Biology subjects

Narang, A.

Publications and source records attributed to Narang, A..

16 recordsLinked to original sources

bioRxiv2026

Characterization of variants associated with Cerebral Small Vessel Disease identifies a functional SNV in Versican

BackgroundSingle nucleotide variants in the non-coding genome can significantly alter disease risk, but identifying the function of SNVs is a challenge. Increasing numbers of variants of unknown significance have been associated with the risk of Stroke, Cerebral Small Vessel Disease and burden of White Matter Hyperintensities, but without biological validation, the significance of these findings is uncertain. MethodsWe use a Multiplexed Parallel Reporter Assay (MPRA) to assay the function of 44 SNVs associated with Cerebral Small Vessel Disease and stroke in EFEMP1, FOXF2, HAAO, KCNK3, NMT1, OPA1, RASL12, STAT3 and VCAN. A functional SNV in versican was further probed using transcriptional reporter and Chromatin Immunoprecipitation assays. ResultsWe identify 26 allele-specific enhancers in where the SNV either increases or decreases transcriptional activity. We validate rs13176921 as an SNV that significantly modulates an intronic enhancer in the matrisome protein Versican and show it affects mRNA levels of the gene. We identify that the transcription factor NKX3.1 binds to the region of this SNV. ConclusionsThus, using MRPA we were able to gain mechanistic insight into which GWAS-identified SNVs modulate transcriptional activity, and validate a functionally important SNV in Versican and provide a mechanism by which it controls its transcription.

genetics↗

bioRxiv2023

A genetic program for vascular pericyte precursors

Brain pericytes are one of the critical cell types that regulate endothelial barrier function and activity, thus ensuring adequate blood flow to the brain. The genetic pathways guiding undifferentiated cells into mature pericytes are not well understood. We show here that pericyte precursor populations from both neural crest and head mesoderm of zebrafish express the transcription factor nkx3.1 develop into brain pericytes. We identify the gene signature of these precursors, and show that an nkx3.1, foxf2a, and cxcl12b -expressing pericyte precursor population is present around the basilar artery prior to artery formation and pericyte recruitment. The precursors later spread throughout the brain and differentiate to express canonical pericyte markers. Cxcl12b-Cxcr4 signaling is required for pericyte attachment and differentiation. Further, both nkx3.1 and cxcl12b are necessary and sufficient in regulating pericyte number as loss inhibits and gain increases pericyte number. Through genetic experiments we have defined a precursor population for brain pericytes and identified genes critical for their differentiation.

developmental biology↗

bioRxiv2022

Noise-induced symmetry breaking in a network of excitable ecological systems

Noise-induced symmetry breaking has barely been unveiled on the ecological grounds, though its occurrence may elucidate mechanisms responsible for maintaining biodiversity and ecosystem stability. Here, for a network of excitable consumer-resource systems, we show that the interplay of network structure and noise intensity manifests a transition from homogeneous steady state to inhomogeneous steady states, resulting in noise-induced symmetry breaking. On further increasing the noise intensity, there exist asynchronous oscillations, leading to heterogeneity crucial for maintaining a systems adaptive capacity. The observed collective dynamics can be understood analytically in the framework of linear stability analysis of the corresponding deterministic system.

ecology↗

bioRxiv2022

In-vivo phase-dependent enhancement and suppression of brain oscillations by transcranial alternating current stimulation (tACS)

Transcranial alternating current stimulation (tACS) can influence human perception and behavior, with recent evidence also suggesting its potential impact in clinical settings, but the underlying mechanisms are poorly understood. Behavioral and indirect physiological evidence indicates that phase-dependent constructive and destructive interference between the tACS electric field and ongoing brain oscillations may play an important role, but direct in-vivo validation was infeasible because stimulation artifacts impeded such assessment. Using stimulation artifact source separation (SASS), a real-time compatible artifact suppression approach, we overcame this limitation and provide direct evidence for millisecond-by-millisecond phase-dependent enhancement and suppression of ongoing brain oscillations during amplitude-modulated tACS (AM-tACS) across 29 healthy human volunteers. We found that AM-tACS enhanced and suppressed targeted brain oscillations by 11.7 {+/-} 5.14% and 10.1 {+/-} 4.07% respectively. Millisecond-precise modulation of oscillations predicted modulation of behavior (r = 0.65, p < 0.001). These results not only provide direct evidence for constructive and destructive interference as a key mechanism of AM-tACS but suggest superiority of phase-locked (closed-loop) AM-tACS over conventional (open-loop) AM-tACS to purposefully enhance or suppress brain oscillations. SignificanceThe presented data provide direct evidence for a key mechanism underlying neurophysiological and behavioral effects of transcranial alternating current stimulation (tACS), a broadly used neuromodulation approach that yields promising clinical results but also raised controversies because of its variable effects. Our findings not only elucidate the underlying mechanisms of tACS, but also provide the rationale for closed-loop tACS protocols that will enable targeted enhancement and suppression of brain oscillations related to various brain functions such perception, memory or cognition. Towards this end, we introduce the technical prerequisites to establish millisecond-to-millisecond precise closed-loop tACS protocols that will be important to advance tACS as a neuroscientific and clinical tool, for example in the treatment of neuropsychiatric disorders.

