bioRxiv : the preprint server for biology最新文献

{"title":"Conformational biosensors delineate endosomal G protein regulation by GPCRs.","authors":"Brian Wysolmerski, Emily E Blythe, Mark von Zastrow","doi":"10.1101/2025.05.12.653522","DOIUrl":"10.1101/2025.05.12.653522","url":null,"abstract":"<p><p>Many GPCRs trigger a second phase of G protein-coupled signaling from endosomes after initiating signaling from the plasma membrane. This inherently requires receptors to increase the concentration of active-state G proteins on the endosome membrane, but how this is achieved remains incompletely understood. We addressed this question by dissecting the regulation of G protein abundance and activity on endosomes following activation of several G _s -coupled GPCRs-the β2-adrenergic receptor, the VIP-1 receptor, and the adenosine 2b receptor-that are natively co-expressed and differ in their ability to internalize after activation. We first verify GPCR-triggered redistribution of Gα _s from the plasma membrane to a mixed population of intracellular membranes, including endosomes, that is both reversible after receptor inactivation and triggered irrespective of the ability of the GPCR to internalize. We next show that GPCRs trigger this redistribution process at native expression levels and describe a method, using conformational biosensors, to detect endosomal activation of endogenous Gα _s . Applying this method, we show that GPCR-mediated production of active-state Gα _s on endosomes depends on receptor endocytosis, whereas increasing the net amount of Gα _s on endosomes does not. Our results support a model for G _s regulation on endosomes mediated by two spatially separated receptor coupling events-one at the plasma membrane controlling endosomal G _s abundance and another at endosomes controlling G _s activity. Additionally, our results reveal location-bias in the selectivity of G protein activation on endosomes that is differentially programmed by GPCRs in a receptor-specific manner.</p>","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-06-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12132277/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144218202","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Cognitive reserve linked to network-specific brain-ventricle coupling modes.","authors":"Fulvia Francesca Campo, Elvira Brattico, Vânia Miguel, Vicente Magalhães, Salvatore Nigro, Benedetta Tafuri, Giancarlo Logroscino, Joana Cabral","doi":"10.1101/2025.01.04.631289","DOIUrl":"10.1101/2025.01.04.631289","url":null,"abstract":"<p><p>Despite showing significant impact in cognitive preservation, the relationship between brain activity captured with functional Magnetic Resonance Imaging (fMRI) in gray matter and ventricular cerebrospinal fluid dynamics remains poorly understood. We analyzed 599 fMRI scans from 163 elderly participants at rest with varying degrees of cognitive impairment employing a unified phase coupling analysis that breaks from convention by incorporating both tissue and ventricular signal fluctuations. This whole-brain approach identified distinct brain-ventricle coupling modes that differentiate between cognitive status groups and correlate with specific cognitive abilities. Beyond the previously reported anti-phase coupling between global brain signals and ventricles-which we confirm occurs more frequently in cognitively normal controls-our analysis method uncovered additional coupling modes where signals in specific brain networks temporarily align with ventricle signals. At the cortical level, these modes reveal patterns corresponding to known resting-state networks: one overlapping with the Default Mode Network occurs significantly less frequently in Alzheimer's Disease patients, while another revealing the Frontoparietal Network correlates positively with memory scores. Our findings demonstrate that different brain-ventricle coupling modes correlate with specific cognitive domains, with particular modes predicting memory, executive function, and visuospatial abilities. The coupling between signals in brain ventricles and established resting-state networks challenges our current understanding of functional network formation, suggesting an integral link with brain fluid motion. This reconceptualization of brain dynamics through the lens of fluid-tissue interactions establishes a fundamental physical basis for cognitive preservation, suggesting that therapeutic interventions targeting these interactions may prove more effective than approaches focused solely on cellular or molecular mechanisms.