Biology subjects

Rai, V.

Publications and source records attributed to Rai, V..

15 recordsLinked to original sources

bioRxiv2026

Reversible m6Am methylation of snRNA by FTO controls morphine reward and tolerance without altering analgesia

Mu opioids, such as morphine, are effective analgesics, but their reward and tolerance drive opioid use disorder. A major goal is to achieve analgesia without these harmful effects. Here we show that morphine reward and tolerance require the RNA demethylase FTO. Genetic depletion and pharmacologic inhibition of FTO each reduced morphine reward, measured by conditioned-place preference, and reduced antinociceptive tolerance to morphine and fentanyl, without altering analgesia. Although FTO is known to erase m6A on mRNA, we found no effect of FTO depletion on m6A sites, but markedly increased levels of m6Am on snRNA. The effects of FTO depletion were suppressed in mice that cannot make m6Am, supporting the role of m6Am in morphine reward and tolerance. We show that FTO depletion regulates a gene expression network linked to morphine signaling. FTO inhibitors may therefore provide useful adjuvants to mu opioids in pain management and treatment of opioid use disorder.

neuroscience↗

bioRxiv2026

Integration of QTL Mapping, Transcriptomics, and Genome Resequencing Identifies Yield-Associated Genes for Salt Stress in Rice

Salinity and sodicity stresses adversely affect rice growth and yield. To overcome yield losses, suitable tolerant rice cultivars can be developed through a marker-assisted breeding (MAB) program. In the present study, genomic regions associated with sodicity stress tolerance at the reproductive stage were identified using a high-density 50kSNP array in a recombinant inbred line (RIL) population derived from the contrasting rice genotypes CSR11 and MI48. A total of 50 QTLs were detected for various yield-related traits; further, 19 QTLs with [≥]15% of phenotypic variance were selected for integrated (omics) analysis. RNA sequencing of leaves and panicles at the reproductive stage under sodic stress conditions was employed to find differentially expressed genes. A total of 1368 and 1410 SNPs; 104 and 144 indels were found for MI48 and CSR11, respectively, within the QTL regions from resequencing. At chromosomes 1 and 6, colocalized QTLs (qPH1-1/qGP1-1 and qGP6-2/qSSI6-2) were discovered. Differentially expressed genes (DEGs) were mapped over the QTL regions selected, and SNP variations and indels were screened for colocalized QTLs. Potential candidate genes, namely Os-pGlcT1 (Os01g0133400), OsHKT2;1 (Os06g0701600) and OsHKT2;4 (Os06g0701700), OsANTH12 (Os06g0699800), and OsPTR2 (Os06g0706400), were identified as being responsible for glucose transport, ion homeostasis, pollen germination, and nitrogen use efficiency, respectively, under salt stress. Finally, our study provides important insights into the genes and potential mechanisms affecting grain yield under sodic stress in rice, which will contribute to the development of molecular markers for rice breeding programs.

plant biology↗

bioRxiv2023

Population-scale skeletal muscle single-nucleus multi-omic profiling reveals extensive context specific genetic regulation

Skeletal muscle, the largest human organ by weight, is relevant in several polygenic metabolic traits and diseases including type 2 diabetes (T2D). Identifying genetic mechanisms underlying these traits requires pinpointing cell types, regulatory elements, target genes, and causal variants. Here, we use genetic multiplexing to generate population-scale single nucleus (sn) chromatin accessibility (snATAC-seq) and transcriptome (snRNA-seq) maps across 287 frozen human skeletal muscle biopsies representing nearly half a million nuclei. We identify 13 cell types and integrate genetic variation to discover >7,000 expression quantitative trait loci (eQTL) and >100,000 chromatin accessibility QTLs (caQTL) across cell types. Learning patterns of e/caQTL sharing across cell types increased precision of effect estimates. We identify high-resolution cell-states and context-specific e/caQTL with significant genotype by context interaction. We identify nearly 2,000 eGenes colocalized with caQTL and construct causal directional maps for chromatin accessibility and gene expression. Almost 3,500 genome-wide association study (GWAS) signals across 38 relevant traits colocalize with sn-e/caQTL, most in a cell-specific manner. These signals typically colocalize with caQTL and not eQTL, highlighting the importance of population-scale chromatin profiling for GWAS functional studies. Finally, our GWAS-caQTL colocalization data reveal distinct cell-specific regulatory paradigms. Our results illuminate the genetic regulatory architecture of human skeletal muscle at high resolution epigenomic, transcriptomic, and cell-state scales and serve as a template for population-scale multi-omic mapping in complex tissues and traits.

