Biology subjects

Shankar, A.

Publications and source records attributed to Shankar, A..

At least 19 recordsLinked to original sources

bioRxiv2026

Hummingbird torpor recapitulates key molecular signatures of hibernation without large-scale transcriptomic remodelling

Torpor is a physiological strategy used by which some species conserve energy by lowering metabolic rates and body temperatures. While mammalian hibernation is well-studied, the molecular mechanisms governing the rapid entry into avian torpor remain poorly understood. This study represents the first multi-tissue whole-transcriptomic analysis of torpor entry in an avian system. By combining real-time thermal imaging and respirometry with transcriptomic profiling across seven tissues, we identified the key molecular pathways orchestrating this transition in Anna's hummingbirds (Calypte anna). Our results reveal that avian torpor entry is characterised by a subtle transcriptomic change (<5% of the genome differentially expressed across tissues) compared to mammalian hibernation (10%-60%). Most of these genes are differentially expressed before torpor entry is complete, rather than tracking body temperature linearly. This indicates that active transcriptional reprogramming precedes and potentially drives the transition. Thus, hummingbird torpor entry is not a passive shutdown, but a highly regulated, tissue-specific process. Vital organs, such as the heart and lungs, remain transcriptionally stable to maintain essential functions, while the liver and gut exhibit extensive metabolic rewiring. We found evidence of global transcriptional and translational suppression, and cell-cycle arrest: the three major contributors to cellular energy budgets. We hypothesise that avian torpor entry is orchestrated through an arrest of apoptosis, a metabolic switch from carbohydrate to lipid utilisation, coupled with alterations in alternative splicing and circadian rhythm regulation. Finally, the counterintuitive upregulation of genes involved in mitochondrial metabolism suggests a preparation for rapid arousal despite the depressed metabolic state.

physiology↗

bioRxiv2025

Supergene control of chiral development in mirror-image flowers

How genes determine the left-versus right-handed development of chiral structures is a fascinating question. The reciprocal placement of female and male organs on opposite sides of the midline in mirror-image flowers limits selfing and promotes efficient cross-pollination. Here we identify the molecular and developmental basis of floral handedness in butterfly lilies. Female and male organs deflect by a combination of genetically controlled chirality and gravitropism, orienting left and right with respect to an external rather than internal reference axis. Coordinated organ placement is controlled by a hemizygous supergene containing two causal loci, MIR156-R and YUCCA-R, responsible for opposite female and male organ orientation, respectively. This genomic architecture results in differential placement of the supergene alleles on the pollinators and maintenance of the reproductive polymorphism.

plant biology↗

bioRxiv2025

What's next for Indian Ornithology? 101 key research questions

India has a rich history of ornithology, and bird research in this field has expanded considerably in recent decades, spurred by a growing number of birdwatchers and ornithologists. Despite this progress, critical gaps remain. This paper highlights key areas where further research is needed and identifies pressing questions that will shape Indian ornithology in the coming years. Drawing from diverse inputs, we present a curated list of 101 research questions spanning across the various disciplines in ornithology - Natural History, Physiology and Disease Ecology, Behaviour, Population and Community Ecology, Habitat Ecology, Macroecology and Biogeography, Population Genetics and Evolution, Applied/Economic Ornithology and Conservation. The list was compiled through a multi-stage process, starting with a public open call for questions, followed by review and curation by a smaller panel of subject specialists. Each question was independently scored by a panel of experts based on three criteria: generality, novelty, and relevance. To account for variation in scoring styles, scores were normalised using Z-scores. The top 101 research questions were then selected based on these standardised scores. Each question is accompanied by an annotation that describes the significance of the question, and highlights opportunities to address it. While our list of research questions highlights significant research priorities, it is not intended to be exhaustive. Rather, it reflects the perspectives of those involved in its curation, who deemed these questions particularly relevant and impactful towards advancing Indian ornithology. We expect these questions to spark new project ideas among students, researchers, and citizen scientists, while guiding funders, managers, and policymakers toward priority research areas.

ecology↗

bioRxiv2025

The Old genetically heterogeneous Mouse Model Recapitulates Chronic and Persistent Idiopathic Pulmonary Fibrosis with Strong Senescence Signatures

