Biology subjects

Sharma, A.

Publications and source records attributed to Sharma, A..

At least 289 records · Page 16Linked to original sources

bioRxiv2023

PI(3,5)P2 Controls the Signaling Activity of Class I PI3K

3-Phosphoinositides are ubiquitous cellular lipids that play pivotal regulatory roles in health and disease. Among 3-phosphoinositides, phosphatidylinositol-3,5-bisphosphate (PI(3,5)P2) remains the least understood species in terms of its spatiotemporal dynamics and physiological function due to the lack of a specific sensor that allows spatiotemporally resolved quantitative imaging of PI(3,5)P2. Using a newly developed ratiometric PI(3,5)P2 sensor engineered from the C-terminal SH2 domain of Class I phosphoinositide 3-kinases (PI3K)-p85 subunit we demonstrate that a unique pool of PI(3,5)P2 is generated on lysosomes and late endosomes in response to growth factor stimulation. This PI(3,5)P2, the formation of which is mediated sequentially by Class II PI3KC2{beta} and PIKfyve, plays a crucial role in terminating the activity of growth factor-stimulated Class I PI3K, one of the most frequently mutated proteins in cancer, via specific interaction with its regulatory p85 subunit. A small molecule inhibitor of p85-PI(3,5)P2 binding specifically blocks the feedback inhibition of Class I PI3K by PI(3,5)P2 and thus serves as a PI3K activator that promotes neurite growth. Furthermore, cancer-causing mutations of the Class I PI3K-p85 subunit inhibit p85-PI(3,5)P2 interaction and thereby induce sustained activation of Class I PI3K. Our results unravel a hitherto unknown spatiotemporally specific regulatory function of PI(3,5)P2 that links Class I and II PI3Ks and modulates the magnitude of PI3K-mediated growth factor signaling. These results also suggest new therapeutic possibilities for treating cancer patients with p85 mutations and promoting wound healing and tissue regeneration.

biochemistry↗

bioRxiv2023

Deciphering the phenotypic heterogeneity and drug response in cancer cells using genome-wide activity and interaction of chromatin domains.

The effect of co-localization of genes in the topologically associated domains (TADs) and their activity as a regulatory unit in cancer samples and cells, together with drug-response, needs comprehensive analysis. Here, we analyzed the activity of TADs using cancer-cell transcriptomes along with chromatin-interaction and epigenome profiles to understand their relationship with drug-response. Our analysis of 819 cancer cell-line transcriptomes revealed that their response to multiple drugs was more correlated with the activity of individual TADs than genes. Applying our approach to 9014 cancer patients data (20 different cancer types) also revealed a higher association between survival and the activity of thousands of individual TADs in comparison to their genes. CRISPR-mediated knock-out of regulatory sites inside a TAD associated with cisplatin-response of oral cancer cells and discovery of primate-specific gain of synteny of genes within a TAD containing EGFR gene and its contribution towards cancer malignancy demonstrate greater utility of TAD-activity based analysis.

cancer biology↗

bioRxiv2023

Impact of urbanization on the taxonomic and functional diversity of spider assemblages in Guwahati City, Assam, India

The homogenous nature of the urban environment rapidly alters community dynamics of extant flora and fauna due to short-term spatial and temporal factors. However, such impacts of urbanization are mostly investigated in terms of taxonomic diversity, while its impact on functional diversity remains poorly understood. Whereas taxonomic information is limited to the identity of species, functional traits determine the relationship between species identity and ecosystem functioning. Studies investigating the role of urbanization in altering these ecological parameters have mostly focused on avian communities or plant species, while arthropods such as spiders which are integral components of urban households have largely been overlooked. This study aims to understand the impact of urbanization on both taxonomic diversity and functional diversity of spider assemblages across an urban-semi-urban-forest gradient in Guwahati, a rapidly growing city in northeast India. We surveyed spiders at 13 sites representing four habitat types (urban, urban parks, semi-urban, and forests) using belt transects, and also recorded functional traits relating to key life history processes. Spider species composition differed significantly between various habitats. The taxonomic diversity of spiders was highest in forests and lowest in urban parks. The turnover component was the major contributor to changing the {beta}-diversity of spiders. Reduced diversity in urban regions was likely due to the dominance of a few synanthropic species. Generalised linear mixed-effects model analysis indicated that the habitat types significantly impacted spider abundance. Functional richness was maximum in forests (Fric = 23.43) and minimum in urban habitats (Fric = 12.98), while functional divergence was maximum in urban sites (Fdiv = 0.79). Our study demonstrates that urban land-use change can alter the structure and functioning of the spider community.