genomics↗

bioRxiv2022

Red cell enzyme polymorphisms in Muslim population of Eastern UP, India

BackgroundRed cell enzyme polymorphisms have been used to study genetic variations in several human populations/countries worldwide. Owing to considerable ethnic and cultural heterogeneity in the Indian population, it is imperative to study different caste and religion of different regions. Aims and ObjectiveTo determine allele frequency of five Red Cell Enzymes (ADA, AK1, ESD, GLO1) in Muslim population of Eastern Uttar Pradesh Materials and methodsBlood samples were collected from 200 unrelated individuals belonging to Muslim community of eastern Uttar Pradesh. The phenotypes of ADA, AK1, ESD and GLO1 systems were determined by agarose/starch gel electrophoresis. The allele frequencies were calculated by gene count method. ResultsThe calculated frequencies of the alleles are as follows: ADA*1= 0.907, ADA*2= 0.092; AK*1= 0.92, AK*2= 0.08; ESD*1= 0.765, ESD*2= 0.235; GLO*1= 0.27,GLO*2 =0.73 ConclusionThe comparison of the allele frequencies of the four RBC enzymes studied in the present report with those of Asian populations showed that the allele frequencies are close to other Asian populations.

genomics↗

bioRxiv2021

RFX6-mediated dysregulation defines human β cell dysfunction in early type 2 diabetes

A hallmark of type 2 diabetes (T2D), a major cause of world-wide morbidity and mortality, is dysfunction of insulin-producing pancreatic islet {beta} cells1-3. T2D genome-wide association studies (GWAS) have identified hundreds of signals, mostly in the non-coding genome and overlapping {beta} cell regulatory elements, but translating these into biological mechanisms has been challenging4-6. To identify early disease-driving events, we performed single cell spatial proteomics, sorted cell transcriptomics, and assessed islet physiology on pancreatic tissue from short-duration T2D and control donors. Here, through integrative analyses of these diverse modalities, we show that multiple gene regulatory modules are associated with early-stage T2D {beta} cell-intrinsic defects. One notable example is the transcription factor RFX6, which we show is a highly connected {beta} cell hub gene that is reduced in T2D and governs a gene regulatory network associated with insulin secretion defects and T2D GWAS variants. We validated the critical role of RFX6 in {beta} cells through direct perturbation in primary human islets followed by physiological and single nucleus multiome profiling, which showed reduced dynamic insulin secretion and large-scale changes in the {beta} cell transcriptome and chromatin accessibility landscape. Understanding the molecular mechanisms of complex, systemic diseases necessitates integration of signals from multiple molecules, cells, organs, and individuals and thus we anticipate this approach will be a useful template to identify and validate key regulatory networks and master hub genes for other diseases or traits with GWAS data.

cell biology↗

bioRxiv2021

I-M-150847, a novel GLP-1 and GIP receptor dual agonist, reduces body weight gain and improves glycemic control in the rodent model of type 2 diabetes and obesity.

