Biology subjects

Balasubramanian, S.

Publications and source records attributed to Balasubramanian, S..

At least 19 recordsLinked to original sources

bioRxiv2026

Topoisomerase IIβ Kinase: A protein processed from HIV-1 envelope by cysteine proteases

Topoisomerase II{beta} (TopoII{beta}) is activated by TopoII{beta} kinase (TopoII{beta}K) during HIV-1 infection. This study demonstrates that TopoII{beta}K is produced within 15-30 minutes post-infection and is conserved across the major HIV-1 subtypes (A, B, C, and D), although its formation kinetics vary among subtypes. Immunological mapping using specific anti-gp120 antibodies suggests that TopoII{beta}K is derived from the N-terminal region of gp120. Notably, TopoII{beta}K co-localizes with endolysosomes shortly after viral entry. Inhibition of cysteine proteases using E64d and Z-FY-CHO abrogates TopoII{beta}K production in both HIV-1-infected and envelope-transfected cells. These findings suggest that TopoII{beta}K is a conserved polypeptide product of gp120 processing within endolysosomes during the early stages of HIV-1 infection, highlighting a potentially conserved mechanism that regulates early viral infection across major HIV-1 subtypes.

molecular biology↗

bioRxiv2026

An update on the mosquito fauna of Aguascalientes, Mexico: morphological and molecular identifications, host-feeding patterns, and the removal of Aedes idahoensis (Theobald) from Mexico

To better understand taxonomic identity and feeding patterns of mosquitoes in all physiographic regions and sub-regions of Aguascalientes, Mexico, we conducted surveillance followed by morphologic analysis and DNA metabarcoding. We targeted the Sierra Madre Occidental, Central Plateau, and Neo-Volcanic Axis. We sampled natural larval habitat for immature stages and adults were collected using Shannon and CDC light traps, mechanical aspirators, and human landing catch method. In addition, curated specimens from Aguascalientes deposited in a local institution were re-examined. Overall, 5,227 mosquito specimens consisting of 357 larvae, 199 larval exuviae, 373 pupal exuviae, 33 pupae, 3,000 females, 1,264 males, and 1 male genitalia were examined using taxonomic keys. Most immature and adult species (n = 20/34 species representing 58.8% coverage) were barcoded for molecular species designation, and a subsample (n = 64) of engorged female mosquitoes were analyzed for blood feeding patterns. Two subfamilies, four tribes, seven genera, 14 subgenera, and 34 species were identified, which one tribe, three genera, nine subgenera, and 22 species are new records. Phylogenetic analysis of specimens from Aguascalientes identified 20 species. Morphological observation of mosquitoes deposited in entomological collections resulted in the removal of Aedesidahoensis from Mexico, leaving the country with a total of 255 species documented. Bloodmeal metabarcoding was successful in 23 mosquitoes of five species, revealing evidence of feeding on more than a single vertebrate species in 17 individuals. Birds were the most common host with the cattle egret (Ardea ibis) found in 18 out of 23 mosquitoes. This update on the taxonomic identity and mosquito richness and feeding patterns from Aguascalientes affords a better understanding of the ecology of medically important mosquito species.

zoology↗

bioRxiv2026

G4SCOPE identifies sequence features and epigenetic contexts of chromatin G-quadruplexes

Cancer-associated epigenetic remodeling involves a complex interplay between DNA secondary structures and covalent cytosine modifications, yet predicting endogenously folded, chromatin-constrained G-quadruplex (G4) dynamics remains challenging. Here, we develop G4SCOPE, a multi-task deep learning framework that models chromatin-associated G4 occupancy and reconstructs quantitative high-resolution CUT&Tag profiles directly from primary DNA sequence alone. We initially trained G4SCOPE on genotype-stratified G4 enriched cut&tag landscapes generated across an isogenic series of human breast epithelial cells (WT, TP53-/-, TP53-/-;BRCA1-/-, and TP53-/-;BRCA2-/-). G4SCOPE integrates convolutional motif learning with transformer self-attention to decode long-range sequence contexts. The model robustly distinguishes chromatin-associated G4s from GC-matched loci with intrinsic in vitro folding potential, generalizes across distinct breast lineages, and transfers accurately to an independent K562 cellular context. Strikingly, genotype-resolved mapping reveals a profound divergence in genome maintenance states: BRCA1 deficiency indicated a global inflation of chromatin-embedded G4 density, whereas BRCA2 loss was associated with systemic, chromosome-wide structural depletion. Furthermore, unsupervised clustering of model-derived latent sequence representations identified distinct biological G4 subclasses that occupy unique regulatory class genomic environments associated with distinct local 5-methylcytosine and 5-hydroxymethylcytosine landscapes. Together, our framework decodes the primary sequence grammar governing cell-based G4 occupancy and demonstrates that sequence-defined G4 topologies harbor intrinsic and distinct local epigenetic features.