Idiopathic Pulmonary Fibrosis (IPF) is a chronic and progressive lung disease that primarily afflicts people over the age of 65. IPF is characterized by lung scarring, an elevated senescence burden, and interstitial pneumonia, resulting in disability and mortality. The growing aging population worldwide, limited effectiveness of current treatments, and high economic burden underscore the need for robust models to investigate the underlying mechanisms and test novel interventions. Despite broad preclinical use, the bleomycin-induced murine model has notable limitations. Animals subjected to a single dose of bleomycin administration undergo recovery in weight and behavior between 21 and 28 days after administration, which is contrary to the progressive nature of IPF. Previous reports have shown that repetitive instillation of bleomycin phenocopies this aspect of the human disease. However, these methods are time-consuming and complex. Although IPF is typically associated with advanced age, most research is conducted in 6 to 8-week-old mice, which lack the age-related structural and metabolic deficits seen in humans. In this study, we report an improved model of IPF using 17-month-old UM-HET3 mice subjected to a single oropharyngeal bleomycin dosing that better mimics the persistent nature of the disease. Lung histology and immunohistochemistry (IHC) confirm persistence of fibrosis and senescence in mice 10 weeks after bleomycin administration. Furthermore, bulk RNA sequencing (RNA-Seq) analysis revealed a distinct set of gene expression signatures that is more consistent with chronic human fibrosis. This model offers greater insight into IPF pathogenesis, and we anticipate that it will enhance confidence in the human translatability of candidate therapeutic interventions.

molecular biology↗

bioRxiv2025

A Case Study: Using Passive Acoustic Monitoring Devices In A Growing Urban Landscape To Monitor Avian Diversity

With the increase of urbanization around the world, key habitats such as grasslands and scrublands are disappearing, posing significant threats to species that rely on such habitats. Passive acoustic monitoring (PAM) has started to gain interest as a reliable tool for biodiversity monitoring. This study assesses whether PAM can be an effective way to monitor biodiversity with relatively low effort when compared to traditional survey methods. Using PAM, a mixed grassland and scrubland ecosystem was monitored for five months for avifaunal diversity. Data that was collected from dusk to dawn using audio recorders deployed on the study site were run through BirdNET analyzer under default detectors. Top detections for each species were compared with avian vocalization libraries manually. Out of 135 species detected, 76 were true positives, resulting in a species identification accuracy of 56.3%. Notably, among the species that were true detections, 21 species were found to have confidence scores larger than 0.99. In addition, 15 of the detected species were found to be migratory in this area, and three were found to be rare. This study demonstrates how PAM can be used to monitor biodiversity in a species-rich but understudied area such as Southern India, to identify both cryptic and nocturnal species that might be omitted from standard field surveys.

ecology↗

bioRxiv2025

Temporal and cell-specific changes to cellular iron sequestration and lipid peroxidation in a murine model of neonatal hypoxic-ischemic brain injury.

BackgroundIron accumulation and lipid peroxidation are pathophysiologic mechanisms that drive neonatal hypoxic-ischemic (HI) brain injury. Characterization of spatiotemporal changes in these processes will help elucidate their role in ischemic neuronal injury as an initial step towards developing targeted interventions. MethodsHI was induced in post-natal day 9 mice using the modified-Vannucci model. Hippocampal tissue from ipsilateral HI exposed, contralateral hypoxia exposed and sham animals was collected at 6h, 24h, 72h and 7d post-HI. Tissue was subsequently evaluated for markers of cell death (TUNEL), intracellular iron changes (FerroOrange, fluorescent in situ and immunofluorescence), and lipid peroxidation (real time PCR, Gpx4 immunofluorescence and mass spectrometry). Mass spectrometry measured isoprostanes (15-F2t-IsoP) and neuroprostanes (4-F4t-NP) as lipid peroxidation markers of arachidonic (ARA) and docosahexaenoic acid (DHA), respectively. ResultsCompared to sham, the HI hippocampus showed increased intracellular labile iron levels that was maximal at 6h post-HI with subsequent elevation in only neuroprostanes at 24h post-HI. TUNEL labeling peaked at 24h post-HI. At 72h, labile iron levels and lipid peroxidation declined corresponding with peak infiltration of ferritin positive microglia/macrophages and the start of TUNEL staining decline. In addition, surviving neurons had increased expression of Gpx4 peaking at 72h post-HI that normalized by 7d post-HI. ConclusionsThese findings suggest that following HI, an acute increase in labile iron and DHA peroxidation are correlated with markers of cell death that peak at 24h post-HI. Microglial/macrophage iron sequestration and neuronal antioxidant responses may ameliorate further injury and represent targets for neuroprotective therapies.