ecology↗

bioRxiv2022

On the origin and evolution of the mosquito male-determining factor Nix

The mosquito family Culicidae is divided into two subfamilies named the Culicinae and Anophelinae. Nix, the dominant male-determining factor, has only been found in the culicines Aedes aegypti and Ae. albopictus, two important arboviral vectors that belong to the subgenus Stegomyia. Here we performed sex-specific whole-genome sequencing and RNAseq of divergent mosquito species and explored additional male-inclusive datasets to investigate the distribution of Nix. Except for the Culex genus, Nix homologs were found in all species surveyed from the Culicinae subfamily, including 12 additional species from three highly divergent tribes comprising 4 genera, suggesting Nix originated at least 133-165 MYA. Heterologous expression of one of three divergent Nix ORFs in Ae. aegypti resulted in partial masculinization of genetic females as evidenced by morphology and doublesex splicing. It is not clear whether insufficient transgene expression or sequence divergence or both are responsible for the lack of phenotype for the other two. Phylogenetic analysis suggests Nix is related to femaleless (fle), a recently described intermediate sex-determining factor found exclusively in anopheline mosquitoes. Nix from all species has a conserved structure, including three RNA-recognition motifs (RRMs), as does fle. However, Nix has evolved at a much faster rate than fle. The RRM3 of both Nix and fle are related to the single RRM of a widely distributed and conserved splicing factor transformer-2 (tra2). RRM3-based phylogenetic analysis suggests this domain in Nix and fle may have evolved from tra2 in a common ancestor of mosquitoes. Our results provide insights into the evolution of sex-determination and homomorphic sex chromosomes in mosquitoes, and will inform broad applications of mosquito-control strategies based on manipulating sex ratios towards the non-biting males.

evolutionary biology↗

bioRxiv2022

Multi-omics analysis of paracetamol exposure identifies dysregulated genes involved in neurotoxicity and neuronal differentiation of human embryonic stem cells

Prenatal paracetamol exposure has been associated with neurodevelopmental outcomes in childhood. Pharmacoepigenetic studies show differences in cord blood DNA methylation between paracetamol exposed and unexposed neonates. However, causal implications and impact of long-term prenatal long-term paracetamol exposure on brain development remain unclear. Using a multi-omics approach, we investigated the effects of paracetamol on a model of early human brain development. We exposed human embryonic stem cells undergoing in vitro neuronal differentiation to daily media changes with paracetamol concentrations corresponding to maternal therapeutic doses. Single-cell RNA-seq and ATAC-seq integration identified paracetamol-induced chromatin-opening changes linked to gene expression. Differentially methylated and/or expressed genes were involved in signalling, neurotransmission, and cell fate-determination trajectories. Some genes involved in neuronal injury and development-specific pathways, such as KCNE3, overlapped with differentially methylated genes previously identified in cord blood associated with prenatal paracetamol exposure. Our data suggest that paracetamol may play a causal role in impaired neurodevelopment. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=191 HEIGHT=200 SRC="FIGDIR/small/519620v2_ufig1.gif" ALT="Figure 1"> View larger version (53K): org.highwire.dtl.DTLVardef@e1a75forg.highwire.dtl.DTLVardef@b36a1forg.highwire.dtl.DTLVardef@fc25e4org.highwire.dtl.DTLVardef@1bb1c8_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2022

STOmics-GenX: CRISPR based approach to improve cell identity specific gene detection from spatially resolved transcriptomics

The spatial organisation of cells defines the biological functions of tissue ecosystems from development to disease. Recently, an array of technologies have been developed to query gene expression in a spatial context. These include techniques such as employing barcoded oligonucleotides, single-molecule fluorescence in situ hybridization (smFISH), and DNA nanoball (DNB)-patterned arrays. However, resolution and efficiency vary across platforms and technologies. To obtain spatially relevant biological information from spatially resolved transcriptomics, we combined the Stereo-seq workflow with CRISPRclean technology to develop the STOmics-GenX pipeline. STOmics-GenX not only allowed us to reduce genomic, mitochondrial, and ribosomal reads, but also lead to a [~]2.1-fold increase in the number of detected genes when compared to conventional Stereo-seq (STOmics). Additionally, the STOmics-GenX pipeline resulted in an improved detection of cell type specific genes, thereby improving cellular annotations. Most importantly, STOmics-GenX allowed for enhanced detection of clinically relevant biomarkers such as Alpha-fetoprotein (AFP), enabling the identification of two spatially distinct subsets of hepatocytes in hepatocellular carcinoma tissue. Thereby, combining CRISPRclean technology with STOmics not only allowed improved gene detection but also paved the way for spatial precision oncology by improved detection of clinically relevant biomarkers.

molecular biology↗

bioRxiv2022

Molecular mechanisms regulating the pH-dependent pr/E interaction in yellow fever virus.

