How MCM10 drives this process is unclear owing to a lack of structural information. Here, by determining structures of yeast CMG-Mcm10 complexes, and of human CMG-Pol {varepsilon} dimers assembled by DONSON and bound to MCM10 and the helicase activator RECQL4, we reveal a conserved mechanism of CMG helicase activation in eukaryotes. MCM10 targets CMG dimers through highly conserved and species-specific interactions, that in human also involve RECQL4. Our data indicate this arrangement allows MCM10 to stimulate DNA unwinding by CMG and to utilise the associated conformational changes to drive single-stranded DNA ejection between MCM2 and MCM5. This mechanism provides an explanation for synchronized activation of two CMG helicases at origins of bidirectional replication.

The chromatin reader Rhino (Rhi) is an HP1-paralog and master regulator of piRNA biogenesis in Drosophila that drives the transcription of piRNA precursors. While Rhi binds the heterochromatic mark H3K9me3, this interaction is insufficient to explain its specific occupancy, as Rhi is excluded from the majority of H3K9me3-enriched loci. Instead, we find that Rhi recruitment is orchestrated by several competing pathways, including the piRNA-guided protein Panoramix (Panx) and the DNA-binding protein Kipferl (Kipf). We demonstrate that Panx functions as a piRNA-guided modular scaffold that directs Rhi to its targets through a dual-mode mechanism: its N-terminus recruits the H3K9 methyltransferase machinery, while its C-terminus directly binds the Rhi chromodomain. While H3K9me3 deposition provides a necessary foundation, it acts in synergy with the direct Panx-Rhi physical bridge to drive robust Rhi occupancy. Furthermore, Rhi recruitment is amplified by the cytoplasmic inheritance of maternal piRNAs, forming a transgenerational feed-forward loop. Our results reveal that the piRNA pathway imparts sequence-specificity to the H3K9me3 code, utilizing a direct physical bridge to program the genomic distribution of the chromatin reader Rhi.

In animals, plants, and some fungi, Polycomb Repressive Complex 2 (PRC2) catalyzes trimethylation of histone H3 lysine 27 (H3K27me3) to establish transcriptionally repressed chromatin. Here, we identify the histone acetyltransferase RTT109 as a key regulator of PRC2-repressed domains in the model fungus Neurospora crassa. Although RTT109 interacts with the VPS75 homolog Nucleosome Assembly Factor 2 (NAF-2), we show that proper structure and function of PRC2-methylated chromatin require RTT109 catalytic activity but are independent of NAF-2 and H3K56 acetylation. We further demonstrate that H3K27me3 can be stably propagated over multiple rounds of mitosis in the absence of sequence-specific PRC2 targeting, and that RTT109 is essential for maintenance of the repressed state. These findings uncover a replication-linked mechanism for epigenetic memory and establish RTT109 as a key regulator of Polycomb-mediated chromatin inheritance.

Smith-Kingsmore syndrome (SKS) is a rare neurodevelopmental disorder caused by gain-of-function mutations in MTOR, yet whether these mutations phenocopy TSC2 loss or establish a distinct signaling state remains unclear. Using quantitative proteomics, phosphoproteomics, and transcriptomics in isogenic cell models of SKS (MTOR{Delta}4aa), TSC2 loss (TSC2-/-), and wild-type controls under glucose depletion and refeeding, we find that MTOR{Delta}4aa and TSC2-/- cells occupy fundamentally distinct regulatory states. TSC2-/- cells exhibit broad anabolic remodeling and a transcriptional program dominated by NF-{kappa}B- and STAT-driven inflammatory responses. MTOR{Delta}4aa cells instead display enrichment of nuclear and RNA processing programs, E2F/MYC-driven transcription, and a constrained proteomic dynamic range across nutrient states. Phosphoproteomic analysis of MTOR{Delta}4aa reveals rerouting of nutrient-responsive signaling toward MAPK/ERK- and Ca2+/CaMK-dependent pathways with limited canonical mTORC1/S6K1 engagement. These findings establish SKS as a signaling rewiring disorder distinct from classical mTORC1 hyperactivation, with implications for therapeutic targeting.

The ATR-enforced S/G2 checkpoint activates during DNA replication to restrain CDK1-dependent phosphorylation of FOXM1 and subsequent transactivation of the G2/M gene network until the end of S phase. However, the extent to which this checkpoint ensures the completion of DNA replication and whether it safeguards genomic integrity has remained unknown. Here, we induce S/G2 checkpoint failure throughout S phase in non-malignant human epithelial cells using multiple ATR pathway inhibitors. Consequently, the mitotic kinase complex cyclin B1-CDK1 prematurely shuts-down the DNA replication program, preventing the completion of genome duplication. In turn, this leads to the retention of inactive replisomes on chromatin and unfired origins into the G2 phase, which induce subsequent accumulation of pan-nuclear {gamma}H2AX and mitotic failure. Collectively, these findings indicate the S/G2 checkpoint ensures replication completion and genome stability.