neuroscience↗

bioRxiv2021

PAOX1 expression in mixed-substrate continuous cultures of Komagataella phaffii (Pichia pastoris) is completely determined by methanol uptake regardless of the secondary carbon source: a simplifying principle for predicting recombinant protein production.

The expression of recombinant proteins by the AOX1 promoter of Komagataella phaffii is typically induced by adding methanol to the cultivation medium. Since growth on methanol imposes a high oxygen demand, the medium is often supplemented with an additional secondary carbon source which serves to reduce the consumption of methanol, and hence, oxygen. Early research recommended the use of glycerol as the secondary carbon source, but more recent studies recommend the use of sorbitol because glycerol represses PAOX1 expression. To assess the validity of this recommendation, we measured the steady state concentrations of biomass, residual methanol, and LacZ expressed from PAOX1 over a wide range of dilution rates (0.02-0.20 h-1) in continuous cultures of the Mut+ strain fed with methanol + glycerol (repressing) and methanol + sorbitol (non-repressing). We find that under these conditions, the specific PAOX1 expression rate is completely determined by the specific methanol consumption rate regardless of the type (repressing/non-repressing) of the secondary carbon source. In both cultures, the specific PAOX1 expression rate is proportional to the specific methanol consumption rate provided that the latter is below 0.15 g/(gdw-h); beyond this threshold consumption rate, the specific PAOX1 expression rate of both cultures saturates to the same value. Analysis of the data in the literature shows that the same phenomenon also occurs in continuous cultures of Escherichia coli fed with mixtures of lactose plus repressing/non-repressing carbon sources. The specific Plac expression rate is completely determined by the specific lactose consumption rate regardless of the type of secondary carbon source, glycerol or glucose. Key pointsO_LIPAOX1 expression rate is completely determined by the methanol consumption rate. C_LIO_LISorbitol is not necessarily superior secondary carbon source than glycerol. C_LI

bioengineering↗

bioRxiv2021

Aggregation state of Mycobacterium tuberculosis impacts host immunity and augments pulmonary disease pathology

Phagocytosis of Mycobacterium tuberculosis (Mtb) aggregates, rather than similar numbers of single bacilli, induces host macrophage death and favors bacterial growth. Here, we examined whether aggregation contributes to enhanced Mtb pathogenicity in vivo in rabbit lungs. Rabbits were exposed to infectious aerosols containing mainly Mtb-aggregates (Mtb-AG) or Mtb-single cells (Mtb-SC). The lung bacterial load, histology, and immune cell composition were investigated over time. Genome-wide transcriptome analysis, cellular and tissue-level assays, and immunofluorescent imaging were performed on lung tissue to define and compare differential immune activation and pathogenesis between Mtb-AG and Mtb-SC infection. Lung bacillary loads, disease scores, lesion size, and structure were significantly higher in Mtb-AG than in Mtb-SC infected animals. A differential immune cell distribution and activation were noted in the lungs and spleen of the two groups of infected animals. Mtb-AG infected animals also showed early induction of inflammatory network genes associated with necrosis and reduced host cell viability. Consistently, larger lung granulomas with clumped Mtb, extensive necrotic foci, and elevated matrix metalloproteases expression were observed in Mtb-AG infected rabbits. Our findings suggest that bacillary aggregation increases Mtb fitness for improved growth and accelerated lung inflammation and cell death, thereby exacerbating disease pathology in the lungs.

microbiology↗

bioRxiv2020

Human PRE-PIK3C2B exhibits long-range intra- and inter-chromosomal interactions with genomic regions enriched in repressive marks.

