Biology subjects

Tyagi, S.

Publications and source records attributed to Tyagi, S..

At least 37 records · Page 2Linked to original sources

bioRxiv2024

H3K4me3 methyltransferase KMT2F promotes pre-initiation complex formation by RNA Polymerase I to regulate ribosomal RNA transcription.

Trimethylation of histone 3 lysine 4 (H3K4me3) is mark of active transcription and its regulatory role in RNA polymerase II-mediated transcription has been well-studied. However, if and how this mark regulates RNA polymerase I (RNA Pol I) is not known. Here we used customized genome assemblies for rDNA to demonstrate that KMT2A and KMT2F bind to entire rDNA loci. The binding of these enzymes were mirrored by the binding of H3K4me2 and H3K4me3 marks. Using biochemical assays, we demonstrate the interaction of KMT2- specific subunits with RNA Pol I transcriptional machinery. Our findings reveal KMT2F as the primary KMT depositing the H3K4me3 on rDNA. Loss of H3K4me3 adversely affects the epigenetic landscape and promotes heterochromatization of rDNA locus. Mechanistically, we show that KMT2F promotes pre-initiation complex formation of RNA Pol I. Our findings highlights the thus far undiscovered role of H3K4me3 in the transcriptional initiation of rDNA genes.

molecular biology↗

bioRxiv2024

MLL/WDR5 complex recruits KIF2C to midbody to ensure MT depolymerization and furrow compaction during cytokinesis

Mixed-lineage leukemia (MLL) protein is a well characterized epigenetic regulator whose non-canonical activities remain under appreciated. Here we show that MLL and its associated protein WDR5, localize to the midbody. Loss of MLL/WDR5 results in defective midbody formation, which displays a wide midzone-like microtubule structure, along with chromosome bridges, resulting in binucleated cells. We show that MLL and WDR5 interact with kinesin 13 motor--KIF2C, and targets it to the midbody. The depolymerase activity of KIF2C promotes correct localization of centralspindlin complex, compaction of midzone MTs and finally furrow completion. By characterizing the previously undiscovered role of MLL and KIF2C in the regulation of cytokinesis, our work underscores the importance of these proteins at the interface of actin and microtubule cytoskeleton regulation, pathways that are frequently altered in oncogenesis.

cell biology↗

bioRxiv2024

Regulation of alternative polyadenylation isoforms of Timp2 is an effector event of RAS signaling in cell transformation

Alternative polyadenylation (APA) generates mRNA isoforms with different lengths of the 3 untranslated region (3 UTR). The tissue inhibitor of metalloproteinase 2 (TIMP2) plays a key role in extracellular matrix remodeling under various developmental and disease conditions. Both human and mouse genes encoding TIMP2 contain two highly conserved 3UTR APA sites, leading to mRNA isoforms that differ substantially in 3UTR size. APA of Timp2 is one of the most significantly regulated events in multiple cell differentiation lineages. Here we show that Timp2 APA is highly regulated in transformation of NIH3T3 cells by the oncogene HRASG12V. Perturbations of isoform expression with long 3UTR isoform-specific knockdown or genomic removal of the alternative UTR (aUTR) region indicate that the long 3UTR isoform contributes to the secreted Timp2 protein much more than the short 3UTR isoform. The short and long 3UTR isoforms differ in subcellular localization to endoplasmic reticulum (ER). Strikingly, Timp2 aUTR enhances secreted protein expression but no effect on intracellular proteins in reporter assays. Furthermore, downregulation of Timp2 long isoform mitigates gene expression changes elicited by HRASG12V. Together, our data indicate that regulation of Timp2 protein expression through APA isoform changes is an integral part of RAS-mediated cell transformation and 3UTR isoforms of Timp2 can have distinct impacts on expression of secreted vs. intracellular proteins.

molecular biology↗

bioRxiv2024

Arabidopsis AtGELP53 modulates polysaccharide acetylation and defense response through oligosaccharide-mediated signaling