The nonfunctional rRNA decay (NRD) pathway eliminates defective ribosomes to maintain protein synthesis integrity. Although the Mms1-Rtt101 E3 ligase is known to trigger 25S NRD to clear defective 60S subunits, the specific molecular marks and targets it recognizes remain unknown. Here, we demonstrate that the late-stage maturation factor Reh1 functions as a specific molecular sensor for these defects. While Reh1 is normally displaced from the polypeptide exit tunnel (PET) during successful translation initiation, it is persistently retained on nonfunctional 80S ribosomes incapable of peptide bond formation. This prolonged retention, driven by the absence of a nascent peptide, provides a physical mark that recruits the Mms1 complex via Reh1s N-terminal domain, triggering site-specific ubiquitination of ribosomal protein Rpl19 (uL6). Our findings reveal that the cell repurposes a maturation factor as a sentinel to monitor translation competence, achieving robust detection of diverse ribosomal and maturation defects through a single molecular pathway.

Musashi-2 (MSI2) is an RNA-binding protein implicated in stem cell regulation and cancer, yet reports of its regulatory activity span translational activation, repression, and effects on mRNA stability, sometimes within the same cellular context. The basis for this diversity has remained unclear. Here, we identify alternative splicing as a determinant of MSI2 regulatory activity, acting through isoform-specific subcellular localization. Using a tethered reporter assay, we show that the canonical MSI2-328 isoform promotes translation without changing mRNA abundance. Truncation and mutation analysis identify a 40-amino-acid region (residues 194-234) as necessary and sufficient for cytoplasmic localization and necessary for translational activation. In contrast, the alternatively spliced MSI2-324 isoform localizes predominantly to the nucleus and fails to promote translation. We map this difference to an 18-amino-acid sequence introduced by an alternative 3 splice acceptor in exon 12; this sequence is sufficient to direct nuclear localization, and its removal restores MSI2-328-like cytoplasmic localization and translational activation. Consistent with these compartmental differences, the two isoforms associate with distinct protein networks, MSI2-328 with translation factors and ribosomal proteins, and MSI2-324 with chromatin and pre-mRNA processing factors. These isoform-specific activities are conserved across cell types, and the relative abundance of MSI2 isoforms shifts toward MSI2-324 in several cancers. Altogether, alternative splicing controls MSI2 subcellular localization, interaction networks, and regulatory output, providing a mechanistic framework for the context-dependent roles of MSI2 in gene regulation.

The insulin-like growth factor 2 mRNA-binding proteins (IGF2BP1-3) are oncofetal RNA regulators that control translation, stability, and localization of several transcripts, yet display paralog-specific functions despite high structural similarity. Each paralog contains six RNA-binding domains (two RRMs and four KH domains) linked by intrinsically disordered segments. mTORC2 phosphorylates IGF2BP1 and IGF2BP3 at a single conserved serine within the disordered linker between the RRM2 and KH1 domains, a modification required for proper regulation of mRNA translational fate. Pairing site-specific phosphoserine incorporation with structural and biophysical interrogations, we show that this phosphorylation acts as a configurational switch that reorganizes long-range arrangements of RNA-binding domains and linkers without altering the secondary structure, and with only modest effects on RNA-binding affinity. Critically, pSer-driven rearrangements occur both in the RNA-free state and upon RNA engagement, and the resulting architectures differ markedly between IGF2BP1 and IGF2BP3 despite >70% sequence identity. These paralog-specific, phosphorylation-dependent configurational landscapes likely underlie differences in mRNA recognition modes and functional outcomes. Our work identifies a post-translational mechanism that tunes IGF2BP paralog dynamics across free and RNA-bound states to program target mRNA selection, processing, and translational fate.

The INO80 chromatin-remodeling complex is a multi-subunit regulator of DNA-templated processes, yet the mechanisms that control remodeler function in vivo are not completely known. In this study, we report that the Ies6 subunit of the INO80 complex encodes a prion-like domain (PLD) within a larger region of predicted disorder. After transient inducible overexpression, both full-length Ies6 and the PLD domain alone aggregate in a manner that evades proteasome-mediated degradation, suggestive of prion-like behavior. Cytosolic aggregates are also visible with fluorescent microscopy following expression of the PLD alone. Loss of the protein chaperone Hsp70 increases Ies6 aggregation. In addition, deletion of ARP5, another INO80 subunit and binding partner of Ies6, also results in elevated protein aggregation. Finally, transcriptome analysis indicates that loss of PLD-mediated aggregation alters the expression of metabolic stress-responsive genes, including glucose-starvation and respiratory programs, even in glucose-replete conditions. Together, these findings support a model in which Ies6 couples the INO80 complex to metabolic gene regulation via prion-like behavior, providing a potential new mechanism for tuning chromatin-based metabolic adaptation.