Human PRE-PIK3C2B is a dual nature polycomb response element that interacts with both polycomb as well as trithorax members. In the current study, using 4C-Seq (Capturing Circular Chromosomal Conformation-Sequencing), we identified long-range chromatin interactions associated with PRE-PIK3C2B and validated them with 3C-PCR. We identified both intra-as well as inter-chromosomal interactions, a large proportion of which were found to be closely distributed around transcriptional start sites (TSS). A significant number of interactions were also found to be associated with heterochromatic regions. Meta-analysis of ENCODE ChIP-Seq data identified an overall enrichment of YY1, CTCF as well as histone modification such as H3K4me3 and H3K27me marks in different cell lines. Almost 90% interactions were derived from either intronic or intergenic regions. among which large proportions of intronic interactors were either unique sequences or LINE/SINE derived. In case of intergenic interactions, majority of the interaction were associated with LINE/SINE repeats. We further found that genes proximal to the interactor sequences were co-expressed, they showed reduced expression. To the best of our knowledge this is one of the early demonstrations of long-range interaction of PRE sequences in human genome.

genetics↗

bioRxiv2020

Deconstructing glucose-mediated catabolite repression of the lac operon of Escherichia coli: II. Positive feedback exists and drives the repression

The expression of the lac operon of E. coli is subject to positive feedback during growth in the presence of gratuitous inducers, but its existence in the presence of lactose remains controversial. The key question in this debate is: Do the lactose enzymes, Lac permease and β-galactosidase, promote accumulation of allolactose? If so, positive feedback exists since allolactose does stimulate synthesis of the lactose enzymes. Here, we addressed the above question by developing methods for determining the intracellular allolactose concentration as well as the kinetics of enzyme induction and dilution. We show that during lac induction in the presence of lactose, the intracellular allolactose concentration increases with the lactose enzyme level, which implies that lactose enzymes promote allolactose accumulation, and positive feedback exists. We also show that during lac repression in the presence of lactose + glucose, the intracellular allolactose concentration decreases with the lactose enzyme levels, which suggests that under these conditions, the positive feedback loop turns in the reverse direction. The induction and dilution rates derived from the transient data show that the positive feedback loop is reversed due to a radical shift of the steady state induction level. This is formally identical to the mechanism driving catabolite repression in the presence of TMG + glucose.Competing Interest StatementThe authors have declared no competing interest.View Full Text

systems biology↗

bioRxiv2020

Genome and transcriptome analysis of the mealybug Maconellicoccus hirsutus: A model for genomic Imprinting

In mealybugs, transcriptional inactivation of the entire paternal genome in males, due to genomic imprinting, is closely correlated with sex determination. The sequencing, de-novo assembly and annotation of the mealybug, Maconellicoccus hirsutus genome and its comparison with Planococcus citri genome strengthened our gene identification. The expanded gene classes, in both genomes relate to the high pesticide and radiation resistance; the phenotypes correlating with increased gene copy number rather than the acquisition of novel genes. The complete repertoire of genes for epigenetic regulation and multiple copies of genes for the core members of polycomb and trithorax complexes and the canonical chromatin remodelling complexes are present in both the genomes. Phylogenetic analysis with Drosophila shows high conservation of most genes, while a few have diverged outside the functional domain. The proteins involved in mammalian X-chromosome inactivation are identified in mealybugs, thus demonstrating the evolutionary conservation of factors for facultative heterochromatization. The transcriptome analysis of adult male and female M.hirsutus indicates the expression of the epigenetic regulators and the differential expression of metabolic pathway genes and the genes for sexual dimorphism. The depletion of endosymbionts in males during development is reflected in the significantly lower expression of endosymbiont genes in them. Author summaryThe mealybug system offers a unique model for genomic imprinting and differential regulation of homologous chromosomes that pre-dates the discovery of dosage compensation of X chromosomes in female mammals. In the absence of robust genetics for mealybugs, we generated and analysed the genome and transcriptome profile as primary resources for effective exploration. The expanded gene classes in the mealybugs relate to their unique biology; the expansion of pesticide genes, trehalose transporter, SETMAR and retrotransposons correlate with pesticide, desiccation and radiation resistance, respectively. The similarity in the genomic profile of two species of mealybugs strengthens our gene prediction. All the known epigenetic modifiers and proteins of the primary complexes like the PRC1,2 and the trithorax are conserved in mealybugs, so also the homologues of mammalian proteins involved in X chromosome inactivation. The high copy number of genes for many partners in these complexes could facilitate the inactivation of a large part of the genome and raise the possibility of formation of additional non-canonical complexes for sex specific chromosome inactivation. In adult males and females, the status of epigenetic regulation is likely to be in a maintenance state; therefore, it is of interest to analyze the expression of epigenetic regulators during development.