O-acetylation is a crucial substitution found in hemicelluloses and pectin which are necessary for maintaining the flexibility and structural integrity of the cell. A balanced polysaccharide O-acetylation level is maintained by cell wall acetyl transferases and esterases present in different cell organelles. Specifically, the role of esterases in cell wall acetylation metabolism is less explored. Therefore, we investigated the role of AtGELP53 from the GELP family of esterases or lipases. Here, we show that AtGELP53 is localized in the plasma membrane. Analysis of AtGELP53 overexpressing independent transgenic lines revealed a decrease in xyloglucan acetylation, changes in other polysaccharide acetylation and alteration in cell wall composition. The series of elicitor-based, transcriptomic and proteomic analyses in AtGELP53 overexpressing lines suggested that oligosaccharide-mediated signalling activates the cell wall and defence-related genes primarily because of xyloglucan deacetylation. Furthermore, AtGELP53 overexpression plants showed resistance against Pseudomonas syringae and Ralstonia solanacearum through activation of elicitor-mediated defense response. Overall, our findings outline the role of AtGELP53 in polysaccharide acetylation, cell wall remodelling and defense through the activation of plant cell wall integrity.

plant biology↗

bioRxiv2024

Type-B response regulators MaRR_B9 and MaRR_B12 coordinate cytokinin-mediated negative regulation of anthocyanin biosynthesis in banana fruits

O_LIAnthocyanins are pigments responsible for vibrant plant colors and play vital roles in plant physiology. Comparing two banana varieties, grand naine (GN) and red banana (RB), which display significant contrast in anthocyanin pigmentation. C_LIO_LITranscriptomic analysis of GN and RB peel and pulp tissue highlighted cytokinin-specific response regulators, MaRR_B9 and MaRR_B12, as regulators of anthocyanin biosynthesis. C_LIO_LIThrough a combination of physiological, molecular, and biochemical analyses, we demonstrate that MaRR_B9 and MaRR_B12 exert direct regulatory control over key structural genes of anthocyanin biosynthesis, dihydroflavanol reductase (MaDFR) and anthocyanidin synthase (MaANS). MaRR_B9 and MaRRB_12 interact with the promoters of MaDFR and MaANS, repressing the concerned genes in vivo. Overexpression of MaRR_B9 and MaRR_B12 in banana fruits leads to a reduction in anthocyanin content, particularly that of the cyanidin derivative, along with altered expression patterns of MaDFR and MaANS. C_LIO_LIThus, the present study identifies novel regulators of anthocyanin biosynthesis in banana and provides further evidence that the cytokinin regulatory network modifies anthocyanin accumulation in plants. In conclusion, our findings reveal new molecular targets, in the form of MaRRs for the genetic manipulation of anthocyanin content and thereby for the development of stress-resilient and nutritionally enriched crop plants. C_LI

plant biology↗

bioRxiv2024

pH dependent direct sulfhydrylation pathway is required for pathogenesis of Mycobacterium tuberculosis

Methionine is essential for the survival of Mycobacterium tuberculosis (M. tuberculosis) inside the host. However, the transsulfuration pathway, a major contributor of methionine, is dispensable for the growth of M. tuberculosis suggesting redundancy in the methionine biosynthesis pathway. Orthologues of MetZTB in other bacterial species are known to operate a redundant single-step methionine biosynthesis pathway called direct sulfhydrylation. In this study, we demonstrate that genetic disruption of the metZ-mediated direct sulfhydrylation pathway in M. tuberculosis hinders growth at low pH, an effect mitigated by methionine supplementation. Computational analyses, including in-silico molecular docking and molecular dynamics (MD) simulations, reveal enhanced binding of the MetZ substrate, O-succinyl homoserine (OSH), to the active site of MetZ at acidic pH. Intriguingly, despite increased intracellular ATP levels, a relative decrease in the frequency of Bedaquiline (BDQ)-induced persisters is observed in metZ-deficient strain, suggesting a role of direct sulfhydrylation pathway in modulating BDQ sensitivity. Finally, we demonstrated that the absence of metZ impedes the ability of M. tuberculosis to grow inside the host.

microbiology↗

bioRxiv2024

Phosphoglucomutase A mediated regulation of carbon flux is essential for antibiotic and disease persistence in Mycobacterium tuberculosis