bioinformatics↗

bioRxiv2026

Changes in peripheral sensory afference do not alter predictive motor planning: evidence from carpal tunnel syndrome

Anticipatory control organises motor output prior to predictable perturbations and is expressed in multi-digit tasks as anticipatory synergy adjustments (ASAs), which coordinate digit forces before movement onset. Whether such feedforward coordination depends on peripheral sensory input remains unclear. Carpal tunnel syndrome provides a model of altered median nerve afference with within-subject restoration following surgical decompression. We quantified ASA onset and amplitude in eleven individuals with carpal tunnel syndrome performing a multi-finger grasp-and-release task before and three weeks after decompression surgery. Postoperatively, sensory function improved, and total grip force decreased significantly across task phases, indicating more efficient force regulation. In contrast, ASA onset timing and amplitude were unchanged. Equivalence testing confirmed that pre- and post-operative ASA measures fell within predefined bounds of practical equivalence. These findings demonstrate a central-peripheral dissociation: feedback-mediated grip force scaling is sensory-dependent and rapidly recalibrates following afferent restoration, whereas feedforward synergy coordination remains stable despite months of degraded peripheral input. The preserved ASA suggests that central motor planning circuits maintain anticipatory coordination through efferent copy or cerebellar-mediated internal models that do not require continuous peripheral recalibration. This resilience may reflect the brains ability to maintain predictive motor planning despite chronic sensory degradation, with implications for understanding compensatory mechanisms in peripheral neuropathies and the limits of sensory-dependent motor adaptation.

neuroscience↗

bioRxiv2025

Insights into the mechanism of succinimide formation in an archaeal glutaminase.

Succinimide (SNN), an intermediate formed during asparaginyl deamidation or aspartyl dehydration in proteins, is generally hydrolysis-prone, leading to isomerization to L/D /{beta}-aspartyl residue, with the latter being considered deleterious to protein structure and function. An unusually stable SNN-mediated conformational rigidity through restriction of the backbone dihedral angle, {psi}, enhances the thermostability of glutamine amidotransferase (GATase) from Methanocaldococcus jannaschii (Mj). Although several structural features involved in maintaining a stable SNN and imparting SNN-mediated thermostability have been identified in MjGATase, the residues in the protein that catalyse the rapid and complete conversion of Asn109 to SNN remain unknown. Here, we investigated several site-directed mutants of MjGATase for their ability to retain Asn109 side chain in the unmodified form. Mass spectrometric analysis of 10 single mutants enabled the identification of residues that impacted the proportion of SNN and Asn population in the protein sample. This led to the generation of two double mutants that retained intact Asn109 side chain as observed in the mass spectra and crystal structures. These mutants with intact Asn residue at position 109, displayed lower thermal stability than the protein with the SNN modification. Further understanding of the deprotonation mechanism was addressed using QM/MM MD metadynamics simulations. HighlightsO_LIStable succinimide (SNN) arising from deamidation of Asn109 residue imparts hyperthermostability to MjGATase. C_LIO_LIExamination of the structure of MjGATase suggests neighbouring residues playing possible roles in deamidation and cyclization. C_LIO_LIExamination by LC-MS of single site-directed mutants of residues contacting SNN revealed varied levels of intact Asn109 enabling generation of double mutants with complete absence of deamidation. C_LIO_LIPresence of intact Asn109 confirmed by X-ray crystallography highlights the role of Y158, D110, and K151 in mediating SNN formation. C_LIO_LIQM/MM MD metadynamics simulations support experimental findings. C_LI