neuroscience↗

bioRxiv2025

γδ T Cells Target and Ablate Senescent Cells in Aging and Alleviate Pulmonary Fibrosis

A variety of physiological and pathological stimuli elicit the cellular senescence response. Immune cells are known to execute surveillance of infected, cancerous, and senescent cells, and yet senescent cells accumulate with age and drive inflammation and age-related disease. Understanding the roles of different immune cells in senescent cell surveillance could enable the development of immunotherapies against biological aging and age-related disease. Here, we report the role of human gamma delta ({gamma}{delta}) T cells in eliminating senescent cells. Human donor V{gamma}9v{delta}2 T cells selectively remove senescent cells of different cell types and modes of induction while sparing healthy cells, with parallel findings in mouse cells. We find that senescent cells express high levels of multiple {gamma}{delta} T cell ligands, including cell-surface BTN3A1. Individually blocking NKG2D or {gamma}{delta} TCR of {gamma}{delta} T cells only partially reduces V{gamma}9v{delta}2 T cell cytotoxicity, evidencing their versatility in senescence removal. {gamma}{delta} T cells expand in response to the induction of a mouse model of idiopathic pulmonary fibrosis (IPF), accompanied by the emergence of senescent cells, and colocalize with senescent cells in lung tissue from patients with IPF. Finally, we show that adoptive cell transfer of {gamma}{delta} T cells into an IPF mouse model reduces the number of p21-expressing senescent cells in affected lung tissue and improves outcomes. {gamma}{delta} T cells or modalities that activate their surveillance activity present a potent approach for removing senescent cells and their attendant contribution to aging and disease.

immunology↗

bioRxiv2025

STREAMLINING HISTOPATHOLOGY: INSTAPRESERVE TISSUESAFE A SINGLE-STEP FIXATIVE THAT IMPROVES TISSUE QUALITY AND WORKFLOW EFFICIENCY

In clinical pathology, tissue processing is crucial in generating a valuable report for faster diagnosis. Formalin-fixed paraffin-embedded tissues are the standard specimens for clinical and molecular analyses. Though the demand persists for faster diagnosis, neutral buffered formalin (NBF) -based fixation and processing have not been replaced with a simple, faster, and user-friendly method. The alcohol-based fixatives were evaluated as an alternative to formalin, yet none have replaced formalin for various reasons. InstaPRESERVE Tissuesafe is an alcohol-based, biodegradable, and user-friendly fixative solution. The clinical specimens are well preserved and suitable for histopathology, genomics, and proteomics studies. The efficacy of instaPRESERVE Tissuesafe with ethanol or isopropyl alcohol and a modified tissue processing method without alcohol dehydration steps was studied. The pigs organs, brain, and liver tissues were fixed with NBF and InstaPRESERVE Tissuesafe solutions (ethanol/isopropyl alcohol). Based on the alcohol content of instaPRESERVE Tissuesafe, the dehydration step(s) were skipped during tissue processing. Serial sections from fixed tissues were processed and stained with H&E. The intactness of the sections with instaPRESERVE Tissuesafe fixation was comparable to that of NBF fixation. No autolysis/ decomposition was observed with InstaPRESERVE Tissuesafe (both) and NBF. The H&E staining scoring was satisfactory with well-preserved cell boundaries and organelles in both liver and brain tissue sections. The key factors of any fixative are its penetration, temperature, and time taken for fixation. In this study, the penetration rate of InstaPRESERVE Tissuesafe with either ethanol or isopropyl alcohol was the same as NBF within 6 to 12 hrs. The results indicated that increased concentration of alcohol in instaPRESERVE Tissuesafe did not affect the histology, and overall quality of the tissue sections processed was comparable to formalin fixation. The cytoplasmic and nuclear details, erythrocyte integrity, and lymphocytic appearance were well maintained. The time was reduced to 6 hrs from 9 hrs of the standard method. This study has addressed the modification of tissue processing with reduced time in histopathology with instaPRESERVE Tissuesafe. The outcome of this study has shown that instaPRESERVE Tissuesafe may be an alternative to formalin and helps in faster diagnosis.

