Biology subjects

Singhal, A.

Publications and source records attributed to Singhal, A..

At least 19 recordsLinked to original sources

bioRxiv2026

The basal cell state maintains pancreatic cancers by controlling an immunosuppressive circuit

Intra-tumoral heterogeneity is a cardinal feature of solid tumors, yet how distinct cancer cell states functionally contribute to malignant and stromal diversity in situ remains poorly understood. Using mouse models to lineage-trace or genetically ablate the two predominant cancer cell states in autochthonous pancreatic ductal adenocarcinoma (PDAC), we discover that basal cancer cells are highly plastic, whereas classical cancer cells exhibit limited plasticity. Strikingly, ablation of the basal, but not the classical, state induced rapid and durable tumor collapse, driven by loss of immunosuppressive cancer-associated fibroblasts, macrophage repolarization, and reprogramming of the tumor cytokine milieu, culminating in tumor destruction by cytotoxic lymphocytes. Knockout of a single cytokine, GM-CSF, specifically in basal cells recapitulated macrophage repolarization and lymphocyte recruitment observed upon basal state ablation and shrank tumors. These results reveal the basal cell state controls an immunosuppressive cell circuit critical for PDAC maintenance, motivating therapeutic targeting of the basal cells.

cancer biology↗

bioRxiv2026

NR4A1 limits CD8⁺ T Cell effector responses and protection in tuberculosis

During Mycobacterium tuberculosis (Mtb) infection, CD8+ T cells exhibit dysfunction with impaired cytotoxicity and limited localization to granuloma cores. Using knockout mice, adoptive-transfer models and validation in macaque and human datasets, we identified the nuclear receptor NR4A1 as a key restrainer of CD8+ T cell immunity in tuberculosis (TB). Mtb-infected Nr4a1-/- mice displayed reduced bacterial burden, attenuated pathology, higher lung CD8+/CD4+ T cell ratios, and enhanced CD8+ T cell effector functions. Bulk and single-cell RNA sequencing revealed suppression of gene expression program linked with exhaustion, and expansion of Nkg7+ and Granzyme+ cytotoxic CD8+ T cell subsets in Nr4a1-/- mice. Spatial analyses demonstrated increased infiltration of Nkg7+ activated CD8+ T cells in Nr4a1-/- lesions. ChIP-qPCR showed NR4A1 binding to Nkg7 promoter, and Nkg7 knockdown abrogated the enhanced cytotoxicity of Nr4a1-/- CD8+ T cells. Pharmacologic inhibition of NR4A1 reduced Mtb burden and pathology, and restored Nkg7 expression and CD8+ T cell infiltration in the lung. Together, these findings identify NR4A1 as a negative regulator of CD8+ T cell-mediated immunity in TB and suggest the NR4A1-NKG7 axis as a novel host-directed therapeutic target. A one-sentence summary of your paperNR4A1 suppresses CD8+ T cell infiltration and cytotoxicity in TB lesions, and its inhibition enhances host resistance to Mtb infection.

immunology↗

bioRxiv2025

Neonatal BCG Vaccination Engages the Vasculature to Elicit γδ T Cell-Mediated Protection against Tuberculosis

The Bacillus Calmette-Guerin (BCG) vaccine remains the only approved vaccine against tuber-culosis (TB). Although its efficacy against pulmonary TB in adults is limited, BCG provides re-markable protection against miliary TB when administered during infancy. Despite more than 100 million infants worldwide receiving BCG annually, the mechanisms underlying its neonatal protective effects remain poorly defined. Here, we demonstrate that subcutaneous neonatal BCG vaccination (BCG-sc) induces a marked expansion of {gamma}{delta} T cells producing IL-17 and IL-22, which mediated protection against subsequent Mycobacterium tuberculosis (Mtb) experimental infection. A similar expansion of {gamma}{delta} T cells was observed in a longitudinal cohort of infants, from birth to three months of infants followed after intradermal BCG vaccination. Mechanistical-ly, BCG-mediated protection in neonates was linked to its early vascular dissemination through the distinct structure of neonatal skin, resembling the protective effects of intravenous BCG in adults. Moreover, neonatal BCG-sc vaccination generated a distinct BCG-induced microbiome signature, characterized by enrichment of Prevotellaceae, Tannerellaceae, and Bifidobacteriaceae, which was associated with protection. Together, these findings identify {gamma}{delta} T cells as key mediators of early-life BCG-induced immunity and highlight the role of the gut-lung axis in long-term protection against TB from infancy into adulthood.