The long-term survival of Mtb mandates judicious utilization of the available resources inside the host. Uninterrupted access to host-derived nutrients holds the key to the success of Mtb. Phosphoglucomutase enzyme besides synthesizing glycogen, which serves as a nutrient reservoir, also helps modulate the carbon flux in different pathogens. Studies on the role of glycogen metabolism in disease progression, reactivation, and drug susceptibility in tuberculosis are severely lacking. To investigate this, we generated an Mtb strain ({Delta}pgmA) devoid of the gene that encodes for the enzyme phosphoglucomutase A (pgmA). The absence of pgmA impedes the ability of the pathogen to survive under nutrient-limiting and reactivation conditions. In the current study, we demonstrate that the absence of cell membrane-associated glycolipids in {Delta}pgmA compromised the cell wall integrity and increased the susceptibility of {Delta}pgmA to various stresses. Interestingly, in comparison to the wild type, low cAMP levels in {Delta}pgmA imparted an enhanced growth phenotype on cholesterol. Differential gene expression and carbon flux analysis suggest that stored carbon in the form of glycogen is essential for the survival of Mtb under nutrient-limiting conditions. Finally, we demonstrate that the pgmA gene of Mtb is essential for the growth of Mtb inside the host. Overall, this study unveils the significance of pgmA-mediated regulation of membrane glycolipids and its implication on antibiotic and disease persistence in tuberculosis. Additionally, information derived from this study will help design anti-TB strategies that are novel, short, and more efficient.

microbiology↗

bioRxiv2024

Contribution of telacebec to novel drug regimens in a murine tuberculosis model

The clinical efficacy of combination drug regimens containing the first generation diarylquinoline (DARQ) bedaquiline in the treatment of multidrug-resistant tuberculosis has validated ATP synthesis as a vulnerable pathway in Mycobacterium tuberculosis. New DARQs in clinical development may be even more effective than bedaquiline, including against emerging bedaquiline-resistant strains. Telacebec (T) is a novel cytochrome bc1:aa3 oxidase inhibitor that also inhibits ATP synthesis. Based on its demonstrated efficacy as a monotherapy in mice and in a phase 2a clinical trial, we used an established BALB/c mouse model of tuberculosis (TB) to test the contribution of T to novel combination therapies against two strains of M. tuberculosis (H37Rv and HN878) in an effort to find more effective regimens. Overall, T was more effective in regimens against the HN878 strain than against the H37Rv strain, a finding that supports the greater vulnerability of the former strain to T and to genetic depletion of QcrB. Against both strains, combinations of a DARQ, clofazimine (CFZ), and T were highly bactericidal. However, only against HN878 did T contribute synergistically, whereas an antagonistic effect was observed against H37Rv. These results demonstrate the therapeutic potential of T and highlight how differences in the susceptibility of M. tuberculosis strains could lead to different conclusions about a drugs potential contribution to novel drug regimens.

microbiology↗

bioRxiv2023

Hypothetical gene Rv0495c regulates redox homeostasis in Mycobacterium tuberculosis

Mycobacterium tuberculosis (Mtb) has evolved sophisticated surveillance mechanisms to regulate and neutralize redox imbalances and associated lethal consequences. Failing this, the accumulated ROS induces toxicity by oxidizing a variety of biological molecules including proteins, nucleic acids and lipids. In the present study we identified Mtbs Rv0495c gene as an important regulator of oxidized cytosolic environment. Compared to wild type Mtb strain lacking the Rv0495c gene, {Delta}Rv0495c, had increased ROS and NAD+/NADH ratio creating a highly oxidized intracellular environment. {Delta}Rv0495c strain demonstrated slow growth phenotype under in vitro and ex-vivo growth conditions and demonstrated enhanced susceptibility to drugs, oxidative, nitrosative and hypoxic growth conditions. In addition, the increase in the superoxide radicals triggered a Fenton-like reaction rendering the {Delta}Rv0495c susceptible to free iron. The increase in the intracellular ROS levels of the {Delta}Rv0495c was further corroborated by an increase in the expression of proteins involved in antioxidant defense and enhanced ROS-mediated oxidation and degradation of mycobacterial lipids. This superoxide-induced lipid degradation resulted in altered colony morphology and loss of membrane integrity in the {Delta}Rv0495c. Surprisingly, despite showing a growth defect phenotype in an ex-vivo macrophage infection model, the absence of the Rv0495c gene in Mtb enhanced the pathogenicity and augmented the ability of the Mtb to grow inside the host. Gene expression analysis revealed a Rv0495c mediated immunomodulation of the host controls inflammation and helps creates a favorable niche for long-term survival of Mtb inside the host. In summary, the current study underscores the fact that the truce in the war between the host and the pathogen favors long-term disease persistence in tuberculosis. We believe targeting Rv0495c could potentially be explored as a strategy to potentiate the current anti-TB regimen.