biochemistry↗

bioRxiv2025

The Desmoglein 2 interactome in primary neonatal cardiomyocytes

Mechanical coupling and chemical communication between cardiomyocytes are facilitated through a specialized adhesive structure known as the intercalated disc (ICD). The ICD is essential for heart organization and contraction. Yet, the network of adhesion, adaptor, and signaling proteins that form the ICD remains poorly defined. Here, we combined proximity labeling and quantitative mass spectrometry to identify proteins associated with the desmosomal cadherin, Desmoglein 2 (DSG2), in cultured neonatal cardiomyocytes. We identified over 300 proteins in the DSG2 interactome; half of which are shared with the N-cadherin (CDH2) interactome in cardiomyocytes. Proteins unique to DSG2 include the gap junction protein connexin 43 and the plakin family of cytolinker proteins. Comparison of the cardiomyocyte DSG2 interactome with the interactomes of desmosomal proteins from epithelia revealed only a small number of shared proteins. In cardiomyocytes, plakoglobin (JUP) and plakophilin 2 (PKP2) were the most abundant shared proteins between the DSG2 and CDH2 interactomes. PKP2 is a dynamic protein whose membrane recruitment in cardiomyocytes is tension-dependent. Our analysis of the DSG2 interactome provides a critical new dimension to the proteomic atlas of the essential molecular complexes required for cardiomyocyte adhesion.

cell biology↗

bioRxiv2025

Advancing the design of the kissing bug kill trap for surveillance of triatomines

Standardized surveillance and control of kissing bugs (Hemiptera: Reduviidae: Triatominae), the insect vectors of the Chagas disease parasite Trypanosoma cruzi, which causes Chagas disease, remains difficult. The Kissing Bug Kill Trap consists of solar powered LED lights mounted over a column of black funnels. It operates autonomously to capture, kill and preserve adult triatomines. We conducted experiments from 2022-2024 testing potential ways to improve trap performance, ease of deployment, and minimize cost. Thirteen prototypes evaluated in Texas, Guatemala, and Mexico captured 1,531 triatomines. In 2022-2023 we selected a six-funnel trap suspended from a single support pole with an angle bracket, and with four LED lights and a solar panel mounted above the rain-guard, as a reference trap. In 2023, traps with smaller funnels, blue funnels, and blue lights were inferior to the reference trap based on high by-catch of other arthropods and/or fewer triatomines caught per day. In 2024, traps with more or fewer than six funnels or with LED lights mounted on or below the rain guard did not outperform the reference trap. The experiments added five new triatomine species to the four already known to be caught by the Kissing Bug Kill Trap and revealed differences and similarities in phenology of dispersal flights of Triatoma gerstaeckeri over a three-year period in Texas. The reference trap was selected as the pre-commercial prototype, based on its suitability for triatomine surveillance and potential for reducing the risk of T. cruzi infection by intercepting dispersing adult triatomines before they reach human habitats.

ecology↗

bioRxiv2025

Variant Classification Using Proteomics-Informed Large Language Models Increases Power of Rare Variant Association Studies and Enhances Target Discovery

Rare variant association analysis, which assesses the aggregate effect of rare damaging variants within a gene, is a powerful strategy for advancing knowledge of human biology. Numerous models have been proposed to identify damaging coding variants, with the most recent ones employing deep learning and large language models (LLM) to predict the impact of changes in coding sequences. Here, we use newly available proteomics data on 2,898 proteins across 46, 665 individuals to evaluate and refine LLM predictors of damaging variants. Using one of these refined models, we evaluate association between rare damaging variants and human phenotypes at 241 positive control gene-trait pairs. Among these gene-trait pairs, our proteomics-guided model outperforms an ensemble of conventional approaches including PolyPhen2, Mutation Taster, SIFT, and LRT, as well as newer machine learning approaches for identifying damaging missense variants, such as CADD, ESM-1v, ESM-1b and AlphaMissense. When attempting to recover known associations by correctly separating damaging singleton missense variants from other singleton variants, our approach recapitulates 36.5% of gene-trait pairs with known associations, exceeding all the alternatives we considered. Furthermore, when we apply our model to 10 exemplary traits from the UK Biobank, we identify 177 gene-trait associations - again exceeding all other approaches. Our results demonstrate that summary statistics from large-scale human proteomics data enable evaluation and refinement of coding variant classification LLMs, improving discovery potential in human genetic studies.

bioinformatics↗

bioRxiv2025

Mutations of short tandem repeats explain abundant trait heritability in Arabidopsis