</p>","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-06-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11722378/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142974359","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Phospholipid Scramblases TMEM16F and Xkr8 mediate distinct features of Phosphatidylserine (PS) externalization and immune suppression to promote tumor growth.","authors":"Varsha Gadiyar, Rachael Pulica, Ahmed Aquib, James A Tranos, Christopher Varsanyi, Trevor Frederick, Ziren Wang, Luis Fernandez Almansa, Lawrence Gaspers, Mariana S De Lorenzo, Sergei V Kotenko, Sushil Tripathi, Roger W Howell, Alok Choudhary, David C Calianese, Raymond B Birge","doi":"10.1101/2025.04.17.649445","DOIUrl":"10.1101/2025.04.17.649445","url":null,"abstract":"<p><p>The phospholipid scramblases Xkr8 and TMEM16F externalize phosphatidylserine (PS) by distinct mechanisms. Xkr8, is activated by caspase-mediated proteolytic cleavage, and in synergy with inactivation of P4-ATPase flippases, results in the irreversible externalization of PS on apoptotic cells and an \"eat-me\" signal for efferocytosis. In contrast, TMEM16F is a calcium activated scramblase that reversibly externalizes PS on viable cells via the transient increase in intracellular calcium in live cells. The tumor microenvironment (TME) is abundant with exposed PS, resulting from prolonged oncogenic and metabolic stresses and high apoptotic indexes of tumors. Such chronic PS externalization in the TME has been linked to host immune evasion from interactions of PS with inhibitory PS receptors such as TAM and TIM receptors. Here, in an effort to better understand the contributions of apoptotic vs live cell PS-externalization to tumorigenesis and immune evasion, we employed an E0771 orthotopic breast cancer model and genetically ablated Xkr8 and TMEM16F using CRISPR/Cas9. While neither the knockout of Xkr8 nor TMEM16F showed defects in cell intrinsic properties related to proliferation, tumor-sphere formation, and growth factor signaling, both knockouts suppressed tumorigenicity in immune-competent mice, but not in NOD/SCID or RAG-KO immune-deficient strains. Mechanistically, Xkr8-KO tumors suppressed macrophage-mediated efferocytosis, and TMEM16F-KO suppressed ER stress/calcium-induced PS externalization. Our data support an emerging idea in immune-oncology that constitutive PS externalization, mediated by scramblase dysregulation on tumor cells, supports immune evasion in the tumor microenvironment. This links apoptosis/efferocytosis and oncogenic stress involving calcium dysregulation, contributing to PS-mediated immune escape and cancer progression.</p>","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-06-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12087989/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144103482","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Ligand binding represses bacterial histidine kinase activity by inhibiting its dimerization.","authors":"Gaurav D Sankhe, Jiawei Xing, Merissa Xiao, John Buglino, Huilin Li, Igor B Zhulin, Michael S Glickman","doi":"10.1101/2025.05.18.654591","DOIUrl":"10.1101/2025.05.18.654591","url":null,"abstract":"<p><p>Two component systems (TCS) mediate bacterial signal transduction in response to specific environmental conditions. The two components are the sensor kinase (SK), which senses the signal and autophosphorylates on a histidine residue, and a response regulator (RR), which is phosphorylated by the kinase and modifies gene expression. Despite intensive study, the mechanisms of signal sensing by sensor kinases are incompletely defined