We report the discovery of a novel unimolecular glucagon-like peptide-1 (GLP-1) and glucose-dependent insulinotropic polypeptide (GIP) receptor dual agonist that exhibits potent glycemic control and weight loss in diet-induced obese mice. The dual agonism of GLP-1 and GIP receptor was achieved by replacing the tryptophan cage of exendin-4 with the C-terminal undecapeptide sequence of oxyntomodulin along with a single amino acid substitution from histidine to tyrosine at the amino terminus of the peptide. The structural modification places lysine 30 of the novel incretin agonist in frame with the corresponding lysine residue in the native GIP sequence. The novel incretin receptor dual agonist, named I-M-150847, induces rapid redistribution of GLP-1R at the plasma membrane following activation ensuring the maintenance of the receptor in a sensitized state. I-M-150847 promotes glucose-stimulated insulin exocytosis in cultured pancreatic beta cells and augments insulin-stimulated glucose uptake in mouse adipocytes. Chronic administration of I-M-150847 enhances insulin sensitivity, improves glycemic control, and achieves significant weight loss relative to the control or exendin-4-treated DIO-mice demonstrating the therapeutic efficacy of dual agonist in ameliorating type 2 Diabetes and Obesity. Significance statement.O_LIReplacement of the Trp-cage with the C-terminal oxyntomodulin undecapeptide along with the tyrosine substitution at the amino terminus converts the selective GLP-1R agonist exendin-4 to a novel GLP-1R and GIPR dual agonist I-M-150847. C_LIO_LIThe GLP-1R and GIPR dual agonist I-M-150847 induces the expeditious redistribution of GLP-1R at the plasma membrane following initial activation thereby maintaining the receptor in a sensitized state. C_LIO_LIThe incretin receptor dual agonist I-M-150847 enhances insulin sensitivity and delivers superior glycemic control and weight loss compared to exendin-4 in the rodent model of diabetes and obesity. C_LI Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=197 HEIGHT=200 SRC="FIGDIR/small/471325v2_ufig1.gif" ALT="Figure 1"> View larger version (30K): org.highwire.dtl.DTLVardef@1e27480org.highwire.dtl.DTLVardef@4e88acorg.highwire.dtl.DTLVardef@1eee9e7org.highwire.dtl.DTLVardef@3e41c9_HPS_FORMAT_FIGEXP M_FIG C_FIG

physiology↗

bioRxiv2020

Human and rat skeletal muscle single-nuclei multi-omic integrative analyses nominate causal cell types, regulatory elements, and SNPs for complex traits

BackgroundSkeletal muscle accounts for the largest proportion of human body mass, on average, and is a key tissue in complex diseases, mobility, and quality of life. It is composed of several different cell and muscle fiber types. ResultsHere, we optimize single-nucleus ATAC-seq (snATAC-seq) to map skeletal muscle cell-specific chromatin accessibility landscapes in frozen human and rat samples, and single-nucleus RNA-seq (snRNA-seq) to map cell-specific transcriptomes in human. We capture type I and type II muscle fiber signatures, which are generally missed by existing single-cell RNA-seq methods. We perform cross-modality and cross-species integrative analyses on 30,531 nuclei, representing 11 libraries, profiled in this study, and identify seven distinct cell types ranging in abundance from 63% (type II fibers) to 0.9% (muscle satellite cells) of all nuclei. We introduce a regression-based approach to infer cell types by comparing transcription start site-distal ATAC-seq peaks to reference enhancer maps and show consistency with RNA-based marker gene cell type assignments. We find heterogeneity in enrichment of genetic variants linked to complex phenotypes from the UK Biobank and diabetes genome wide association studies in cell-specific ATAC-seq peaks, with the most striking enrichment patterns in muscle mesenchymal stem cells ([~]3% of nuclei). Finally, we overlay these chromatin accessibility maps on GWAS data to nominate causal cell types, SNPs, and transcription factor motifs for creatinine levels and type 2 diabetes signals. ConclusionsThese chromatin accessibility profiles for human and rat skeletal muscle cell types are a useful resource for investigating specific cell types and nominating causal GWAS SNPs and cell types.

genomics↗

bioRxiv2020

"Prevalence of of ABO and Rhesus (Rh) Blood Groups in Eastern UP Population"