pathology↗

bioRxiv2025

Biobanking of Biological Samples at Room Temperature

Biospecimens have become an integral part of life science research, pharma and drug development. There is increased demand for biospecimens from patients with assured quality of collection, processing, and storage. Establishing a biobank with high-quality biospecimens is an expensive aspect due to the requirement of costly freezers and liquid nitrogen facilities. Many studies have explored various storage reagents for biological samples. Still, the need of the hour is the one that can preserve biological samples at ambient room temperature and suitable for diagnosis and research. InstaPRESERVE is an eco/user-friendly solution with long-term sustainable alternative for freezer or liquid nitrogen systems for biobanking. Blood and saliva specimens were collected and stored in InstaPRESERVE at room temperature and conventional storage conditions. The genomics and proteomics analysis of the DNA, RNA, and protein extracted from the -80{degrees}C and InstaPRESERVE stored specimens and fresh specimens indicated that the specimens were well-conserved at room temperature compared to frozen specimens. Innovative technologies and approaches are being evaluated in biobanks for sample integrity, reducing collection, processing, and storage costs, increasing speed and throughput, and reducing energy expenditure. Preserving the biospecimens in InstaPRESERVE at room temperature eliminates expensive storage systems, cold-chain during transportation, and pre-processing requirements. The qualitative and quantitative results of DNA, RNA, and protein ensured stabilized storage for a longer period. The use of InstaPRESERVE as a specimen storage medium is emerging as an alternative in biobanking for specimen storage at room temperature. The existing and proposed biobanks may consider employing InstaPRESERVE as a reliable resource for biospecimens storage.

molecular biology↗

bioRxiv2025

Inhibition of PIKfyve kinase induces senescent cell death by suppressing lysosomal exocytosis and leads to improved outcomes in a mouse model of idiopathic pulmonary fibrosis

Cellular senescence is a pivotal hallmark of aging, which limits lifespan and contributes to the development of age-related diseases. Efforts to identify senolytics - drugs that selectively eliminate senescent cells, have so far yielded candidates with limited translational potential. Here, we characterize the senescent cell surface proteomic landscape and identify proteins that are abnormally present on the plasma membrane of senescent cells. Many of these proteins are lysosomal enzymes, pointing to lysosomal exocytosis as a likely mechanism that leads to their persistent display on the cell surface. Blocking lysosomal exocytosis via PIKfyve kinase inhibition with a small molecule drug apilimod results in selective killing of senescent cells in vitro, while this treatment does not affect quiescent and proliferating cells. Furthermore, apilimod can be safely administered in vivo and effectively removes senescent cells and reduces tissue remodeling in a bleomycin mouse model of pulmonary fibrosis. We conclude that apilimod is an effective and well-tolerated senolytic that may be useful for the treatment of senescence-associated diseases of aging.

molecular biology↗

bioRxiv2025

Cell-Surface LAMP1 is a Senescence Marker in Aging and Idiopathic Pulmonary Fibrosis

The accumulation of senescent cells (SEN) with aging produces a chronic inflammatory state that accelerates age-related diseases. Eliminating SEN has been shown to delay, prevent, and in some cases reverse aging in animal disease models and extend lifespan. There is thus an unmet clinical need to identify and target SEN while sparing healthy cells. Here, we show that Lysosomal-Associated Membrane Protein 1 (LAMP1) is a membrane-specific biomarker of cellular senescence. We have validated selective LAMP1 upregulation in SEN in human and mouse cells. Lamp1+ cells express high levels of prototypical senescence markers p16, p21, Glb1, and have low Lmnb1 expression as compared to Lamp1- cells. The percentage of Lamp1+ cells is increased in mice with fibrotic lungs after bleomycin instillation. Finally, we use a dual antibody-drug conjugate (ADC) strategy to eliminate LAMP1+ senescent cells.

molecular biology↗

bioRxiv2023

Edge Community Entropy is a Novel Neural Correlate of Aging and Moderator of Fluid Cognition

Decreased neuronal specificity of the brain in response to cognitive demands (i.e., neural dedifferentiation) has been implicated in age-related cognitive decline. Investigations into functional connectivity analogues of these processes have focused primarily on measuring segregation of nonoverlapping networks at rest. Here, we used an edge-centric network approach to derive entropy, a measure of nodal specialization, from spatially overlapping communities during cognitive task fMRI. Using Human Connectome Project Lifespan data (713 participants, 36-100 years old), we characterized a pattern of nodal despecialization differentially affecting the medial temporal lobe and limbic, visual, and subcortical systems. Global entropy uniquely covaried with age when controlling for network segregation. Importantly, relationships between both metrics and fluid cognition were age-dependent, although entropys relationship with cognition was specific to older adults. These results suggest entropy is a potentially important metric for examining how neurological processes in aging affect functional specialization at the nodal, network, and whole-brain level.