and the mechanisms by which SKs can sense multiple ligands are unclear. <i>Mycobacterium tuberculosis</i> PdtaS/PdtaR is a soluble TCS pair that participates in the Rip1 signal transduction cascade to control virulence by responding to copper and nitric oxide (NO). In contrast to paradigmatic ligand activated SKs, PdtaS is constitutively active without ligand and directly inhibited by Cu or NO, yet it remains unclear how such chemically diverse ligands are sensed. Here we show that PdtaS is a dimeric kinase that constitutively autophosphorylates in trans. Cu and NO both inhibit PdtaS phosphorylation by inhibiting dimerization. Phylogenetic analysis of the PdtaS family reveals conservation of the GAF/PAS dimer interface rather than the ligand binding pockets and mutations in the GAF dimer interface that alter dimerization impair multi-ligand sensing both in vitro and in <i>M. tuberculosis</i> cells. These results indicate that a single bacterial kinase can sense chemically diverse inputs through inhibition of dimerization dependent phosphorylation.</p>","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-06-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12132213/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144218345","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transcriptional Elongation-Associated RNA Processing Errors in Induced Cellular Growth Arrest.","authors":"Saeid Parast, Simai Wang, Marta Iwanaszko, Yue He, Deniz G Olgun, Sarah R Gold, Yuki Aoi, Jacob M Zeidner, Benjamin C Howard, William R Thakur, Vijay Ramani, Ali Shilatifard","doi":"10.1101/2025.06.23.660200","DOIUrl":"https://doi.org/10.1101/2025.06.23.660200","url":null,"abstract":"<p><p>Transcription elongation factors control post-initiation steps of gene expression by RNA polymerase II (RNAPII). We have established distinct mechanistic roles for the essential elongation factors PAF1, NELF, SPT5, SPT6, and the Super Elongaiton Complex (SEC) via acute depletion of each individually in auxin-inducible degron lines. Here, we leverage these degron lines to explore the regulatory intersection of transcription elongation control and pre-mRNA processing. Integrating long- and short-read RNA-seq data to quantify transcript isoform usage at single-molecule resolution, we identify elongation factor-specific RNA processing regulons including a cellular senescence-enriched regulon shared by NELF and SPT6. We then show that long-term depletion of NELF or SPT6 results in reversible growth arrest following early upregulation of a small group of genes, which include the senescence-associated genes CDKN1A (p21) and CCN2. We perform genetic suppressor screens that implicate the elongation factor Elongin A (ELOA) in NELF or SPT6 depletion-induced growth arrest. ELOA loss suppresses NELF depletion-induced pre-mRNA processing defects and the 3' extension of RNAPII occupancy past transcription end sites (TES) at genes induced by NELF depletion. ELOA also occupies TES-proximal regions under normal conditions, and acute ELOA depletion results in a loss of RNAPII processivity at the 3' end of genes, opposing the effects of NELF or SPT6 depletion. Finally, we demonstrate that genetic loss of ELOA confers a growth advantage to aging human primary dermal fibroblasts. These findings establish the existence of novel ELOA-dependent mechanisms regulating transcription maturation, and links these mechanisms to the complex phenomena of cellular senescence and aging.</p>","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-06-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12212439/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144546723","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Dual Molecular Identity of Vestibular Kinocilia: Bridging Structural and Functional Traits of Primary and Motile Cilia.","authors":"Zhenhang Xu, Amirrasoul Tavakoli, Samadhi Kulasooriya, Huizhan Liu, Shu Tu, Celia Bloom, Yi Li, Tirone D Johnson, Jian Zuo, Litao Tao, Bechara Kachar, David Z He","doi":"10.1101/2025.04.16.647417","DOIUrl":"https://doi.org/10.1101/2025.04.16.647417","url":null,"abstract":"<p><p>Vestibular