Flavivirus particles bud in the ER of infected cells as immature virions composed of 180 heterodimers of glycoproteins prM and E, associated as 60 (prM/E)3 trimeric spikes. Exposure to the mildly acidic pH of the TGN results in dissociation of the trimeric spikes followed by reassociation of the prM/E protomers into 90 dimers organized in a characteristic herringbone pattern. The furin site in prM is exposed in the dimers for maturation of prM into M and pr. For flaviviruses such as the tick-borne encephalitis virus (TBEV) as well as for dengue virus, it was shown that at neutral pH pr loses affinity for E, such that it dissociates from the mature particle as soon as it reaches the external milieu, which is at neutral pH. Using a soluble recombinant form of E (sE) and pr from yellow fever virus (YFV), we show here that the affinity of pr for recombinant E protein remains high even at neutral pH. The X-ray structure of YFV pr/sE shows more extensive inter-chain hydrogen bonding than does the dengue or TBEV, and also that it retains the charge complementarity between the interacting surfaces of the two proteins even at neutral pH. We further show that pr blocks sE flotation with liposomes when exposed at low pH at a 1:1 stoichiometry, yet in the context of the virus particle, an excess of 10:1 pr:E ratio is required to block virus/liposome fusion. In aggregate, our results show that the paradigm obtained from earlier studies of other flaviviruses does not apply to yellow fever virus, the flavivirus type species. A mechanism that does not rely solely in a change in the environmental pH is thus required for the release of pr from the mature particles upon release from infected cells. These results open up new avenues to understand the activation mechanism that yields mature, infectious YFV particles.

microbiology↗

bioRxiv2022

13C ENDOR Spectroscopy-Guided MD Computations Reveals the Structure of the Enzyme-Substrate Complex of an Active, N-linked Glycosylated Lipoxygenase

Lipoxygenases (LOXs) are enzymes responsible for producing important cell signaling mediators and have been extensively studied for their potential clinical relevance as well as to advance our understanding of enzyme catalysis. The common inability to capture and characterize LOX-substrate complexes by Xray co-crystallography requires the development of alternative structural methods. We previously reported the integration of 13C/1H electron nuclear double resonance (ENDOR) spectroscopy and molecular dynamics (MD) to visualize the complex structure of the paradigmatic LOX from soybean, SLO, with substrate linoleic acid (LA). However, this required substitution of the catalytic mononuclear, nonheme iron by the structurally faithful, yet inactive Mn2+ ion as a spin-probe. Unlike canonical Fe-LOXs from plants and animals, LOXs from pathogenic fungi contain active mononuclear manganese metallocentres. Here, we report the ground-state active-site structure of the native, fully glycosylated fungal LOX from M. oryzae, MoLOX complexed with LA obtained through the 13C/1H ENDOR-guided MD approach. The Mn-oxygen-to-LA donor carbon distance (DAD) for MoLOX-LA, 3.4 {+/-} 0.3 [A], matches the distance in the single representative X-ray co-structure of an animal 8R-LOX with its natural fatty acid substrate, and slightly elongated from that of the SLO-LA complex, 3.1 {+/-} 0.2 [A], despite its carboxylate-out substrate binding orientation versus carboxylate-in for SLO. The results provide unique insight into the evolutionary divergence of the ground-state DAD in the LOX family, which influences the activation barrier for hydrogen tunneling, and give a structural basis for guiding development of MoLOX inhibitors. The work highlights the robustness of ENDOR-guided MD approach to describe LOX-substrate structures that elude conventional X-ray techniques.