Short tandem repeats (STRs) mutations are one of the most important fuels of evolution, but are often largely ignored despite their huge effects on phenotypic variations. Here, we leveraged seven Arabidopsis mutation accumulation lines to assess the STR mutation rate, which ranged from 1.93x10-2 to 4.40x10-3 per STR locus per generation and was much higher than the common SNP mutation rate at the level of 10-9-10-8. Interspecific comparison revealed rapid STR turnover, with a large proportion (71.8%) only present in Arabidopsis. In addition, intraspecific comparison of the ten assembled Arabidopsis genomes revealed that 29.3% of STRs were presence/absence variation (PAV), 36.5% of STRs were length variation (LV), 13.0% of STRs were no variation (NV) and the 21.1% STR loci with both LV and PAV. Based on 413 RNA-seq datasets, we identified that length variation of 3,871 STR loci (eSTRs) was associated with gene expression and 651 STR loci (sSTRs) were associated with splicing variation, and over one thousand eSTRs or sSTRs were linked with published genome-wide association study signals. In addition, a direct association between STR length variation and phenotypic variation uncovered a series of STR-trait associations. More notably, using the expression levels of 24,175 genes, the splice strength values of 12,784 splice sites, and 16 phenotypes of natural Arabidopsis populations, we revealed that the STR heritability is 0.111, 0.143 and 0.101, respectively. Overall, our results not only revealed the evolutionary dynamics of STRs, but highlighted the importance of STR variations as an important contributor to missing heritability in the regulation of complex traits.

evolutionary biology↗

bioRxiv2025

Lysine-specific demethylase 1a is obligatory for gene regulation during kidney development

Histone methyltransferases and demethylases play crucial roles in gene regulation and are vital for proper functioning of multiple tissues. Lysine-specific histone demethylase 1A (Kdm1a), is responsible for the demethylation of specific lysines, namely K4 and K9, on histone H3. In this study, we investigated the functions of Kdm1a during mouse kidney development upon targeted deletion in renal progenitor cells. Loss of Kdm1a in Six2-positive nephron progenitors resulted in significant reduction in renal mass, tissue structural changes and impaired function. To further understand the molecular function of Kdm1a during kidney development, we conducted multi-omics analyses that included transcriptome profiling, Chromatin immunoprecipitation (ChIP) sequencing, and methylome assessments. These omic analyses identified Kdm1a as a critical gene regulator required for sustained expression of several nephron segment marker genes, as well as vast number of solute carrier (Slc) genes and a few imprinted genes. Absence of Kdm1a in kidneys led to an increase in global H3K9 methylation peaks, which correlated with the transcriptional downregulation of numerous genes. Among these were markers of nephron progenitors and presumptive tubular precursors. We also observed that specific gene bodies exhibited altered DNA methylation patterns at intragenic differentially methylated regions (DMRs) upon Kdm1a deletion, while the overall global levels of DNA methylation remained unchanged. Our data point to a key regulatory role for Kdm1a in the renal progenitor epigenome, influencing kidney specific gene expression in the developing nephrons. Together the study highlights an indispensable role for Kdm1a for proper development of mouse kidneys, and its absence leading to significant developmental and functional impairment.

developmental biology↗

bioRxiv2024

Comparable neural and behavioural performance in dominant and non-dominant hands during grasping tasks

Hand dominance has long been associated with differences in neural control and motor performance, with the dominant hand typically exhibiting better coordination in reaching tasks. However, the extent to which this dominance influences performance in finger force control remains unclear. This study aimed to examine the behavioural and neural features of the dominant and non-dominant hands during grasping and lifting tasks in healthy young adults, focusing on the synergy index, EEG band power, and EEG-EMG coherence as key measures. Twenty right-handed adults (mean age = 26.95, STD = 2.68) participated in this study. Participants engaged in an experimental task where they grasped a handle for the initial five seconds, followed by lifting and holding it for an additional five seconds. There were two task conditions: fixed (thumb platform secured) and free (thumb platform movable). They performed 25 trials with both the dominant and non-dominant hands in the two task conditions, with the order of trials and hands block randomized to eliminate potential order effects. Contrary to the dynamic dominance hypothesis, we found statistical equivalence in the synergy index, EEG band power, and EEG-EMG coherence between the dominant and non-dominant hands across both fixed and free task conditions. These findings suggest that both hands are capable of achieving similar levels of performance in tasks emphasizing steady-state force maintenance, despite the typical advantages of the dominant hand in other motor tasks. While task-dependent modulations in behavioural and neural features were observed due to changes in friction, these adjustments were non-different between the dominant and non-dominant hands.

neuroscience↗

bioRxiv2024

Vinculin Y822 phosphorylation regulates cardiomyocyte adhesion dynamics and adherens junction maturation in the heart