microbiology↗

bioRxiv2023

VapC12 ribonuclease toxin modulates host immune response during Mycobacterium tuberculosis infection

Mechanistic understanding of antibiotic persistence is a prerequisite in controlling the emergence of MDR cases in Tuberculosis (TB). We have reported that the cholesterol-induced activation of VapC12 ribonuclease is critical for disease persistence in TB. In this study, we observed that relative to the wild type, mice infected with {Delta}vapC12 induced a proinflammatory response, had a higher pathogen load, and responded better to the anti-TB treatment. In a high-dose infection model, all the mice infected with {Delta}vapC12 succumbed early to the disease. Finally, we reported that the above phenotype of {Delta}vapC12 was dependent on the presence of the TLR4 receptor. Overall, the data suggest that the inability of {Delta}vapC12 to resolve neutrophil-mediated inflammation reduced bacterial killing by altering the T-cell response. In conclusion, our findings suggest the role of the VapC12 toxin in modulating the hosts innate immune response in ways that favor the long-term survival of the pathogen inside the host.

microbiology↗

bioRxiv2023

genomicBERT and data-free deep-learning model evaluation

The genome, which serves as the inherent language directing the blueprint of life, offers significant analysis prospects by combining Natural Language Processing (NLP) and machine learning (ML). Integrating biological sequences with other digital healthcare information has potential to transform data-driven diagnostics. Large language models (LLMs) can be harnessed to decode the genomic language. This endeavor encounters three critical challenges: First, long biomolecular sequences require segmentation into smaller subunits, which is non-trivial since many biological "words" remain unknown. Second, the analysis of extended DNA sequences using LLMs demands a compute-intensive infrastructure. Third, ensuring reproducibility and reusability of modeling workflows remains an unresolved issue. To tackle these challenges, we introduce an empirical DNA tokenisation approach and a versatile, semantic-aware, genome language model --genomicBERT. The model is species-agnostic and operates seamlessly at the DNA or RNA levels. By introducing a reduced and specialized DNA vocabulary, our approach minimizes computational overhead and optimizes performance. Our benchmarking demonstrates that the genomicBERT matches or surpasses the performance of contemporary tools on the same datasets under different experimental conditions. To encourage collaboration and ease of access, we introduce genomicBERT as an integral component of the openly accessible conda package, genomeNLP. Validated across diverse case studies, genomicBERT lowers the barriers to decoding genomic language, relying solely on sequence data to extract meaningful insights. HighlightsO_LIThis novel model offers a compelling solution for DNA sequence analysis by significantly reducing model size and computational costs without compromising performance, setting a new standard for efficient model development. C_LIO_LIWe demonstrate that a powerful vocabulary and tokenization method helps to derive patterns from biological sequence data while accounting for hidden semantic rules. C_LIO_LIOur method is agnostic to species or biomolecule type as it is data-driven. Hence, it can be applied to DNA and RNA C_LIO_LIWe validate the important genomicBERT tokens by mapping back to the biologically significant motifs. C_LIO_LIWe present a publicly available genome language modeling toolkit called genomeNLP, specifically designed to combine computational linguistics and genomics, enabling researchers from biology backgrounds to analyze and interpret genomic sequences effectively. C_LI

bioinformatics↗

bioRxiv2023

Metabolic alterations unravel the materno fetal immune responses with disease severity in pregnant women infected with SARS-CoV-2