biochemistry↗

bioRxiv2022

Hematopoiesis and cell growth are differentially regulated by TAL1 isoforms

T-cell acute lymphoblastic leukemia (T-ALL) protein 1 (TAL1) is a central transcription factor in hematopoiesis. The timing and level of TAL1 expression orchestrate the differentiation to specialized blood cells and its overexpression is a common cause of T-ALL. Here we studied the two protein isoforms of TAL1, short and long, that are generated by the use of alternative promoters as well as by alternative splicing. We analyzed the expression of each isoform by deleting an enhancer or insulator, or by opening chromatin at the enhancer location. Our results show that each enhancer promotes expression from a specific TAL1 promoter. Expression from a specific promoter gives rise to a unique 5 UTR with differential regulation of translation. Moreover, our study suggests that the enhancers regulate TAL1 exon 3 alternative splicing by inducing changes in the chromatin at the splice site, which we demonstrate is mediated by KMT2B. Furthermore, our results indicate that TAL1-short binds more strongly to TAL1 E-protein partners and functions as a stronger transcription factor than TAL1-long. Specifically TAL1-short has a unique transcription signature promoting apoptosis. Finally, when we expressed both isoforms in mice bone-marrow, we found that while overexpression of both isoforms prevents lymphoid differentiation, expression of TAL-short alone leads to hematopoietic stem cell exhaustion. Furthermore, we found that TAL1-short promoted erythropoiesis and reduced cell survival in the CML cell line K562. While TAL1 and its partners are considered promising therapeutic targets in the treatment of T-ALL, our results show that TAL1-short could act as a tumor suppressor and suggest that altering TAL1 isoforms ratio could be a preferred therapeutic approach.

molecular biology↗

bioRxiv2022

Cerebral malaria is regulated by host mediated changes in Plasmodium gene expression

Cerebral Malaria (CM), the deadliest complication of Plasmodium infection, is a complex and unpredictable disease. However, our understanding of the host and parasite factors that cause CM is limited. Using a mouse model of CM, experimental CM (ECM), we performed a three-way comparison between: ECM susceptible C57BL/6 mice infected with ECM-causing Plasmodium ANKA (Pb ANKA) parasites (ANKA(C57BL/6)); ECM resistant Balb/c mice infected with Pb ANKA (ANKA(Balb/c)); and C57BL/6 mice infected with Pb NK65 that does not cause ECM (NK65(C57BL/6)). All ANKA(C57BL/6) mice developed CM. In contrast in ANKA(Balb/c) and NK65(C57BL/6) infections do not result in CM and proceed similarly in terms of parasite growth, disease course and host immune response.. However, parasite gene expression in (ANKA(C57BL/6)) was remarkably different than in ANKA(Balb/c) but similar to the gene expression in NK65(C57BL/6). Thus, Pb ANKA has a ECM-specific gene expression profile that is only activated in susceptible hosts providing evidence that the host has a critical influence on the outcome of infection.

microbiology↗

bioRxiv2022

Defining the Parameters to Improve Plant Regeneration with Developmental Regulators

Tissue culture methods which serve as the standard to regenerate modified plants are challenging and have limited the capacity to engineer new accessions. To improve upon these techniques, genome modifying reagents have been combined with developmental regulators to create gene edited plant tissues in both monocot and eudicot species. Co-culturing seedlings with Agrobacterium strains encoding developmental regulatory genes has proved to be effective at producing de novo meristems in multiple eudicot species. In order to see that this technology scales well beyond proof of concept experiments, various parameters were tested for refinement. Improvements have been observed at the key stages of growth induction and progression to shooting by manipulating the vector design, developmental regulator choice, Agrobacterium strain selection, and regulatory gene removal systems. Having defined these parameters as viable optimization points, the avenues to apply developmental regulators for plant regeneration in more diverse species have become more feasible.

plant biology↗

bioRxiv2022

Temporal Vascular Endothelial Growth Factor Sub-type gene Switching in SARS-CoV Pathogenesis. Interpretation through in vivo Murine C57BL Models

This study examines temporal gene expression (GE) patterns in a murine model of SARS-CoV infection. We focused on a Temporal Gene Set (TGS) comprising pro-inflammatory genes (TNF, NFKB1, VEGF-A) and VEGF-B. A systematic search of the NCBI Geo database for MA15 (SARS-CoV) pulmonary studies using C57BL Wild (WT) mice and filtering according to TGS GE patterns eluded seven datasets for further analysis. Encompassing the GE profiles from these datasets alluded to a rising and falling pattern in TNF and NFKB1 GE. Also, our findings reveal a temporal decrease in VEGF-A GE coinciding with an increase in VEGF-B GE post-immunogenic stimulation. Notably, differential responses were observed with the MA15 dosage and in comparison, to other antigens (dORF6 and NSP16). Further, the human SARS-CoV-2 gene enrichment in this murine study confirms the MA15 murine models relevance for SARS research. Our study also suggests potential interactions between SARS-CoV-2 Spike protein and VEGF-related receptors, hinting at other pathophysiological mechanisms. Our results indicate severe inflammation may lead to a flattened VEGF-B GE response, influencing VEGF-Bs cell survival role. We underline the significance of considering VEGF-A/B interactions, particularly temporal differences, in manipulating angiogenic processes. Future research needs to consider temporal changes in VEGF-A and VEGF-B GE, in terms of time-associated gene-switching, in line with changing host inflammation.