In the heart, cell-matrix and cell-cell adhesions reorganize in response to increased cardiac demand and growth to promote cardiomyocyte maturation. Vinculin, a mechanosensitive adaptor protein, links filamentous actin to cell-matrix and cell-cell adhesions and is thus positioned to regulate adhesion reorganization. However, how the two adhesion systems are coordinated in the heart, and the role of vinculin in this process is poorly understood. Here, we define the role of vinculin phosphorylation at tyrosine residue 822 (pY822) in cardiomyocyte adhesion and heart function. We found that pY822 correlated with dynamic junction remodeling in the developing heart but was lost as junctions matured postnatally. We then mutated Y822 to phenylalanine (Y822F) in the mouse to determine pY822 function in vivo. Homozygous mutant Vcl Y822F mice were viable and exhibited normal cardiac function at ten weeks of age; however, cardiac dysfunction was observed at 28 weeks. Vinculin and adherens junction proteins were reduced at cardiomyocyte junctions in Y822F hearts. In contrast, 5/{beta}1 integrin and fibronectin increased along the lateral border of Y822F cardiomyocytes. Our results demonstrate that vinculin Y822 phosphorylation regulates the balance between cadherin and integrin adhesion organization, highlighting the importance of post-translational modification in modulating vinculin function in heart physiology.

cell biology↗

bioRxiv2024

5-methylcytosine and 5-hydroxymethylcytosine are synergistic biomarkers for early detection of colorectal cancer

Early cancer detection has the potential to significantly improve treatment outcomes and survival rates. This study investigates the roles of 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) as biomarkers for early-stage colorectal cancer (CRC) detection in cell-free DNA (cfDNA). Using whole genome sequencing, we analyzed cfDNA from 37 treatment-naive CRC patients and 32 healthy controls. Our findings indicate that combining measurements of 5mC and 5hmC significantly enhances diagnostic accuracy (AUC = 0.95) compared to traditional approaches that conflate these markers (modified C, AUC = 0.66). Notably, 71.7% of differentially methylated regions (DMRs) exhibiting an increase in 5hmC in stage I cfDNA also showed a corresponding decrease in 5mC in stage IV, suggesting that 5hmC can effectively track regions undergoing demethylation during tumor development. These results support the hypothesis that distinguishing between 5mC and 5hmC can improve the sensitivity of liquid biopsy tests for early cancer detection.

cancer biology↗

bioRxiv2024

The TissueTractor, a device for applying large strains to tissues and cells for simultaneous high-resolution live cell microscopy.

Mechanical strain substantially influences tissue shape and function in various contexts, from embryonic development to disease progression. Disruptions in these processes can result in congenital abnormalities and short-circuit mechanotransduction pathways. Manipulating strain in live tissues is crucial for understanding its impact on cellular and subcellular activities. Existing tools, such as optogenetic modulation of strain, are limited to small strain over limited distance and durations. Here, we introduce a high-strain stretcher system, the TissueTractor, designed for high-resolution spatiotemporal imaging of live tissues, enabling strain application varying from 0% to over 150%. This system is needed to unravel the intricate connections between mechanical forces and developmental processes. We demonstrated the stretcher with Xenopus laevis organotypic explants, human umbilical endothelial cells, and mouse neonatal cardiomyocytes to highlight the stretchers adaptability. These demonstrations underscore the potential of this stretcher to deepen our understanding of the mechanical cues governing tissue dynamics and morphogenesis. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=170 SRC="FIGDIR/small/600827v3_ufig1.gif" ALT="Figure 1"> View larger version (46K): org.highwire.dtl.DTLVardef@207163org.highwire.dtl.DTLVardef@1f424e7org.highwire.dtl.DTLVardef@1a2e9e1org.highwire.dtl.DTLVardef@a8d785_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2024

Romiumeter: An Open-Source Inertial Measurement Unit-Based Goniometer for Range of Motion Measurements

Range of motion (ROM) serves as a crucial metric for assessing movement impairments. Traditionally, clinicians use goniometers to measure the ROM, but this method relies on the clinicians skill, in particular for difficult joints such as the shoulder and neck joints. Recent studies have explored the use of wearable inertial measurement units (IMUs) as an alternative. IMUs exhibit excellent agreement with goniometers, but the lack of affordable, accessible, and clinically validated tools remains an issue. This paper introduces the Romiumeter, a single IMU-based device designed to measure the ROM of the neck and shoulder movements. To validate its accuracy, the Romiumeter was tested on 34 asymptomatic individuals for shoulder and neck movements, using an optical motion capture system as the ground truth. The device demonstrated good accuracy, with a maximum absolute error of less than 5{degrees} with moderate to good reliable measurements(inter-rater reliability: 0.69 - 0.87 and intra-rater reliability: 0.76 - 0.87). Additionally, the Romiumeter underwent validation for different algorithms, including the complementary and Madgwick filters. Interestingly, no significant differences were found between the algorithms. Overall, the Romiumeter provides reliable measurements for assessing shoulder and neck ROM in asymptomatic individuals.