neuroscience↗

bioRxiv2022

Large-scale in vivo CRISPR screens identify SAGA complex members as a key regulators of HSC lineage commitment and aging

The biological mechanisms that sustain the vast blood production required for healthy life remain incompletely understood. To search for novel regulators of hematopoiesis, we performed genome-wide in vivo hematopoietic stem cell (HSC)-based CRISPR knockout screens for regulators of hematopoiesis. We discovered SAGA complex members, including Tada2b and Taf5l, as key regulators of hematopoiesis. Loss of Tada2b or Taf5l strongly inhibited hematopoiesis in vivo, led to a buildup of immature hematopoietic cells in the bone marrow, and was associated with upregulation of interferon pathway genes. Loss of these factors also enhanced the cell outgrowth and the interferon pathway in an in vivo human myelodysplastic syndrome model, suggesting that loss of SAGA complex activity could contribute to hematological disease progression. In summary, this study has identified the SAGA complex as an important regulator of hematopoiesis.

genetics↗

bioRxiv2021

Facultative variation across a shallow to deep torpor spectrum in hummingbirds

Many small endotherms use torpor, saving energy by a controlled reduction of their body temperature and metabolic rate. Some species (e.g. arctic ground squirrels, hummingbirds) enter deep torpor, dropping their body temperatures by 23-37 {degrees}C, while others can only enter shallow torpor (e.g., pigeons, 3-10 {degrees}C reductions). However, deep torpor in mammals can increase predation risk (unless animals are in burrows or caves), inhibit immune function, and result in sleep deprivation, so even for species that can enter deep torpor, facultative shallow torpor might help balance energy savings with these potential costs. Deep torpor occurs in three avian orders. Although the literature hints that some bird species can use both shallow and deep torpor, little empirical evidence of such an avian torpor spectrum exists. We infrared imaged three hummingbird species that are known to use deep torpor, under natural temperature and light cycles, to test if they were also capable of shallow torpor. All three species used both deep and shallow torpor, often on the same night. Depending on the species, they used shallow torpor for 5-35% of the night. The presence of a bird torpor spectrum indicates a capacity for fine-scale physiological and genetic regulation of avian torpid metabolism.

ecology↗

bioRxiv2021

Employing connectome-based models to predict working memory in multiple sclerosis

BackgroundIndividuals with multiple sclerosis (MS) are vulnerable to deficits in working memory, and the search for neural correlates of working memory in circumscribed areas has yielded inconclusive findings. Given the widespread neural alterations observed in MS, predictive modeling approaches that capitalize on whole-brain connectivity may better capture individual-level working memory in this population. MethodsHere, we applied connectome-based predictive modeling to functional MRI data from working memory tasks in two independent samples with relapsing-remitting MS. In the internal validation sample (ninternal = 36), functional connectivity data were used to train a model through cross-validation to predict accuracy on the Paced Visual Serial Addition Test, a gold-standard measure of working memory in MS. We then tested its ability to predict performance on the N-back working memory task in the external validation sample (nexternal = 36). ResultsThe resulting model successfully predicted working memory in the internal validation sample but did not extend to the external sample. We also tested the generalizability of an existing model of working memory derived in healthy young adults to people with MS. It showed successful prediction in both MS samples, demonstrating its translational potential. We qualitatively explored differences between the healthy and MS models in intra- and inter-network connectivity amongst canonical networks. DiscussionThese findings suggest that connectome-based predictive models derived in people with MS may have limited generalizability. Instead, models identified in healthy individuals may offer superior generalizability to clinical samples, such as MS, and may serve as more useful targets for intervention. Impact StatementWorking memory deficits in people with multiple sclerosis have important consequence for employment, leisure, and daily living activities. Identifying a functional connectivity-based marker that accurately captures individual differences in working memory may offer a useful target for cognitive rehabilitation. Manglani et al. demonstrate machine learning can be applied to whole-brain functional connectivity data to identify networks that predict individual-level working memory in people with multiple sclerosis. However, existing network-based models of working memory derived in healthy adults outperform those identified in multiple sclerosis, suggesting translational potential of brain networks derived in large, healthy samples for predicting cognition in multiple sclerosis.