Approximately 300 different types of blood groups are identified so far, the ABO and Rh antigens are still the clinically most significant and genetically most polymorphic of all human blood group systems to date. A total of 200 unrelated individuals from Uttar Pradesh were studied for the phenotype and allele frequency distribution of ABO and Rh (D) blood groups. In total 200 samples analyzed, phenotype B blood type has the highest frequency 36.5% (n=73), followed by O (34.5%; n=69), A (20.5%; n=41) and AB (8.5%; n=17). The O, A and B frequencies were 0.5849, 0.1571 and 0.2580 respectively. The overall phenotypic frequencies of ABO blood groups were B>O>A>AB. The variation in phenotypic frequencies between male and female might be due to small sample size of male sample. The allelic frequency of Rh-negative was 0.2.

genetics↗

bioRxiv2019

Molecular Screening of Hemoglobin S Variant in Anemia Patients of Eastern UP Population

Hemoglobinopathies are the most common type of inherited disease in human. in India the most frequent and clinically significant hemoglobin structural variants are HbS, HbD and HbE. The HbS mutation, in which a glutamic acid at position 6 in the {beta} chain is substituted for valine Sickle cell disease is a major health problem in some parts of India. 2 ml blood sample was collected from 350 anemia patient and PCR-RFLP method was used for hemoglobin S analysis. Out of 350 samples, in four individuals, HbS mutation was found in homozygous ({beta} 6/{beta} 6) condition. All four individuals are Sickle cell cases. In conclusion, the percentage of Sickle cell disease was observed as 1.14% in Eastern UP anemic patients.

molecular biology↗

bioRxiv2019

A Study of Association of ABO Blood Group types with Cancer Risk

More than 30 blood group systems have been recognized by International Society of Blood Transfusion (ISBT). ABO blood group is one of the most studied blood group system. ABO blood group system consist of three alleles A, B and O, out which A and B are co-dominant and O is recessive. Many researchers and investigators have found association between ABO blood group and cancer risk. It was found from the recent data that blood group A and AB is associated with increased pancreatic and gastric cancer risk. In the present study data of ABO blood group of 243 patients, both males and females, with confirmed cases of cancer was obtained from Sir Sunderlal hospital, Institute of Medical Science (IMS), Banaras Hindu University (BHU) and Apex hospital, DLW Road, Varanasi. 250 Samples of both males and females were taken as control. Out of 243 cancer patients 117 were males and 126 were females. In 243 cases enrolled in present study, highest number of cases were of breast cancer among women and lowest were rectal cancer. It was found that A blood group was associated with breast cancer, oral cancer, liver cancer and ovarian cancer as compared to other blood group and blood group O was associated with lung cancer, gastric cancer, colon cancer, skin cancer and endometrial cancer.

genetics↗

bioRxiv2019

MTHFR gene A1298C polymorphism and Alzheimer’s disease susceptibility

Methylenetetrahydrofolate reductase (MTHFR) is a crucial enzyme involved in homocysteine/methionone metabolism. It catalyzes the conversion of 5,10methlenetetrahydrofolate in to 5methyltetrahydrofolate. A number of studies have examined the association of MTHFR A1298C polymorphism as risk factor for Alzheimers disease (AD), but the results were contradictory. To clarify the influence of MTHFR A1298C polymorphism on Alzheimers disease (AD), a meta-analysis of ten case-control studies was carried out. Four electronic databases were searched up to August, 2019 for suitable articles. The pooled odds ratios (ORs) with 95% confidence intervals (95% CIs) were used to evaluate the association. All statistical analyses were performed by MetaAnalyst program.\n\nThe results of meta-analysis suggested that except allele contrast model, A1298C polymorphism is not risk for Alzheimers disease using overall comparisons in three genetic models (C vs. A: OR= 1.26, 95%CI= 0.912-1.76, p= 0.04; CC+AC vs. AA: OR= 1.43; 95%CI= 0.85-2.44; p=0.05; CC vs. AA: OR= 1.16, 95%CI= .88-1.55, p= 0.51; AC vs. AA: 1.55; 95%CI= 0.81-2.93,p=0.07). Publication bias was absent in all five genetic models. In conclusion, results of present meta-analysis showed no significant association between MTHFR A1298C polymorphism and AD risk.

