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Choi, J. Y.

Publications and source records attributed to Choi, J. Y..

At least 19 recordsLinked to original sources

Biogeographic cline is associated with the global plant telomere length variation

Telomeres have the crucial role of protecting chromosome ends and its length varies significantly between organisms. What evolutionary factor shapes this natural variation has been a long standing question, with answers providing insights into chromosome function and evolution. In animals life-history variation relating to senescence or tumorigenesis explains telomere length variation. For plants, however, we lack knowledge of what factor is driving their length variation in nature. Is life-history differences also driving telomere length variation among plant species? We answer this question by analyzing the telomeres of 257 plant species spanning the major orders of the green plant kingdom. Telomere lengths were estimated for species that vary significantly in their life-history, geographical distribution, and trait characters. Results showed telomere length increased with the evolution of terrestrialization, where Chlorophytes had the shortest telomeres and Spermatophytes had the longest telomeres. Surprisingly, plants with different life-histories had minimal telomere length differences, but biogeographic clines had significant effect on telomere length variation. Plant telomere length increases closer to the equator, while telomere length decreases at higher altitude. Domestication was previously proposed to lengthen telomeres, but we found no consistent domestication effect on telomere lengths comparing crops and their wild progenitors. From our results we conclude plant telomere length contrasts with animal telomeres, in that life-history has minimal effect on length variation. Instead we propose the ecological adaptation hypothesis, where telomere length in plants is determined by selection from abiotic conditions, and suggest temperature is a major factor shaping telomere length in plants.

evolutionary biology↗

Rapid evolution and functional divergence of the monkeyflower Mimulus lewisii telomerase

Telomeres are nucleoprotein structures that protect chromosome ends and are maintained by the Telomerase Reverse Transcriptase (TERT) protein that uses a noncoding Telomerase RNA (TR) as a template. In monkeyflowers, Mimulus lewisii had an ancient TR gene duplication, synthesizing an evolutionarily atypical sequence heterogeneous telomere. How TERT interacts with both TR paralogs during telomere maintenance is unknown and answers can shed novel insights underlying telomere function. Using new genome assemblies we discovered TERT is rapidly evolving in lineages sharing the TR duplication. We investigated the functional consequences arising from the rapid evolution, first by using yeast three-hybrid and testing the physical binding between conspecific and heterospecific TERT-TR combinations. Results showed TERT binds both ancestral (TR1) and derived (TR2) TR paralogs in M. lewisii, but not in species without a functioning TR2. We located the region of TR binding to amino acids near the KRxR motif. We then combined next-generation sequencing with Telomeric Repeat Amplification Protocol and discovered M. lewisii had high telomerase activity. Comparative transcriptomics indicated no strong evidence of expression divergence in telomere maintenance genes for M. lewisii, suggesting rapid evolution shaped TERT protein sequence. In vivo activity of M. lewisii telomerase was investigated by analyzing F1 telomeres generated by crossing M. lewisii and M. verbenaceus, which doesnt have a functioning TR2. Results showed M. verbenaceus chromosome ends in the F1 had converted into M. lewisii telomeres, suggesting dominance of the M. lewisii telomerase. We demonstrate TERT-TR coevolution can have significant consequences on the evolution of plant telomeres. Significance statementTelomeres protect chromosome ends and are maintained by the telomerase complex. We discovered the catalytic component of the telomerase (TERT) was rapidly evolving in monkeyflowers (Mimulus) and studied the molecular consequences. In M. lewisii, TERT evolved lineage-specific amino acids to bind two sequence divergent telomerase RNA paralogs. Telomerase activity assay showed M. lewisii synthesized more telomere repeats compared to its sister species without the TR duplication, and transcriptomics indicated this was not due to a change in telomere maintenance gene expression. Genetic experiments in interspecies hybrids showed M. lewisii telomerase could convert chromosome ends in sister species into M. lewisii-like telomeres suggesting functional dominance. We show rapid evolution of the telomerase can have significant effects on telomere evolution.

evolutionary biology↗

Identification of a new mycobacterial peptide that controls the activity of the iron-dependent regulator, IdeR.