neuroscience↗

bioRxiv2020

MicrobeTrace: Retooling Molecular Epidemiology for Rapid Public Health Response

MotivationOutbreak investigations use data from interviews, healthcare providers, laboratories and surveillance systems. However, integrated use of data from multiple sources requires a patchwork of software that present challenges in usability, interoperability, confidentiality, and cost. Rapid integration, visualization and analysis of data from multiple sources can guide effective public health interventions. ResultsWe developed MicrobeTrace to facilitate rapid public health responses by overcoming barriers to data integration and exploration in molecular epidemiology. Using publicly available HIV sequences and other data, we demonstrate the analysis of viral genetic distance networks and introduce a novel approach to minimum spanning trees that simplifies results. We also illustrate the potential utility of MicrobeTrace in support of contact tracing by analyzing and displaying data from an outbreak of SARS-CoV-2 in South Korea in early 2020. Availability and ImplementationMicrobeTrace is a web-based, client-side, JavaScript application (https://microbetrace.cdc.gov) that runs in Chromium-based browsers and remains fully-operational without an internet connection. MicrobeTrace is developed and actively maintained by the Centers for Disease Control and Prevention. The source code is available at https://github.com/cdcgov/microbetrace. Contactells@cdc.gov

bioinformatics↗

bioRxiv2020

Spatiotemporal dynamics between interictal epileptiform discharges and ripples during associative memory processing

We describe the spatiotemporal course of cortical high-gamma activity (HGA), hippocampal ripple activity and interictal epileptiform discharges (IEDs) during an associative memory task in 15 epilepsy patients undergoing invasive electroencephalography. Successful encoding trials manifested significantly greater HGA in hippocampus and frontal regions. Successful cued recall trials manifested sustained HGA in hippocampus compared to failed responses. Hippocampal ripple rates were greater during successful encoding and retrieval trials. IEDs during encoding were associated with 15% decreased odds of remembering in hippocampus (95% CI 6-23%). Hippocampal IEDs during retrieval predicted 25% decreased odds of remembering (15-33%). Odds of remembering were reduced by 25-52% if IEDs occurred during the 500-2000 ms window of encoding or by 41% during retrieval. During encoding and retrieval, hippocampal IEDs were followed by a transient decrease in ripple rate. We hypothesize that IEDs impair associative memory in a regionally and temporally specific manner by decreasing physiologic hippocampal ripples necessary for effective encoding and recall. Because dynamic memory impairment arises from pathological IED events competing with physiological ripples, IEDs represent a promising therapeutic target for memory remediation in patients with epilepsy. SummaryHippocampal interictal epileptiform discharges in hippocampus acutely impair declarative memory, potentially by hijacking physiological processes essential for encoding and recall.

neuroscience↗

bioRxiv2020

Context-dependent functional compensation between Ythdf m6A readers

The N6-methyladenosine (m6A) modification is the most prevalent post-transcriptional mRNA modification, regulating mRNA decay, translation and splicing. It plays a major role during normal development, differentiation, and disease progression. The modification is dynamically regulated by a set of writer, eraser and reader proteins. The YTH-domain family of proteins: Ythdf1, Ythdf2, and Ythdf3, are three homologous m6A binding proteins, which have different cellular functions. However, their sequence similarity and their tendency to bind the same targets suggest that they may have overlapping roles. We systematically knocked out (KO) the Mettl3 writer for each of the Ythdf readers and for the three readers together (triple-KO). We then estimated the effect in-vivo, in mouse gametogenesis and viability, and in-vitro, in mouse embryonic stem cells (mESCs). We show that in gametogenesis, Mettl3-KO severity is increased as the deletion occurs earlier in the process, and Ythdf2 has a dominant role that cannot be compensated by Ythdf1 or Ythdf3, possibly due to differences in readers expression, both in quantity and in spatial location. By knocking out the three readers together and systematically testing offspring genotypes, we have revealed a redundancy in the readers role during early development, a redundancy which is dosage-dependent. Additionally, we show that in mESCs there is compensation between the three readers, since the inability to differentiate and the significant effect on mRNA decay occur only in the triple-KO cells and not in the single KOs. Thus, we suggest a novel model for the Ythdf readers function. There is a dosage-dependent redundancy when all three readers are co-expressed in the same location in the cells.

developmental biology↗