immunology↗

bioRxiv2025

Odyssey: reconstructing evolution through emergent consensus in the global proteome

We present Odyssey, a family of multimodal protein language models for sequence and structure generation, protein editing and design. We scale Odyssey to more than 102 billion parameters, trained over 1.1 x 1023 FLOPs. The Odyssey architecture uses context modalities, categorized as structural cues, semantic descriptions, and orthologous group metadata, and comprises two main components: a finite scalar quantizer for tokenizing continuous atomic coordinates, and a transformer stack for multimodal representation learning. Odyssey is trained via discrete diffusion, and characterizes the generative process as a time-dependent unmasking procedure. The finite scalar quantizer and transformer stack leverage the consensus mechanism, a replacement for attention that uses an iterative propagation scheme informed by local agreements between residues. Across various benchmarks, Odyssey achieves landmark performance for protein generation and protein structure discretization. Our empirical findings are supported by theoretical analysis.

synthetic biology↗

bioRxiv2025

PU.1 Shapes Host Epigenetic Responses to Mycobacterium tuberculosis and Represents a Target for Host Directed Therapy

Mycobacterium tuberculosis (Mtb) infection induces widespread epigenetic changes in monocytes and macrophages. To characterize the critical factor responsible for Mtb-induced epigenetic responses, we performed an integrative analyses of chromatin modification (H3K27ac), transcription factor binding, and gene expression in human monocytes and macrophages. Our data identified PU.1 (SPI1) as a key transcriptional regulator to be upregulated and bound to gene promoters in response to Mtb. PU.1 enrichment was associated with enhanced proinflammatory and anti-apoptotic gene programs. PU.1 expression was also elevated in the lung tissues from Mtb-infected macaques and tuberculosis patients. PU.1 knockdown enhanced human macrophage apoptosis, dampened inflammation and reduced bacterial survival, suggesting its functional role in supporting Mtb infection. Pharmacological inhibition of PU.1 replicated the effects of knockdown, restricting Mtb growth without cytotoxicity. These findings identify PU.1 as a central node in the host epigenetic response to Mtb and a candidate for host-directed therapeutic targeting in tuberculosis.

immunology↗

bioRxiv2025

Translating clinical gene sequencing into a foundational representation of tumor subtype

While gene sequencing is routine in cancer care, translating sequences into treatment decisions remains a challenge. Here we introduce MutationProjector, an AI foundation model that transforms tumor mutation profiles into a compact representation of cancer subtype, with broad implications for diagnosis and therapy. MutationProjector is pre-trained by integrating genomic alterations from >30,000 tumors with extensive molecular knowledge, yielding a model that accurately reconstructs held-out genetic profiles (demonstrating strong generalization) and determines subtype representations from altered molecular pathways (enabling model interpretability). We evaluate MutationProjector in independent tasks related to prediction of immunotherapy response, prediction of chemotherapy response, and classification of metastasis, recording leading performance in all areas. Each task identifies key biomarkers of interest, including KMT2A and KRAS-STK11 alterations which govern immunotherapy response.

systems biology↗

bioRxiv2025

Inflammasomes and DNA Damage Orchestrate Divergent Pyroptotic Fates in Neutrophils