immunology↗

bioRxiv2022

Molecular basis of SARS-CoV-2 Omicron variant evasion from shared neutralizing antibody response

A detailed understanding of the molecular features of the neutralizing epitopes developed by viral escape mutants is important for predicting and developing vaccines or therapeutic antibodies against continuously emerging SARS-CoV-2 variants. Here, we report three human monoclonal antibodies (mAbs) generated from COVID-19 recovered individuals during first wave of pandemic in India. These mAbs had publicly shared near germline gene usage and potently neutralized Alpha and Delta, but poorly neutralized Beta and completely failed to neutralize Omicron BA.1 SARS-CoV-2 variants. Structural analysis of these three mAbs in complex with trimeric spike protein showed that all three mAbs are involved in bivalent spike binding with two mAbs targeting class-1 and one targeting class-4 Receptor Binding Domain (RBD) epitope. Comparison of immunogenetic makeup, structure, and function of these three mAbs with our recently reported class-3 RBD binding mAb that potently neutralized all SARS-CoV-2 variants revealed precise antibody footprint, specific molecular interactions associated with the most potent multi-variant binding / neutralization efficacy. This knowledge has timely significance for understanding how a combination of certain mutations affect the binding or neutralization of an antibody and thus have implications for predicting structural features of emerging SARS-CoV-2 escape variants and to develop vaccines or therapeutic antibodies against these.

immunology↗

bioRxiv2022

Cross-species conservation and phenotypic directionality switching in non-genetic inheritance

Evidence supporting non-DNA sequence-based inheritance in animals has increasingly been described in recent years, often under short-term, intergenerational inheritance or longer, transgenerational epigenetic inheritance (TEI). Existence of the latter, a stronger indicator of germline transmission, though established in invertebrates remains controversial in mammals due to inherent confounding factors. Besides evolutionary conservation, physiological implications of TEI also remain unclear. Leveraging invertebrate evidence of TEI to assess possible instances in mammals, and dissecting already described models to gain further insights are suggested approaches to address uncertainties in non-genetic inheritance. Here, in an unbiased approach, we compared existing transcriptomic data associated with so far available Drosophila models of inter- and trans-, and rodent models of inter-generational inheritance, observed phenotypic cross-species conservation and cross-generation directionality shift therein, and confirmed these observations experimentally in flies. Specifically, previous models of cold and diet induced inheritance in both flies and mice were commonly associated with altered regulation of proteolysis genes. Besides, fly TEI models were in general characterized by opposite phenotypic regulation between inter- and trans-generational offspring. As insulin producing cell (IPC) ablation was also associated with proteolysis gene dysregulation in one of the mouse models, we opted to use genetic ablation of IPCs in flies for the experimental confirmation. Remarkably, the ablation led to transcriptomic alterations across multiple generations, with dysregulated genes showing proteolysis enrichment. Similarly, phenotypic directionality changed in the opposite direction in transgenerational offspring of IPC ablated ancestors. These results support mammalian existence, and physiologically adaptive and maladaptive consequences of germline mediated epigenetic inheritance.

genetics↗

bioRxiv2022

Mapping of the bs5 and bs6 non-race-specific recessive resistances against bacterial spot of pepper

Bacterial spot caused by Xanthomonas euvesicatoria is a major disease of pepper (Capsicum annuum L.) in warm and humid production environments. Use of genetically resistant cultivars is an effective approach to manage bacterial spot. Two recessive resistance genes, bs5 and bs6, confer non-race-specific resistance against bacterial spot. The objective of our study was to map these two loci in the pepper genome. We used a genotyping-by-sequencing approach to initially map the position of the two resistances. Segregant populations for bs5 and bs6 were developed by crossing susceptible Early CalWonder (ECW) with near-isogenic lines ECW50R (bs5 introgression) or ECW60R (bs6 introgression). Following fine-mapping, bs5 was delimited to a ~535 Kbp interval on chromosome 3, and bs6 to a ~666 Kbp interval in chromosome 6 of pepper. We also identified 14 and 8 candidate resistance genes for bs5 and bs6, respectively, based on predicted protein coding polymorphisms between ECW and the corresponding resistant parent. Mapping of bs5 and bs6 will facilitate their use in breeding programs through marker-assisted selection and is also a crucial step towards understanding the mechanisms of resistance. Key messageTwo recessive bacterial spot resistance genes were mapped in the pepper genome, which will facilitate their advancement in commercial pepper for management of all races of Xanthomonas euvesicatoria.