BackgroundPregnancy being immune compromised state, COVID-19 disease poses high risk of premature delivery and threat to fetus. Plasma metabolome regulates immune cellular responses and we aimed to analyze the plasma secretome, metabolome and immune cells in COVID-19 positive pregnant mother and cord blood. MethodsCOVID-19 RT-PCR positive pregnant females (n=112) asymptomatic (n=82), or with mild (n=21) or moderate (n=9) disease and control healthy pregnant (n=10) females were included. Mothers blood and cord blood (n=80) was analysed for untargeted metabolome profiling and plasma cytokines by high-resolution mass spectrometry (MS) and multiplex cytokine bead array. Immune scan in mothers was done using flow cytometry. ResultsIn asymptomatic SARS-CoV-2 infection, --the amino acid metabolic pathways such as glycine, serine, L-lactate and threonine metabolism was upregulated, riboflavin and tyrosine metabolism, downregulated. In mild to moderate disease, the pyruvate and NAD+ metabolism (energy metabolic pathways) were mostly altered. In addition to raised TNF-, IFN-, IFN-{gamma}, IL-6 cytokine storm, IL-9 was increased in both mothers and neonates. Pyruvate and NAD+ metabolic pathways along with IL-9 and IFN-{gamma} had impact on non-classical monocytes, increased CD4 T cells and B cells but depleted CD8+ T cells. Cord blood mimicked the mothers metabolomic profiles by showing altered valine, leucine, isoleucine, glycine, serine, threonine in asymptomatic and NAD+ and riboflavin metabolism in mild and moderate disease subjects. ConclusionsOur results demonstrate a graduated immune-metabolomic interplay in mother and fetus in pregnant females with different degrees of severity of COVID-19 disease. IL-9 and IFN- {gamma} regulated pyruvate, lactate TCA metabolism and riboflavin metabolism with context to disease severity are hall marks of this materno-fetal metabolome. HighlightsO_LISARS-CoV-2 infection alters energy consumption metabolic pathways during pregnancy. C_LIO_LIPregnant women with mild to moderate COVID-19 show increased energy demands, and consume stored glucose by upregulating pyruvate and NAD+ metabolism. C_LIO_LIIncreased TNF- and IL-9 in mild COVID-19 disease involve TCA cycle to produce lactate and consume stored glucose by up regulating pyruvate and nicotinamide and nicotinate metabolism. C_LIO_LIWith mild to moderate disease, raised IL-9 and TNF-, decreased riboflavin pathway, exhaustion of T and B cells cause pathogenesis. C_LIO_LICord blood mimics the metabolic profile of mothers peripheral blood, SARS- CoV-2 infection reshapes immune-metabolic profiles of mother-infant dyad. C_LI Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=141 HEIGHT=200 SRC="FIGDIR/small/540101v1_ufig1.gif" ALT="Figure 1"> View larger version (36K): org.highwire.dtl.DTLVardef@657cc3org.highwire.dtl.DTLVardef@e1e76forg.highwire.dtl.DTLVardef@12153f2org.highwire.dtl.DTLVardef@10e5332_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2023

Uncovering Co-regulatory Modules and Gene Regulatory Networks in the Heart through Machine Learning-based Analysis of Large-scale Epigenomic Data

The availability of large scale epigenomic data from different cell types and conditions has provided valuable information to evaluate and learn features that predict co-binding of transcription factors (TF). However, previous attempts to develop models for predicting motif cooccurrence were not scalable for global analysis of any combination of motifs or cross-species predictions. Further, mapping co-regulatory modules (CRM) to their gene regulatory networks (GRN) is crucial in understanding the underlying function. Currently, there is no comprehensive pipeline to locate CRM and GRN on a large scale with speed and accuracy. In this study, we analyzed and evaluated different TF binding characteristics that would facilitate co-binding with biological significance to identify all possible clusters of co-binding TFs. We curated the UniBind database, which contains ChIP-Seq data from over 1983 samples and 232 TFs, and implemented two machine learning models to predict CRMs and potential regulatory networks they operate on. We narrowed our focus to study heart related regulatory motifs. Our findings highlight the importance of the NKX family of transcription factors in cardiac development and provide potential targets for further investigation in cardiac disease.