bioengineering↗

bioRxiv2024

Spatially tuneable multi-omics sequencing using light-driven combinatorial barcoding of molecules in tissues

Mapping the molecular identities and functions of cells within their spatial context is key to understanding the complex interplay within and between tissue neighbourhoods. A wide range of methods have recently enabled spatial profiling of cellular anatomical contexts, some offering single-cell resolution. These use different barcoding schemes to encode either the location or the identity of target molecules. However, all these technologies face a trade-off between spatial resolution, depth of profiling, and scalability. Here, we present Barcoding by Activated Linkage of Indexes (BALI), a method that uses light to write combinatorial spatial molecular barcodes directly onto target molecules in situ, enabling multi-omic profiling by next generation sequencing. A unique feature of BALI is that the user can define the number, size, and shape, and resolution of the spatial locations to be interrogated, with the potential to profile millions of distinct regions with subcellular precision. As a proof of concept, we used BALI to capture the transcriptome, chromatin accessibility, or both simultaneously, from distinct areas of the mouse brain in single tissue sections, demonstrating strong concordance with publicly available datasets. BALI therefore combines high spatial resolution, high throughput, histological compatibility, and workflow accessibility to enable powerful spatial multi-omic profiling.

genomics↗

bioRxiv2024

Genome-wide association study elucidates the genetic architecture of manganese tolerance in Brassica napus

Brassica napus (canola) is a significant contributor to the worlds oil production and is cultivated across continents, yet acidic soils with Al3+ and Mn2+ toxicities limit its production. The genetic determinants underlying acidic soil tolerance in canola are unknown and require to be uncovered for canola breeding and production. Here, through comprehensive phenotyping, whole genome resequencing, and genome-wide association analysis, we identified three QTLs for tolerance to Mn2+ toxicity on chromosomes A09, C03, and C09. Allelism tests between four tolerance sources confirmed that at least one locus on A09 controls Mn2+ tolerance in B. napus. Integrated analysis of genomic and expression QTL and Mn2+ tolerance data reveals that BnMTP8.A09, in conjunction with BnMATE.C03, BnMTP8.C04 and BnMTP8.C08, play a central role in conferring Mn2+ tolerance in B. napus. Gene expression analysis revealed a high correlation (R2 = 0.74) between Mn2+ tolerance and the BnMTP8.A09 expression. Yeast complementation assays show that BnMTP8.A09 can complement manganese-hypersensitive yeast mutant strain PMR1{Delta} and restore Mn2+ tolerance to wild-type levels. Inductively coupled plasma mass spectrometry revealed that Mn2+ tolerant accessions accumulate less Mn in the shoots compared to Mn2+ sensitives, suggesting that the BnMTP8.A09 transporter likely sequesters Mn2+ into the tonoplast. Taken together, our research unveils the genetic architecture of Mn2+ tolerance and identifies BnMTP8.A09 as a major gene imparting tolerance to Mn2+ toxicity in B. napus.

plant biology↗

bioRxiv2024

A basic framework governing splice-site choice in eukaryotes

Changes in splicing are observed between cells, tissues, organs, individuals, and species. These changes can mediate phenotypic variation ranging from flowering time differences in plants to genetic diseases in humans. However, the genomic determinants of splicing variation are largely unknown. Here, we quantified the usage of individual splice-sites and uncover extensive variation between individuals (genotypes) in Arabidopsis, Drosophila and Humans. We used this robust quantitative measure as a phenotype and mapped variation in splice-site usage using Genome-Wide Association Studies (GWAS). By carrying out more than 130,000 GWAS with splice-site usage phenotypes, we reveal genetic variants associated with differential usage of specific splice-sites. Our analysis conclusively shows that most of the common, genetically controlled variation in splicing is cis and there are no major trans hotspots in any of the three analyzed species. High-resolution mapping allowed us to determine genome-wide patterns that govern splice-site choice. We reveal that the variability in the intronic hexamer sequence (GT[N]4 or [N]4AG) differentiates intrinsic splice-site strength and is among the primary determinants of splice-site choice. Experimental analysis validates the primary role for intronic hexamer sequences in conferring splice-site decisions. Transcriptome analyses in diverse species across the tree of life reveals that hexamer rankings explains splice-site choices from yeast to plants to humans, forming the basic framework of the splicing code in eukaryotes.

genetics↗