genomics↗

bioRxiv2020

Genetic differences between extreme and composite constitution types from whole exome sequences reveal actionable variations

Personalized medicine relies on successful identification of genome-wide variations that governs inter-individual differences in phenotypes and system level outcomes. In Ayurveda, assessment of composite constitution types "Prakriti" forms the basis for risk stratification, predicting health and disease trajectories and personalized recommendations. Here, we report a novel method for identifying pleiotropic genes and variants that associate with healthy individuals of three extreme and contrasting "Prakriti" constitutions through exome sequencing and state-of-the-art computational methods. Exome Seq of three extreme Prakriti types from 108 healthy individuals 54 each from genetically homogeneous populations of North India (NI, Discovery cohort) and Western India (VADU, Replication cohort) were evaluated. Fishers Exact Test was applied between Prakriti types in both cohorts and further permutation based p-value was used for selection of exonic variants. To investigate the effect of sample size per genetic association test, we performed power analysis. Functional impact of differentiating genes and variations were inferred using diverse resources -Toppfun, GTEx, GWAS, PheWAS, UK Biobank and mouse knockdown/knockout phenotype (MGI). We also applied supervised machine learning approach to evaluate the association of exonic variants with multisystem phenotypes of Prakriti. Our targeted investigation into exome sequencing from NI (discovery) and VADU (validation) cohorts datasets provide ~7,000 differentiating SNPs. Closer inspection further identified a subset of SNPs (2407 (NI) and 2393 (VADU)), that mapped to an overlapping set of 1181 genes. This set can robustly stratify the Prakriti groups into three distinct clusters with distinct gene ontological (GO) enrichments. Functional analysis further strengthens the potential pleiotropic effects of these differentiating genes/variants and multisystem phenotypic consequences. Replicated SNPs map to some very prominent genes like FIG4, EDNRA, ANKLE1, BCKDHA, ATP5SL, EXOCS5, IFIT5, ZNF502, PNPLA3 and IL6R. Lastly, multivariate analysis using random forest uncovered rs7244213 within urea transporter SLC14A2, that associate with an ensemble of features linked to distinct constitutions. Our results reinforce the concept of integration of Prakriti based deep phenotypes for risk stratification of healthy individuals and provides markers for early actionable interventions.

genomics↗

bioRxiv2020

An urn model approach to stochastic modeling of regulated gene expression yields physically intuitive solutions for probability distributions

Fitting the probability mass functions from analytical solutions of stochastic models of gene expression to the count distributions of mRNA and protein molecules in single cells can yield valuable insights into mechanisms of gene regulation. Solutions of chemical master equations are available for various kinetic schemes but, even for the models of regulation with a basic ON-OFF switch, they take complex forms with generating functions given as hypergeometric functions. Gene expression studies that have used these to fit the data have interpreted the parameters as burst size and frequency. However, this is consistent with the hypergeometric functions only if a gene stays active for short time intervals separated by relatively long intervals of inactivity. Physical insights into the probability mass functions are essential to ensure proper interpretations but are lacking for models of gene regulation. We fill this gap by developing urn models for regulated gene expression, which are of immense value to interpret probability distributions. Our model consists of a master urn, which represents the cytosol. We sample RNA polymerases and ribosomes from it and assign them to recipient urns of two or more colors, which represent time intervals with a homogeneous propensity for gene expression. Colors of the recipient urns represent sub-systems of the promoter states, and the assignments to urns of a specific color represent gene expression. We use elementary principles of discrete probability theory to derive the solutions for a range of kinetic models, including the Peccoud-Ycart model, the Shahrezaei-Swain model, and models with an arbitrary number of promoter states. For activated genes, we show that transcriptional lapses, which are events of gene inactivation for short time intervals separated by long active intervals, quantify the transcriptional dynamics better than bursts. Our approach reveals the physics underlying the solutions, which has important implications for single-cell data analysis.

biophysics↗

bioRxiv2019

Deconstructing glucose-mediated catabolite repression of the lac operon of Escherichia coli: I. Inducer exclusion, by itself, cannot account for the repression.