hair cells (HCs) convert gravitational and head motion cues into neural signals through mechanotransduction, mediated by the hair bundle-a mechanically integrated organelle composed of stereocilia and a kinocilium. The kinocilium, a specialized form of primary cilium, remains incompletely defined in structure, molecular composition, and function. To elucidate its characteristics, we conducted single-cell RNA sequencing of adult vestibular and cochlear HCs, uncovering a selective enrichment of primary and motile cilia-associated genes in vestibular HCs, particularly those related to the axonemal repeat complex. This enrichment of orthologous axonemal-related genes was conserved in zebrafish and human vestibular HCs, indicating a shared molecular architecture. Immunostaining validated the expression of key motile cilia markers in vestibular kinocilia. Moreover, live imaging of bullfrog and mouse HCs from crista ampullaris revealed spontaneous kinociliary motion. Together, these findings define the kinocilium as a unique organelle with molecular features of primary and motile cilia and support its previously unknown role as an active, force-generating element within the hair bundle.</p>","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-06-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12190475/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144500189","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Mechanism of CO ₂ and NH ₃ Transport through Human Aquaporin 1: Evidence for Parallel CO ₂ Pathways.","authors":"Raif Musa-Aziz, R Ryan Geyer, Seong-Ki Lee, Fraser J Moss, Walter F Boron","doi":"10.1101/2025.02.28.640247","DOIUrl":"10.1101/2025.02.28.640247","url":null,"abstract":"&lt;p&gt;&lt;p&gt;The traditional view had been that dissolved gases cross membranes simply by dissolving in and diffusing through membrane lipid. However, some membranes are impermeable to CO &lt;sub&gt;2&lt;/sub&gt; and NH &lt;sub&gt;3&lt;/sub&gt; , whereas some aquaporin (AQP) water channels-tetramers with hydrophobic central pores-are permeable to CO &lt;sub&gt;2&lt;/sub&gt; , NH &lt;sub&gt;3&lt;/sub&gt; , or both. Nevertheless, we understand neither the routes that CO &lt;sub&gt;2&lt;/sub&gt; and NH &lt;sub&gt;3&lt;/sub&gt; take through AQP tetramers, nor the basis of CO &lt;sub&gt;2&lt;/sub&gt; /NH &lt;sub&gt;3&lt;/sub&gt; selectivity. Here, we show- for human AQP1 (hAQP1)-that virtually all NH &lt;sub&gt;3&lt;/sub&gt; and H &lt;sub&gt;2&lt;/sub&gt; O pass through the hydrophilic, monomeric pores. However CO &lt;sub&gt;2&lt;/sub&gt; passes both through the monomeric pores and another pathway. We expressed hAQP1 in &lt;i&gt;Xenopus&lt;/i&gt; oocytes and used microelectrodes to monitor the maximal surface-pH transient (ΔpH &lt;sub&gt;S&lt;/sub&gt; ) caused by CO &lt;sub&gt;2&lt;/sub&gt; or NH &lt;sub&gt;3&lt;/sub&gt; influxes. We found that p-chloromercuribenzene sulfonate (pCMBS)-which reacts with C189 in the monomeric pore-eliminates the entire hAQP1-dependent (*) NH &lt;sub&gt;3&lt;/sub&gt; signal (ΔpH &lt;sub&gt;S&lt;/sub&gt; *) &lt;sub&gt;NH3&lt;/sub&gt; , but only half of the signals for CO &lt;sub&gt;2&lt;/sub&gt; (ΔpH &lt;sub&gt;S&lt;/sub&gt; *) &lt;sub&gt;CO2&lt;/sub&gt; or osmotic water permeability &lt;i&gt;P&lt;/i&gt; &lt;sub&gt;f&lt;/sub&gt; *. 4,4'-diisothiocyanatostilbene-2,2'-disulfonate (DIDS), eliminates the remaining (ΔpH &lt;sub&gt;S&lt;/sub&gt; *) &lt;sub&gt;CO2&lt;/sub&gt; but has no effect on (ΔpH &lt;sub&gt;S&lt;/sub&gt; *) &lt;sub&gt;NH3&lt;/sub&gt; or &lt;i&gt;P&lt;/i&gt; &lt;sub&gt;f&lt;/sub&gt; *. Together, the two drugs completely eliminate the CO &lt;sub&gt;2&lt;/sub&gt; permeability of hAQP1. When we express hAQP1 in &lt;i&gt;Pichia pastoris&lt;/i&gt; , treat spheroplasts with DIDS, and examine hAQP1 by SDS-PAGE, reactivity with an anti-DIDS antibody shows that DIDS crosslinks hAQP1 monomers. Our results provide the first evidence that a molecule can move through an AQP via a route other than the monomeric pore, and raise the possibility that selectivity depends on the extent to which CO &lt;sub&gt;2&lt;/sub&gt; /NH &lt;sub&gt;3&lt;/sub&gt; move through monomeric pores vs. an alternate pathway (e.g., the central pore).