plant biology↗

bioRxiv2022

Fluid flow sensitizes bacterial pathogens to chemical stress

Cells regularly experience fluid flow in natural systems. However, most experimental systems rely on batch cell culture and fail to consider the effect of flow-driven dynamics on cell physiology. Using microfluidics and single-cell imaging, we discover that the interplay of physical shear rate (a measure of fluid flow) and chemical stress trigger a transcriptional response in the human pathogen Pseudomonas aeruginosa. In batch cell culture, cells protect themselves by quickly scavenging the ubiquitous chemical stressor hydrogen peroxide (H2O2) from the media. In microfluidic conditions, we observe that cell scavenging generates spatial gradients of H2O2. High shear rates replenish H2O2, abolish gradients, and generate a stress response. Combining mathematical simulations and biophysical experiments, we find that cells in flow are sensitive to a H2O2 concentration that is 100-1000 times lower than traditionally studied in batch cell culture. Surprisingly, the shear rate and H2O2 concentration required to trigger a transcriptional response closely match their respective values in the human bloodstream. Thus, our results explain a long-standing discrepancy between H2O2 levels in experimental and natural systems. Finally, we demonstrate that the shear rate and H2O2 concentration found in the human bloodstream trigger gene expression in the blood-relevant human pathogen Staphylococcus aureus, suggesting that flow sensitizes bacteria to chemical stress in natural environments.

microbiology↗

bioRxiv2022

Characterizing the targets of transcription regulators by aggregating ChIP-seq and perturbation expression data sets

Mapping the gene targets of chromatin-associated transcription regulators (TRs) is a major goal of genomics research. ChIP-seq of TRs and experiments that perturb a TR and measure the differential abundance of gene transcripts are a primary means by which direct relationships are tested on a genomic scale. It has been reported that there is poor overlap in the evidence across gene regulation strategies, emphasizing the need for integrating results from multiple experiments. While research consortia interested in gene regulation have produced a valuable trove of high-quality data, there is an even greater volume of TR-specific data throughout the literature. In this study, we demonstrate a workflow for the identification, uniform processing, and aggregation of ChIP-seq and TR perturbation experiments for the ultimate purpose of ranking human and mouse TR-target interactions. Focusing on an initial set of eight regulators (ASCL1, HES1, MECP2, MEF2C, NEUROD1, PAX6, RUNX1, and TCF4), we identified 497 experiments suitable for analysis. We used this corpus to examine data concordance, to identify systematic patterns of the two data types, and to identify putative orthologous interactions between human and mouse. We build upon commonly used strategies to forward a procedure for aggregating and combining these two genomic methodologies, assessing these rankings against independent literature-curated evidence. Beyond a framework extensible to other TRs, our work also provides empirically ranked TR-target listings, as well as transparent experiment-level gene summaries for community use.

bioinformatics↗

bioRxiv2022

CRTC-1 Balances Histone Trimethylation and Acetylation to Promote Longevity

Loss of function during ageing is accompanied by transcriptional drift, altering gene expression and contributing to a variety of age-related diseases. CREB-regulated transcriptional coactivators (CRTCs) have emerged as key regulators of gene expression that might be targeted to promote longevity. Here, we define the role of the Caenorhabditis elegans CRTC-1 in the epigenetic regulation of longevity. Endogenous CRTC-1 binds chromatin factors, including components of the COMPASS complex, which trimethylates lysine 4 on histone H3 (H3K4me3). CRISPR editing of endogenous CRTC-1 reveals that the CREB-binding domain in neurons is specifically required for H3K4me3-dependent longevity. However, this effect is independent of CREB but instead acts via the transcription factor AP-1. Strikingly, CRTC-1 also mediates global histone acetylation levels, and this acetylation is essential for H3K4me3-dependent longevity. Indeed, overexpression of an acetyltransferase enzyme is sufficient to promote longevity in wild-type worms. CRTCs, therefore, link energetics to longevity by critically fine-tuning histone acetylation and methylation to promote healthy ageing.

genetics↗