bioinformatics↗

bioRxiv2023

Interferon epsilon restricts Zika virus infection in the female reproductive tract

Interferon {varepsilon} (IFN{varepsilon}) is a unique type I IFN that has been implicated in host defense against sexually transmitted infections (STIs). Zika virus (ZIKV), an emerging pathogen, can infect the female reproductive tract (FRT) and cause devastating diseases, particularly in pregnant women. How IFN{varepsilon} contributes to protection against ZIKV infection in vivo is unknown. Here, we show that IFN{varepsilon} plays a critical role in host protection against vaginal ZIKV infection in mice. We found that IFN{varepsilon} was expressed not only by epithelial cells in the FRT, but also by certain immune and other cells at baseline or after exposure to viruses or specific TLR agonists. IFN{varepsilon}-deficient mice exhibited abnormalities in the epithelial border and underlying tissue in the cervicovaginal tract, and these defects were associated with increased susceptibility to vaginal, but not subcutaneous ZIKV infection. IFN{varepsilon}-deficiency resulted in an increase in magnitude, duration, and depth of ZIKV infection in the FRT. Critically, intravaginal administration of recombinant IFN{varepsilon} protected Ifn{varepsilon}-/- mice and highly susceptible Ifnar1-/-mice against vaginal ZIKV infection, indicating that IFN{varepsilon} was sufficient to provide protection even in the absence of signals from other type I IFNs and in an IFNAR1-independent manner. Our findings reveal a potentially critical role for IFN{varepsilon} in mediating protection against transmission of ZIKV in the context of sexual contact. SignificanceInterferon {varepsilon} (IFN{varepsilon}), a unique Type I IFN that is highly expressed in the epithelium of the female reproductive tract (FRT), is thought to protect the host against sexually transmitted infections (STIs) but the mechanism of action is not defined. Zika virus (ZIKV), a causative agent for preterm birth and other severe diseases in pregnant women, can be spread through vaginal transmission. Here, we show that mice lacking the Ifn{varepsilon} gene have abnormal epithelial development and tissue architecture in the cervicovaginal tract. The role of IFN{varepsilon} in protecting host against ZIKV is FRT-specific and is independent of IFNAR1 signaling. Our findings suggest potential preventive strategies based on harnessing mucosal immunity against STIs.

immunology↗

bioRxiv2023

Rab7 dependent regulation of goblet cell protein CLCA1 modulates gastrointestinal homeostasis

Inflammation in ulcerative colitis is typically restricted to the mucosal layer of distal gut. Disrupted mucus barrier coupled with microbial dysbiosis has been reported to occur prior to the onset of inflammation. Here, we show the involvement of vesicular trafficking protein Rab7 in regulating the colonic mucus system. We identified a lowered Rab7 expression in goblet cells of colon during human and murine colitis. In vivo Rab7 knocked down mice (Rab7KD) displayed a compromised mucus layer, increased microbial permeability and depleted gut microbiota with enhanced susceptibility to dextran sodium-sulfate induced colitis. These abnormalities emerged owing to altered mucus composition, as revealed by mucus proteomics, with increased expression of mucin protease Chloride channel accessory 1 (CLCA1). Mechanistically, Rab7 maintained optimal CLCA1 levels by controlling its lysosomal degradation, a process that was dysregulated during colitis. Overall, our work establishes a role for Rab7 dependent control of CLCA1 secretion required for maintaining mucosal homeostasis.

cell biology↗

bioRxiv2023

Imaging Architecture of Granulomas Induced by Mycobacterium tuberculosis Infections with Single-Molecule FISH