&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Key points: &lt;/strong&gt;Some membranes have little or no CO &lt;sub&gt;2&lt;/sub&gt; permeability, absent protein channels like aquaporin-1 (AQP1). We confirm that, during CO &lt;sub&gt;2&lt;/sub&gt; influx, heterologous expression of human AQP1 (hAQP1) in &lt;i&gt;Xenopus&lt;/i&gt; oocytes increases the magnitude of the transient surface-pH increase by an amount (ΔpH &lt;sub&gt;S&lt;/sub&gt; *) &lt;sub&gt;CO2&lt;/sub&gt; , measured with microelectrodes. During NH &lt;sub&gt;3&lt;/sub&gt; influx, hAQP1 expression increases the magnitude of the transient pH &lt;sub&gt;S&lt;/sub&gt; decrease by (ΔpH &lt;sub&gt;S&lt;/sub&gt; *) &lt;sub&gt;NH3&lt;/sub&gt; . p-chloromercuribenzene sulfonate (pCMBS), which reacts with C189 in the monomeric pore, reduces (ΔpH &lt;sub&gt;S&lt;/sub&gt; *) &lt;sub&gt;CO2&lt;/sub&gt; by; (ΔpH &lt;sub&gt;S&lt;/sub&gt; *) &lt;sub&gt;NH3&lt;/sub&gt; , to zero; and AQP1-dependent osmotic water permeability ( &lt;i&gt;P&lt;/i&gt; &lt;sub&gt;f&lt;/sub&gt; *), by half. 4,4'-diisothiocyanatostilbene-2,2'-disulfonate (DIDS) reduces (ΔpH &lt;sub&gt;S&lt;/sub&gt;","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-06-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11908171/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143653019","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"SpaceBF: Spatial coexpression analysis using Bayesian Fused approaches in spatial omics datasets.","authors":"Souvik Seal, Brian Neelon","doi":"10.1101/2025.03.29.646124","DOIUrl":"10.1101/2025.03.29.646124","url":null,"abstract":"<p><p>Advancements in spatial omics technologies have enabled the measurement of expression profiles of different molecules, such as genes (using spatial transcriptomics), and peptides, lipids, or N-glycans (using mass spectrometry imaging), across thousands of spatial locations within a tissue. While identifying individual molecules with spatially variable expression is a well-studied statistical problem, robust methodologies for detecting spatially varying co-expression between molecule pairs remain limited. To address this gap, we introduce a Bayesian fused modeling framework for estimating molecular coexpression at both local (location-specific) and global (tissue-wide) levels, offering a refined understanding of cell-cell communication (CCC) mediated through ligand-receptor and other molecular interactions. Through extensive simulations, we demonstrate that our approach, termed SpaceBF, achieves superior specificity and power compared to existing methods that predominantly rely on geospatial metrics such as bivariate Moran's I and Lee's L. Applying our framework to real spatial transcriptomics and proteomics datasets, we uncover novel biological insights into molecular interactions across different cancers.</p>","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-06-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11996301/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144003873","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Transcription termination promotes splicing efficiency and fidelity in a compact genome.","authors":"Keaton Barr, Kevin L He, Andreas J Krumbein, Guillaume F Chanfreau","doi":"10.1101/2025.03.12.642901","DOIUrl":"10.1101/2025.03.12.642901","url":null,"abstract":"<p><p>Splicing of terminal introns is coupled to 3'-end processing by cleavage and polyadenylation (CPA) of mRNAs in mammalian genes. Whether this functional coupling is universally conserved across eukaryotes is unclear. Here we show using long read RNA sequencing in <i>S</i> . <i>cerevisiae</i> that splicing inactivation does not result in widespread CPA impairment. We also show that inactivation of CPA has limited impact on splicing efficiency. The negative impact of CPA inactivation on splicing is mainly due to transcription termination defects that promote readthrough transcription, leading to splicing inhibition for downstream intron-containing genes. Splicing impairment due to 5' extensions is length-dependent and can be detected independently from CPA inactivation for endogenous or synthetic genes, and is likely due to an increased distance of splicing signals to the 5' cap. Finally, we found that deficient termination can promote novel intragenic and long-range intergenic splicing events. These results argue against a broad coupling between splicing and CPA in <i>S</i> . <i>cerevisiae</i> but show that efficient CPA-mediated transcription termination is critical for splicing fidelity and efficiency in a compact genome.