The understanding of pyroptotic cell death and its mechanistic insights in neutrophils remains less explored and ambiguous. This study analyzes neutrophil pyroptotic responses under different conditions and dissects distinct pyroptosis-associated events, including IL-1{beta} release and cell death. We decipher the signalling pathways underlying these responses and distinguish them from other cell death mechanisms. Interestingly, we observe IL-1{beta} release and enhanced survival in neutrophils in response to LPS-primed ATP-treatment, in contrast to a combination of IL-1{beta} release with cell death in macrophages. While LPS-primed nigericin-treated neutrophils exhibit IL-1{beta} release and cell death, characterized by nuclear rounding, cell swelling/ ballooning, plasma membrane pore formation, and subsequent cell rupture, confirming the occurrence of pyroptotic cell death. While nigericin alone triggers cytokine uncoupled pyroptosis. Intriguingly, these phenomena do not induce under other death programs, including apoptosis, NETosis. This provides opportunity to unravel the regulation of these pyroptotic responses in neutrophils. Data observed reveal the role of NLRP3 and context-dependent caspase -1 & 11 in IL-1{beta} secretion. While, DNA damage and caspase-7 & 9 regulate pyroptotic death. Intriguingly, forced DNA damage by ATM kinase inhibitor mitigated inflammasome activation and IL-1{beta} release, while spur death. Furthermore, this study identifies perinuclear actomyosin forces driving nuclear rounding and pyroptotic death. Both murine neutrophils exposed to bacteria and human neutrophils treated with nigericin exhibit these pyroptotic processes, highlighting their broad relevance. This study depicts decision whether to secrete cytokines or undergo pyroptotic cell death emphasizing the regulatory role of DNA damage-cytoskeletal axis beyond inflammasome activation. Moreover, LPS and bacteria induced acute lung injury in mice displays nuclear rounding presenting pyroptotic neutrophils and enhanced NLRP3, Caspase-11 activation, and IL-1{beta} release. Together, this study defines intriguing crosstalk of NLRP3, caspases, DNA damage, and actomyosin forces that orchestrate divergent inflammatory fates, potentially leading to opportunities for targeted strategies for combating inflammation. HIGHLIGHTSO_LINeutrophils undergo pyroptotic cell death with nigericin and bacteria, but not with ATP. C_LIO_LILPS priming is essential for IL-1{beta} secretion, while dispensable for cell swelling/ballooning and death. C_LIO_LINLRP3 and Caspase 1/11 regulate IL-1{beta} secretion, while DNA damage and Caspase-7/9 control pyroptotic cell death. C_LIO_LIPerinuclear actomyosin signalling regulates nuclear rounding during pyroptotic cell death. C_LI GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=174 HEIGHT=200 SRC="FIGDIR/small/673694v1_ufig1.gif" ALT="Figure 1"> View larger version (43K): org.highwire.dtl.DTLVardef@102da3forg.highwire.dtl.DTLVardef@46838borg.highwire.dtl.DTLVardef@16648faorg.highwire.dtl.DTLVardef@413bc2_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2025

Rapid cognitive testing predicts real-world driving risk in commercial and medically at-risk drivers

Road safety is a major public and occupational health issue. Safe driving requires numerous cognitive and sensorimotor skills, and past literature suggests that cognitive testing can predict safe or unsafe driving in both healthy and medically at-risk drivers. However, such testing is often time-consuming and inaccessible. In this study, we designed a modified version of the Trail Making Test (TMT) which can be completed on a smartphone in approximately 5 minutes. We recruited 4405 commercially-licensed drivers and 314 medically at-risk drivers to complete the TMT, plus an on-road test of their driving abilities. We then trained and tested a logistic regression model using 50-50 splits on each dataset. The results of the model showed that the longer it took drivers in both groups to complete the TMT, the more likely they were to fail the on-road driving test. Accuracy for the commercial group was 83.8%, with a positive predictive value (PPV) of 34.4% and a negative predictive value (NPV) of 85.3%. Accuracy for the medically at-risk group was 63.1%, with a PPV of 55.8% and an NPV of 65.8%. Overall accuracy was 82.5%, with a PPV of 43.0% and an NPV of 84.3%. Log-transformed reaction time to targets was significantly associated with on-road failure in both driving groups. The results of this study suggest that a rapid and accessible version of the TMT can predict unsafe driving with comparable accuracy to more time-consuming and administratively burdensome means of testing.

neuroscience↗

bioRxiv2025

Telomerase reverse transcriptase is required for resistance to mycobacterial infection

Age is an important risk factor for infections such as tuberculosis (TB). Telomerase is expressed in immune cells yet leukocyte telomere length declines during ageing suggesting an age-dependent loss of telomerase activity in the immune system. Leukocyte telomere length has been correlated with worse outcomes in TB patients, however the mechanisms linking telomere biology to TB susceptibility and response to therapy are unexplored. Here we use the zebrafish-Mycobacterium marinum model to investigate the role of telomerase in TB resistance. We find depletion and inhibition of Tert, the catalytic subunit of telomerase, increases bacterial burden in zebrafish embryos. The Tert depletion infection susceptibility phenotype could not be rescued by p53 or STING depletion suggesting a non-canonical role for Tert in controlling mycobacterial infection. Consistent with a previously described role for Tert in developmental hematopoiesis, we find Tert is necessary for demand-driven emergency myelopoiesis to support containment of extended mycobacterial infection. Our findings establish a previously undescribed role for host telomerase in supporting infection demand-driven hematopoiesis to control infection.

immunology↗

bioRxiv2025

Primary tuberculous mycobacterial granulomas provide a niche for superinfecting Mycobacterium abscessus