The lac operon of Escherichia coli is repressed several 100-fold in the presence of glucose. This repression has been attributed to CRP-mediated transcriptional inhibition and EIIAGlc-mediated inducer exclusion. The growing evidence against the first mechanism has led to the postulate that the repression is driven by inducer exclusion. The literature shows that in fully induced cells, inducer exclusion reduces the permease activity only 2-fold. However, it is conceivable that inducer exclusion drastically reduces the permease activity in partially induced cells. We measured the decline of lactose permease activity due to inducer exclusion in partially induced cells, but found that the permease activity decreased no more than 6-fold. We show that the repression is small because these experiments are performed in the presence of chloramphenicol. Indeed, when glucose is added to a culture growing on glycerol and TMG, but no chloramphenicol, lac is repressed 900-fold. This repression is primarily due to reversal of the positive feedback loop, i.e., the decline of the intracellular TMG level leads to a lower permease level, which reduces the intracellular TMG level even further. The repression in the absence of chloramphenicol is therefore primarily due to positive feedback, which does not exist during measurements of inducer exclusion.Competing Interest StatementThe authors have declared no competing interest.ABBREVIATIONS AND NOTATIONScAMP3’,5’-cyclic adenosine monophosphateCGSCColi Genetic Stock Centre, Yale UniversityCRPcAMP receptor proteinEIIAGlcEnzyme III of glucose transport system, PTS (Previously EIIIGlc)gdwGrams of cell dry weight, gIPTGIsopropyl β-D-thiogalactopyranoside or MeSHLBLuria-Bertani brothMUMiller unitsOD600Optical density at 600 nmONPGortho-nitrophenol-β-D-galactopyranosideRNAPRibonucleic acid (RNA) polymeraseTMGMethyl- β-D-1-thiogalactopyranoside[14C]TMGCarbon-14 labelled isotope of TMGUVUltraviolet (radiation)X-gal5-bromo-4-chloro-3-indolyl-β-D-galactopyranosideNOTATIONSIntracellular concentration of phosphorylated EIIAglc in the absence of glucoseIntracellular concentration of dephosphorylated EIIAglc in the presence of glucoseEgSpecific activity of β-galactosidaseSteady state specific activity of β-galactosidase in the presence of glucoseSteady state specific activity of β-galactosidase in the presence of glycerolEpSpecific activity of Lac permeaseSteady state specific activity of Lac permeaseEp,tSpecific activity of free Lac permease in the absence of glucoseφpFractional reduction of permease activity in the presence of glucose, 1 - Ep/Ep,tk1, k2Proportionality constantsKdDissociation constant for complex OD600Optical density at 600 nmSp. rate of β-galactosidase synthesis in the presence of glucose + glycerol + TMGSp. rate of β-galactosidase synthesis in the presence of glycerol + TMGSpecific rate of diffusive efflux of TMGTIntracellular TMG concentrationSteady-state intracellular TMG concentrationSteady-state intracellular TMG concentration in the presence of glucoseSteady-state intracellular TMG concentration in the presence of glucoseTeExtracellular TMG concentrationµglcSpecific growth rate of E. coli cells on glucoseµglySpecific growth rate of E. coli cells on glycerolXBiomass or cell density, gdw l-1View Full Text

systems biology↗

bioRxiv2019

A comparative analysis of histone methyltransferases and demethylases in insect genome: A meta-analysis

BackgroundThe epigenetic regulation through post-translational modification of histones, especially methylation is well conserved, while DNA methylation is variable, being very low or absent in Drosophila melanogaster. Though there are several insect genomes sequenced, an analysis with a focus on their epigenetic repertoire is limited. We have compared the histone methyltransferases and the demethylases in the genome of Drosophila melanogaster, Aedes aegypti (Diptera), the pea aphid Acyrthosiphon pisum, the triatomid bug Rhodnius prolixus (Hemiptera), the honeybee Apis mellifera (Hymenoptera), the silkworm Bombyx mori (Lepidoptera) and the red flour beetle Tribolium castaneum (Coleoptera).\n\nResultsWe identified 38 clusters consisting of arginine, lysine methyltransferases and demethylases using OrthoFinder. To eliminate false positives, we designed a method based on identifying highly conserved domain within each class designated as the high priority domain. Out of the 9 arginine methyltransferases, Art2, Art6 and Art9 are identified in D.melanogaster only. We observe copy number variation between the genomes; A.pisum has nine copies of eggless gene (H3K9me3 methyltransferase), which can be correlated with the switch between parthenogenesis and sexual reproduction. Other than the high-priority domains, these proteins contain shared and unique domains that can mediate protein-protein interaction. Phylogenetic analysis indicates that the there is a broad conservation within the members of a class while duplication and divergence is observed in LSD1.\n\nConclusionThis meta-analysis provides a method for reliable identification of epigenetic modifiers of histones in newly sequenced insect genomes. Similar approach can be taken for other classes of genes.

genomics↗

bioRxiv2019

The Mut+ strain of Komagataella phaffii (Pichia pastoris) expresses PAOX1 5 and 10 times faster than Muts and Mut- strains: Evidence that formaldehyde or/and formate are true inducers of AOX.