</p><p><strong>Significance statement: </strong>Accurate gene expression requires that the enzyme that polymerizes RNA stops at the proper site (termination). In addition multiple RNA processing reactions, including removal of intervening sequences are necessary to produce mature mRNAs. How these different steps in the RNA biogenesis pathways influence each other is not well understood. In this study, we show that inactivation of termination induces mature RNA formation defects, including long RNAs that retain intervening sequences, or chimeric RNAs containing sequences from genes located next to each other on the genome. This study underscores the importance of proper termination to ensure accurate and efficient splicing of adjacent genes, which is particularly critical for compact genomes in which genes are located close to each other.</p>","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-06-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11952531/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143757511","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Intranasal Leukemia Inhibitory Factor as a late-stage treatment for delayed white matter damage in concussive head injury.","authors":"Veera D'Mello, Jelena Mihailovic, Sidra Ali, Basavaraju G Sanganahalli, Daniel Coman, Fahmeed Hyder, Merisha Fernando, Anita Mampilly, Sridhar S Kannurpatti, Steven W Levison","doi":"10.1101/2025.04.07.647435","DOIUrl":"10.1101/2025.04.07.647435","url":null,"abstract":"<p><p>Leukemia Inhibitory Factor (LIF) is an injury-induced cytokine that peaks 48 hours after a traumatic brain injury (TBI). Juvenile LIF haplodeficient mice exhibit desynchronized glial responses, increased neurodegeneration, decreased axonal conductivity and behavioral deficits after a concussive head injury. Given the necessity of LIF during the acute recovery phase after injury, we hypothesized that intranasal (IN) LIF treatment would prevent neurodegeneration when administered during the chronic recovery period from a mild TBI (mTBI). Young adult male CD1 mice were subjected to a midline, closed-head frontal cortex injury using a flat metal impactor with a 3mm tip to induce a mTBI. In the 6-8 weeks post- mTBI, known to precede axonal atrophy in this mTBI model, two doses of 40 ng and 100 ng of LIF were administered twice daily, 5 days/week for two consecutive weeks. Sensorimotor functions were assessed at 4 and 8 weeks post mTBI, followed by ex-vivo brain magnetic resonance imaging at 9.4T and histopathology. mTBI mice showed sensorimotor deficits at 4 weeks, which worsened by 8 weeks post- injury. IN-LIF treatment prevented the progressive sensorimotor loss seen in the vehicle-treated controls. Increased mean diffusivity (MD) and decreased fractional anisotropy (FA) were observed in the corpus callosum and prefrontal cortex of mTBI brains. In a dose-dependent manner, IN-LIF prevented the mTBI- induced MD increase and FA decrease. Histologically, there was significantly less astrogliosis, microgliosis and axonal injury in the IN-LIF treated mice vs. controls. These results support the therapeutic potential of IN-LIF to reduce delayed neurodegeneration and improve neurological outcomes after mTBIs.</p>","PeriodicalId":519960,"journal":{"name":"bioRxiv : the preprint server for biology","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2025-06-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12026900/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144034923","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}