Prior and concurrent tuberculosis infection are among the most important susceptibility factors for nontuberculous mycobacterial infection in Asia. Here we model this process in zebrafish with a primary Mycobacterium marinum infection followed by a secondary M. abscessus infection. We demonstrate preferential growth of secondary M. abscessus infection inside primary M. marinum granulomas. Granuloma-resident secondary M. abscessus is protected from macrophage-mediated immune control and antibiotic therapy. Successful colonization is driven by expansion of M. abscessus feeding on caseum produced by the primary M. marinum ESX-1 virulence program in a nutritionally separate niche from M. marinum. Our data suggest tuberculous granulomas may provide a long-lasting niche for the growth of the opportunistic pathogen Mycobacterium abscessus.

microbiology↗

bioRxiv2025

Post activation potentiation is greater in human triceps brachii versus triceps surae muscles

Introduction/AimsPost activation potentiation (PAP) is an inherent characteristic of muscle wherein an increase in twitch force is observed after voluntary activation. This phenomenon is believed to be largely due to phosphorylation of the regulatory light chain of myosin. In rodents and other species, PAP occurs predominantly or exclusively in fast twitch muscles. However, it has been suggested that in humans PAP occurs more or less independently of muscle fiber type. Methods18 healthy men and women (27{+/-}8 y) underwent an electrical muscle stimulation protocol during which two sets of four twitches were elicited both pre and post 6 s maximal voluntary contractions of both the triceps surae (60-70% slow twitch) and triceps brachii (60-70% fast twitch) muscles. ResultsUnpotentiated peak twitch torque (PTT) was higher in the larger triceps surae vs. the smaller triceps brachii (i.e., 13.4{+/-}5.3 vs. 3.4{+/-}2.1 Nm; P = 8.22 x 10-13), but time to peak torque was shorter (i.e., 84{+/-}7 vs. 132{+/-}14 ms; P = 6.92 x 10-14) and the relative rate of torque development (RTD) was greater in the triceps brachii (2294{+/-}257 vs. 1425{+/-}102 %/s; P = 1.93 x 10-11). PAP increased PTT and the absolute RTD by 172{+/-}124% and 240{+/-}170% in triceps brachii versus only 20{+/-}20% and 31{+/-}24% in triceps surae, respectively (P = 1.26 x 10-4 and 1.30 x 10-4, respectively). However, PAP-induced changes in half-relaxation time and the relative rate of relaxation did not differ between the two muscle groups. DiscussionWe conclude that PAP influences contraction but not relaxation of human muscle in a fiber type dependent manner.

physiology↗

bioRxiv2025

Proviruses in CD4+ T cells reactive to autologous antigens contribute to nonsuppressible HIV-1 viremia

Antiretroviral therapy (ART) halts HIV-1 replication, reducing plasma virus levels to below the limit of detection, but it is not curative due to a reservoir of latently infected CD4+ T cells. In some people living with HIV-1 (PLWH), plasma HIV-1 RNA becomes persistently detectable despite optimal ART. This nonsuppressible viremia (NSV) is characterized by identical, non-evolving HIV-1 RNA variants expressed from infected CD4+ T cell clones. The mechanisms driving persistent virus production from a specific population of infected cells are poorly understood. We hypothesized that proviruses in cells responding to chronic immunologic stimuli, including self-associated antigens, may drive viral gene expression and NSV. Here, we demonstrate that stimulation of CD4+ T cells with autologous cell lysates induces virus production in an MHC-II-dependent manner. In 7 of 8 participants with NSV, we recovered viral RNA released ex vivo in response to autologous cell lysates that matched plasma virus. This process involves both defective and replication-competent proviruses residing in conventional T cells, and is also observed in PLWH with undetectable viremia. These findings suggest that recognition of self-associated antigens is an important cause of HIV-1 reservoir expression, which can contribute to persistent systemic inflammation and potential rebound upon ART interruption. One sentence summaryHIV-1 viremia not suppressed by effective ART can be caused by proviruses in CD4+ T cells reactive to autologous antigens.

immunology↗

bioRxiv2025

Superinfection with intact HIV-1 results in conditional replication of defective proviruses and nonsuppressible viremia in people living with HIV-1