Granulomas are an important hallmark of Mycobacterium tuberculosis (Mtb) infection. They are organized and dynamic structures created by an assembly of immune cells around the sites of infection in the lungs to locally restrict the bacterial growth and the hosts inflammatory responses. The cellular architecture of granulomas is traditionally studied by immunofluorescence labeling of phenotypic surface markers. However, very few antibodies are available for model animals used in tuberculosis research, such as non-human primates and rabbits; secreted immunological markers such as cytokines cannot be imaged in situ using antibodies; and traditional phenotypic surface markers do not provide sufficient resolution for the detection of many subtypes and differentiation states of immune cells. Using single-molecule fluorescent in situ hybridization (smFISH) and its derivatives, amplified smFISH (ampFISH) and iterative smFISH, we developed a platform for imaging mRNAs encoding immune markers in rabbit and macaque tuberculosis granulomas. Multiplexed imaging for several mRNA and protein markers was followed by quantitative measurement of expression of these markers in single cells in situ. A quantitative analysis of combinatorial expressions of these markers allowed us to classify the cells into several subtypes and chart their distributions within granulomas. For one mRNA target, HIF-1, we were able to image its mRNA and protein in the same cells, demonstrating the specificity of probes. This method paves the way for defining granular differentiation states and cell subtypes from transcriptomic data, identifying key mRNA markers for these cell subtypes, and then locating the cells in the spatial context of granulomas.

immunology↗

bioRxiv2022

Flavonols contrary affect the interconnected glucosinolate and camalexin biosynthesis pathway in Arabidopsis thaliana

Flavonols are structurally and functionally diverse molecules playing roles in plant biotic and abiotic stress tolerance, auxin transport inhibition, pollen development, etc. Despite their ubiquitous occurrence in land plants and multifunctionality, the effect of perturbation of flavonol biosynthesis over global gene expression and pathways other than flavonoid biosynthesis has not been studied in detail. To understand the signaling role of different flavonol metabolites, herein, we used the flavonol deficient Arabidopsis thaliana loss-of-function mutant flavonol synthase1 (fls1-3) as object of study. Comparative transcriptome and metabolic profiling were used to study the effects of genetic flavonol deficiency and exogenous supplementation with flavonol derivatives (kaempferol, quercetin and rutin) on different cellular processes in the seedling. Various flavonol biosynthesis-related regulatory and structural genes were found to be up-regulated in the fls1-3 mutant which could be reversed by exogenous flavonol feeding. Our manifold comparative studies indicated the modulation of various biological processes and metabolic pathways by flavonols. Camalexin biosynthesis was found to be negatively regulated by flavonols. Interestingly, flavonols appeared to promote the accumulation of aliphatic glucosinolate through transcription factor-mediated up-regulation of biosynthesis genes. Overall, this study provides new insights into molecular mechanisms by which flavonols interfere with the relevant signal chains and their molecular targets and adds new knowledge to the expanding plethora of biological activity of flavonols in plants. SignificanceComparative transcriptome and metabolomic profiling of genetic flavonol deficiency and exogenous flavonol supplementation in A. thaliana seedlings, for the first-time revealed the inverse regulation of interconnected specialized metabolite pathways by flavonol aglycones, and -glycosides. Flavonols negatively regulate camalexin biosynthesis, while promoting the accumulation of aliphatic glucosinolates. Our study adds new insights into the expanding plethora of biological activity of flavonols in plants and will help to uncover the molecular mechanisms by which flavonols interfere with the relevant signal chains and their molecular targets.

plant biology↗

bioRxiv2022

MLL family members regulate H3K4 methylation to ensure CENP-A assembly at human centromeres.

The active state of centromeres is epigenetically defined by the presence of CENP-A interspersed with histone H3 nucleosomes. While the importance of dimethylation of H3K4 mark for centromeric transcription has been highlighted in various studies, the identity of the enzyme(s) depositing these marks on the centromere is still unknown. The MLL (KMT2) family play a crucial role in RNA polymerase II (Pol II)-mediated gene regulation by methylating H3K4. Here, we report that MLL family regulate transcription of human centromeres. CRISPR-mediated downregulation of MLL causes loss of H3K4me2, resulting in an altered epigenetic chromatin state of the centromeres. Intriguingly, our results reveal that loss of MLL, but not SETD1A, increases co-transcriptional R-loop formation, and Pol II accumulation at the centromeres. Finally we report that the presence of MLL and SETD1A is crucial for kinetochore maintenance. Altogether, our data reveals a novel molecular framework where both the H3K4 methylation mark and the methyltransferases regulate stability and identity of the centromere.

cell biology↗