neuroscience↗

bioRxiv2019

DRD2 TaqI A polymorphism in Eastern Uttar Pradesh population

Dopamine receptor D2 (DRD2) encoded by DRD2 gene, is located on chromosome 11q22-23. Dopamine plays the central role in motivation, cognition, and reward seeking behaviour. Its dysfunction is implicated in numerous neurological and psychiatric disorders including drug abuse, schizophrenia, ADHD etc. The TaqI A polymorphism is localized 9.8 kb downstream from DRD2 gene in exon 8 of protein kinase gene (ANKK1). It is a SNP demonstrated to cause Glutamate to Lysine substitution at 713 amino acid residue in putative binding domain of ANKK1. Due to the central role of dopamine in reward seeking behavior, DRD2 TaqI A loci is a suitable candidate for investigation of molecular basis of addiction. The aim of the present study is to evaluate the frequency of DRD2 TaqI A polymorphism in Eastern Uttar Pradesh population. 3ml blood samples were collected from 50 individuals randomly selected from Eastern UP. Written informed consent along with profile detail was taken from each subject prior to blood sample collection. DRD2 TaqI A polymorphism analysis was done by PCR-RFLP method. Genomic DNA was extracted from each collected blood samples and amplified using DRD2 Taq1 region specific primers. PCR amplification produced 310bp long amplicon which was digested with Taq I enzyme for polymorphism analysis. In case of A2 allele, Taq1 enzyme cleaved 310bp long fragment into two fragments of 180bp and 130bp. In case of A1 allele, a C to T substitution demolished the restriction site of Taq1, so amplicon of A1 allele remained uncut. In total 50 sample analyzed in present study, A2/A2, A2/A1 and A1/A1 genotype were found in 12, 32 and 06 samples respectively. The genotypic frequencies of mutant homozygous (A1/A1) is 0.12, heterozygous (A2/A1) is 0.64 and normal homozygous (A2/A2) is 0.24. The allelic frequency of A1 is 0.44 and of A2 is 0.56. In conclusion, the results of present study suggests that in TaqI A polymorphism of DRD2 gene, the frequency of allele A2 is higher than that of A1 allele in population of Eastern Uttar Pradesh.

neuroscience↗

bioRxiv2019

Single cell ATAC-seq in human pancreatic islets and deep learning upscaling of rare cells reveals cell-specific type 2 diabetes regulatory signatures

ObjectiveType 2 diabetes (T2D) is a complex disease characterized by pancreatic islet dysfunction, insulin resistance, and disruption of blood glucose levels. Genome wide association studies (GWAS) have identified >400 independent signals that encode genetic predisposition. More than 90% of the associated single nucleotide polymorphisms (SNPs) localize to non-coding regions and are enriched in chromatin-defined islet enhancer elements, indicating a strong transcriptional regulatory component to disease susceptibility. Pancreatic islets are a mixture of cell types that express distinct hormonal programs, and so each cell type may contribute differentially to the underlying regulatory processes that modulate T2D-associated transcriptional circuits. Existing chromatin profiling methods such as ATAC-seq and DNase-seq, applied to islets in bulk, produce aggregate profiles that mask important cellular and regulatory heterogeneity.\n\nMethodsWe present genome-wide single cell chromatin accessibility profiles in >1,600 cells derived from a human pancreatic islet sample using single-cell-combinatorial-indexing ATAC-seq (sci-ATAC-seq). We also developed a deep learning model based on the U-Net architecture to accurately predict open chromatin peak calls in rare cell populations.\n\nResultsWe show that sci-ATAC-seq profiles allow us to deconvolve alpha, beta, and delta cell populations and identify cell-type-specific regulatory signatures underlying T2D. Particularly, we find that T2D GWAS SNPs are significantly enriched in beta cell-specific and cross cell-type shared islet open chromatin, but not in alpha or delta cell-specific open chromatin. We also demonstrate, using less abundant delta cells, that deep-learning models can improve signal recovery and feature reconstruction of rarer cell populations. Finally, we use co-accessibility measures to nominate the cell-specific target genes at 104 non-coding T2D GWAS signals.\n\nConclusionsCollectively, we identify the islet cell type of action across genetic signals of T2D predisposition and provide higher-resolution mechanistic insights into genetically encoded risk pathways.