During replication of some RNA viruses, defective particles can spontaneously arise and interfere with wild-type (WT) virus replication. Recently, engineered versions of these defective interfering particles (DIPs) have been proposed as an HIV-1 therapeutic. However, DIPs have yet to be reported in people with HIV-1 (PWH). Here, we find DIPs in PWH who have a rare, polyclonal form of non-suppressible viremia (NSV). While antiretroviral therapy (ART) rapidly reduces viremia to undetectable levels, some individuals experience sustained viremia due to virus production from cell clones harboring intact or defective proviruses. We characterized the source of NSV in two PWH who never reached undetectable viral load despite ART adherence. Remarkably, in each participant, we found a diverse set of defective viral genomes all sharing the same fatal deletions. We found that this paradoxical accumulation of mutations by viruses with fatal defects was driven by superinfection with intact viruses, resulting in mobilization of defective genomes and accumulation of additional mutations during untreated infection. We show that these defective proviruses interfere with WT virus replication, conditionally replicate, and, in one case, have an R0 > 1, enabling in vivo spread. Despite this, clinical outcomes show no evidence of a beneficial effect of these DIPs.

microbiology↗

bioRxiv2025

Phenotypic pleiotropy of missense variants in human B cell-confinement receptor P2RY8

Missense variants can have pleiotropic effects on protein function and predicting these effects can be difficult. We performed near-saturation deep mutational scanning of P2RY8, a G-protein-coupled receptor that promotes germinal center B cell confinement. We assayed the effect of each variant on surface expression, migration, and proliferation. We delineated variants that affected both expression and function, affected function independently of expression, and discrepantly affected migration and proliferation. We also used cryo-electron microscopy to determine the structure of activated, ligand-bound P2RY8, providing structural insights into the effects of variants on ligand binding and signal transmission. We applied the deep mutational scanning results to both improve computational variant effect predictions and to characterize the phenotype of germline variants and lymphoma-associated variants. Together, our results demonstrate the power of integrating deep mutational scanning, structure determination, and in silico prediction to advance the understanding of a receptor important in human health.

genomics↗

bioRxiv2025

Impaired Macrophage DNase Secretion Promotes Neutrophil Extracellular Trap Mediated Defective Efferocytosis in Atherosclerosis

Neutrophil extracellular traps (NETs) drive atherosclerosis progression and are associated with adverse clinical outcomes like myocardial infarction and stroke. While the triggers of NETosis in atherosclerotic plaque are well-characterized, the mechanisms underlying NET degradation and clearance remain unclear. Moreover, the impact of impaired NET clearance on atherosclerosis progression have not been elucidated. Here we show that macrophages are critical for the release of DNases, which degrade NETs. We identified endoplasmic reticulum (ER) stress mediated activation of PERK-ATF4 pathway as a key driver of impaired macrophage DNase secretion, leading to delayed NET clearance and their persistence. Elevated NET levels trigger cleavage of the efferocytosis receptor Mertk leading to defective macrophage efferocytosis and exacerbation of plaque necrosis. Human atherosclerotic plaques and Ldlr-/- mice treated with ISRIB, a PERK inhibitor, show enhanced DNase secretion and clearance of NETs. Together, the identification of key mechanisms of NET clearance in atherosclerosis offers new therapeutic strategies to stabilize plaques.

pathology↗

bioRxiv2025

Widespread 3D genome reorganization precedes programmed DNA rearrangement in Oxytricha trifallax

Genome organization recapitulates function, yet ciliates like Oxytricha trifallax possess highly-specialized germline genomes, which are largely transcriptionally silent. During post-zygotic development, Oxytrichas germline undergoes large-scale genome editing, rearranging precursor genome elements into a transcriptionally-active genome with thousands of gene-sized nanochromosomes. Transgenerationally-inherited RNAs, derived from the parental somatic genome, program the retention and reordering of germline fragments. Retained and eliminated DNA must be distinguished and processed separately, but the role of chromatin organization in this process is unknown. We developed tools for studying Oxytricha nuclei and apply them to map the 3D organization of precursor and developmental states using Hi-C. We find that the precursor conformation primes the germline for development, while a massive spatial reorganization during development differentiates retained from eliminated regions before DNA rearrangement. Further experiments suggest a role for RNA-DNA interactions and chromatin remodeling in this process, implying a critical role for 3D architecture in programmed genome rearrangement.

genomics↗

bioRxiv2024

Sca-1 expression depicts pro-inflammatory murine neutrophils under steady state and pathological conditions