The methylotrophic yeast Komagataella phaffii is among the most popular hosts for recombinant protein synthesis. Most recombinant proteins were expressed in the wild-type Mut+ host strain from the methanol-inducible promoter PAOX1. Since methanol metabolism has undesirable consequences, two additional host strains, Muts (AOX1-) and Mut- (AOX1- AOX2-), were introduced which consume less methanol and reportedly also express recombinant protein better than Mut+. Both results follow from a simple model based on two widespread assumptions, namely methanol is transported by diffusion and the sole inducer of PAOX1. To test this model, we studied 14C-methanol uptake in the Mut- strain and {beta}-galactosidase expression in all three strains. We confirmed that methanol is transported by diffusion, but in contrast to the literature, Mut+ expressed {beta}-galactosidase 5- and 10-fold faster than Muts and Mut-. These results imply that methanol is not the sole inducer of PAOX1 -- metabolites downstream of methanol also induce PAOX1. We find that formate or/and formaldehyde are probably true inducers since both induce PAOX1 expression in Mut- which cannot synthesize intracellular methanol from formate or formaldehyde. Formate offers a promising substitute for methanol since it does not appear to suffer from the deficiencies that afflict methanol.

bioengineering↗

bioRxiv2019

Analytical expressions and physical principles for single-cell mRNA distributions of the lac operon of Escherichia coli

Mechanistic models of stochastic gene expression are of considerable interest, but their complexity often precludes tractable analytical expressions for mRNA and protein distributions. The lac operon of E. coli is a model system with regulatory elements such as multiple operators and DNA looping that are shared by many operons. Although this system is complex, intuition suggests that fast DNA looping may simplify it by causing the repressor-bound states of the operon to equilibrate rapidly, thus ensuring that the subsequent dynamics are governed by slow transitions between the repressor-free and the equilibrated repressor-bound states. Here, we show that this intuition is correct by applying singular perturbation theory to a mechanistic model of lac transcription with the scaled time constant of DNA looping as the perturbation parameter. We find that at steady state, the repressor-bound states satisfy detailed balance and are dominated by the looped states; moreover, the interaction between the repressor-free and the equilibrated repressor-bound states is described by an extension of the Peccoud-Ycart two-state model in which both (repressor-free and repressor-bound) states support transcription. The solution of this extended two-state model reveals that the steady state mRNA distribution is a mixture of the Poisson and negative hypergeometric distributions which reflects mRNAs obtained by transcription from the repressor-bound and repressor-free states, respectively. Finally, we show that the physics revealed by perturbation theory makes it easy to derive the extended two-state model equations for complex regulatory architectures.

biophysics↗

bioRxiv2019

The regulatory function of dIno80 correlates with its DNA binding activity

The INO80 complex, including the Ino80 protein, forms a highly conserved canonical complex that remodels chromatin in the context of multiple cellular functions. The Drosophila homologue, dIno80, is involved in homeotic gene regulation during development as a canonical Pho-dIno80 complex. Previously, we found that dIno80 regulates homeotic genes by interacting with epigenetic regulators, such as polycomb and trithorax, suggesting the occurrence of non-canonical Ino80 complexes. Here using spectroscopic methods and gel retardation assays, we identified a set of consensus DNA sequences that DNA binding domain of dIno80 (DBINO) interacts with having differential affinity and high specificity. Testing these sequences in reporter assays, showed that this interaction can positively regulate transcription. These results suggest that, dIno80 has a sequence preference for interaction with DNA leading to transcriptional changes.\n\nSIGNIFICANCEThe chromatin remodeling proteins control gene expression by nucleosome sliding and exchange. They are known to function as multi-subunit complexes recruited to chromatin by transcription factors or histone modification readers. Here, we report a sequence specific binding potential for the chromatin remodeler, dIno80. We have carried out in vitro studies with DNA binding domain of dIno80 to elucidate its sequence specific DNA binding. We have also showed that this binding can regulated reporter gene expression in Drosophila cells. Our results suggest a non-canonical role of Ino80 in transcriptional regulation.

developmental biology↗