genomics↗

bioRxiv2019

Loss-of-function genomic variants with impact on liver-related blood traits highlight potential therapeutic targets for cardiovascular disease

Cardiovascular diseases (CVD), and in particular cerebrovascular and ischemic heart diseases, are leading causes of death globally.1 Lowering circulating lipids is an important treatment strategy to reduce risk.2,3 However, some pharmaceutical mechanisms of reducing CVD may increase risk of fatty liver disease or other metabolic disorders.4,5,6 To identify potential novel therapeutic targets, which may reduce risk of CVD without increasing risk of metabolic disease, we focused on the simultaneous evaluation of quantitative traits related to liver function and CVD. Using a combination of low-coverage (5x) whole-genome sequencing and targeted genotyping, deep genotype imputation based on the TOPMed reference panel7, and genome-wide association study (GWAS) meta-analysis, we analyzed 12 liver-related blood traits (including liver enzymes, blood lipids, and markers of iron metabolism) in up to 203,476 people from three population-based cohorts of different ancestries. We identified 88 likely causal protein-altering variants that were associated with one or more liver-related blood traits. We identified several loss-of-function (LoF) variants reducing low-density lipoprotein cholesterol (LDL-C) or risk of CVD without increased risk of liver disease or diabetes, including variants in known lipid genes (e.g. APOB, LPL). A novel LoF variant, ZNF529:p.K405X, was associated with decreased levels of LDL-C (P=1.3x10-8) but demonstrated no association with liver enzymes or non-fasting blood glucose levels. Silencing of ZNF529 in human hepatocytes resulted in upregulation of LDL receptor (LDLR) and increased LDL-C uptake in the cells, suggesting that inhibition of ZNF529 or its gene product could be used for treating hypercholesterolemia and hence reduce the risk of CVD. Taken together, we demonstrate that simultaneous consideration of multiple phenotypes and a focus on rare protein-altering variants may identify promising therapeutic targets.

genomics↗

bioRxiv2018

Ligand Modulates Cross-Coupling between Riboswitch Folding and Transcriptional Pausing

HighlightsO_LIsmFRET, biochemistry and simulations probe co-transcriptional riboswitch folding\nC_LIO_LINascent RNA folding is disfavored by the DNA template and aided by RNAP\nC_LIO_LITranscriptional pausing is stabilized by RNA pseudoknot and destabilized by ligand\nC_LI\n\nSUMMARYNumerous classes of riboswitches have been found to regulate bacterial gene expression in response to physiological cues, offering new paths to anti-bacterial drugs. As common studies of isolated riboswitches lack the functional context of the transcription machinery, we here combine single-molecule, biochemical and simulation approaches to investigate the coupling between co-transcriptional folding of the pseudoknot-structured preQ1 riboswitch and RNA polymerase (RNAP) pausing. We show that pausing at a site immediately downstream of the riboswitch requires a ligand-free pseudoknot in the nascent RNA, a precisely spaced sequence resembling the pause consensus, and electrostatic and steric interactions with the RNAP exit channel. While interactions with RNAP stabilize the native fold of the riboswitch, binding of the ligand signals RNAP release from the pause. Our results demonstrate that the nascent riboswitch and its ligand actively modulate the function of RNAP and vice versa, a paradigm likely to apply to other cellular RNA transcripts.

biophysics↗