Neutrophils play a crucial role in various pathophysiological conditions, yet targeting them for therapeutic intervention has been discouraged due to the associated risk of infections. Thus, identification of neutrophil subsets and their involvement in inflammatory conditions is warranted for targeted therapeutic strategies. This study, through screening of surface proteins on neutrophils isolated from different tissue microenvironments, identified a distinct neutrophil subset, CD11b+Ly6G+Sca1+ neutrophils, expressing Stem cell antigen-1 (Sca-1). Interestingly, these Sca1pos neutrophils were more abundant in the liver than BM, blood, and lungs. Further analysis revealed that Sca1pos neutrophils are mature and activated with enhanced effector functions, including superoxide generation, phagocytosis, degranulation, and NETosis. Tracing studies demonstrated ageing-independent characteristics of Sca1pos neutrophils. Remarkably, Sca1pos pro-inflammatory neutrophils promote T cell proliferation through ROS, while inhibition of Sca-1 restores T cell proliferation and ROS generation. Intriguingly, inflammatory as well as metabolic cues induce the transition of conventional neutrophils (Sca1neg) to Sca1pos neutrophils and differentiation of progenitors (granulocyte monocyte progenitors, GMPs) into Sca1pos neutrophils. Furthermore, in vivo models of acute inflammation, peritonitis, and chronic inflammatory condition, non-alcoholic steatohepatitis (NASH), exhibit an increase of Sca1pos neutrophils at inflammatory sites, while the pharmacological approach using NAC specifically mitigates the expansion of these pro-inflammatory neutrophils. Collectively, our findings unveil a novel subset of Sca1pos neutrophils with implications for inflammation. Significance StatementNeutrophilic inflammation remains the leading driver in infectious and inflammatory diseases. Targeting neutrophil populations remained un-recommended due to hampering the immunological functions of neutrophils. The heterogeneity of neutrophils provides the perspective to target altered neutrophil subsets, but subtle changes defining neutrophil subsets make it complex and ambiguous. Our study identified abundant expression of Sca1on distinct neutrophils under steady state and inflammation. Thus, we reported previously undefined Sca1pos pro-inflammatory neutrophil subsets and elucidated their regulation. This study further established their involvement in acute and chronic inflammatory conditions. This understanding may further pave the way toward targeting specific neutrophil subsets in pathologies characterized by neutrophilic inflammation. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=144 SRC="FIGDIR/small/613221v1_ufig1.gif" ALT="Figure 1"> View larger version (42K): org.highwire.dtl.DTLVardef@62f3eaorg.highwire.dtl.DTLVardef@7baed3org.highwire.dtl.DTLVardef@12da63org.highwire.dtl.DTLVardef@1bfcce9_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LICD11b+Ly6G+Sca1+ neutrophil subset identified with <1% presence in BM and >40% frequency in the liver. C_LIO_LIThese neutrophils are mature and activated, demonstrating enhanced effector functions. C_LIO_LISca1pos neutrophils promote T cell proliferation and display pro-inflammatory characteristics. C_LIO_LIConventional Sca1neg neutrophils transition into Sca1pos neutrophils in response to inflammatory signals, while progenitors undergo differentiation. C_LIO_LIBoth acute and chronic inflammatory models show the expansion of CD11b+Ly6G+Sca1+ neutrophils. C_LI

immunology↗

bioRxiv2024

Cleavage region organizes the structural architecture of the B2 SINE ribozyme

The SINE-encoded B2 retrotransposon is an RNA Polymerase III transcript that gets upregulated during various cellular stress responses. The B2 noncoding RNA can directly inhibit RNA Polymerase II, leading to a significant downregulation of transcripts during stress. Our recent findings have shown that B2 is a self-cleaving epigenetic ribozyme and that cleavage can be induced by interactions with epigenetic factors, co-regulating its function across distinct chromatin-binding target loci. Here, by integrating RNA chemical probing, small angle X-ray scattering, and 3D motif modeling, we determine structural ensemble-to-function relations for the B2 SINE ribozyme RNA. Perturbations of the RNA suggest that the B2 SINE ribozyme has a well-defined secondary structure and dynamic tertiary structure that both critically depend on the presence of the active site of cleavage. In an RNA engineering approach, we examine the effect of point mutations, deletions of the main cleavage site and deletions of the cleavage domain on the structural ensemble of the RNA. By combining this with functional data, we obtain relations of structural ensembles to various functional states. This perturbative approach serves as a template to unravel the relation of structural ensembles to functional states for other ncRNA and mRNA systems.

biophysics↗