Mycobacterium tuberculosis (Mtb) must regulate intracellular iron to survive in the host and cause disease. IdeR (Iron-dependent Regulator) is an essential Mtb protein that governs intracellular iron levels by regulating the expression of genes involved in iron metabolism. IdeR expression, however, is iron independent, and the mechanisms that regulate IdeRs function are not fully understood. Here, we report the discovery of a previously unrecognized Mtb peptide (PRI) that regulates IdeR activity. PRI is induced under iron limitation; it binds to IdeR and restricts its activity. In addition, we demonstrate that altering the balance between PRI and IdeR impairs iron homeostasis and intracellular replication of Mtb in macrophages. The findings reveal a new paradigm in mycobacterial iron regulation and open new avenues for targeting iron homeostatic mechanisms in Mtb, which are crucial for virulence and antibiotic resistance.

microbiology↗

Topsicle: a method for estimating telomere length from whole genome long-read sequencing data

Telomeres protect chromosome ends and its length varies significantly between organisms. Because telomere length variation is associated with various biomedical and eco-evolutionary phenotypes, many biological fields are interest in understanding its biological significance. Here we introduce Topsicle, a computational method that estimates telomere length from whole genome long read sequencing data using k-mer and change point detection analysis. Simulations showed Topsicle was robust to sequencing errors and coverage. Application of Topsicle on plant and human cancer cells showed high accuracy and comparable results to direct telomere length measurements. We predict Topsicle will be a useful tool for studying telomere biology.

genomics↗

Novel mouse model of cerebral microbleeds created by Crispr/Cas9-mediated Col4a1 deletion in adult brain microvessels

Cerebral small vessel disease is a leading cause of cognitive decline and stroke in the elderly, with cerebral microbleeds (CMBs) as one of the key imaging biomarkers. Our understanding of its pathophysiology remains limited due to the lack of appropriate animal models. We report a novel mouse CMB model created by disrupting collagen IV, a core component of the vascular basement membrane (BM), specifically within brain microvessels. Targeted deletion of Col4a1 was achieved in adult mice using brain endothelial-specific AAV vectors with CRISPR/Cas9. MRI revealed numerous CMBs with distributions similar to those of human CMBs. CMB burden increased progressively over six months following Col4a1 deletion in a dose-dependent manner, accompanied by cognitive decline and motor incoordination. Histological examination revealed hemosiderin deposits corresponding to MRI-detected CMBs without evidence of macroscopic hemorrhage or white matter lesions, while ultrastructural analysis demonstrated significant BM thinning in Col4a1-depleted microvessels. Analysis of human MRI and genomic data identified significant associations between CMB susceptibility and genetic variants in TIMP2, an endogenous inhibitor of the matrix-degrading enzyme MMP2, underscoring the clinical relevance of our model. These findings establish a direct causal relationship between microvessel COL4A1 and CMB, suggesting that dysregulated collagen IV homeostasis in BM underlies CMB development.

neuroscience↗

Environment-dependent selection impacts heritable developmental stability and trait canalization in rice

Canalization, or the maintenance of trait values regardless of environmental or genetic variability, is fundamentally important for maintaining developmental stability. While this concept was described decades ago, we still know relatively little about how canalization is influenced by environmental stress, how it is shaped by natural selection, and the genetic underpinnings of canalization. In this study, we examined natural selection on microenvironmental canalization in rice (Oryza sativa) in wet and dry field conditions. We measured developmental stability in genetically identical replicates obtained from geographically widespread Indica and Japonica rice accessions, providing precise estimates of canalization in thousands of plants. We found that drought stress decreased canalization, showing that stress can increase instability. We also found evidence that canalization can evolve, given that canalization of several traits was heritable and under selection. We further uncovered specific genes underlying canalization, with genetic mapping and functional genetic experiments showing that the bZIP transcription factor-encoding gene OsTGA5/rTGA2.3, which is part of a module that balances stress response and plant growth, regulates canalization of several traits in an environment-dependent manner. At a genome-wide scale, canalization was associated with lower gene expression stochasticity at an earlier life stage, indicating that expression variation can reduce canalization and increase instability. Trait canalization was also positively correlated to temperature at accessions source environments, suggesting that selection on canalization can vary among environments. Overall, our study provides novel insights into the molecular genetic basis of environmental differences in developmental stability and how it might be shaped by selection. SignificanceMechanisms stabilizing organismal development in response to genetic mutations or environmental stressors (canalization) have been reported for numerous animals and plants, but their underlying genetic basis and whether they may be shaped by selection remain unclear. Here, we report patterns of drought-induced trait decanalization in populations of rice (Oryza sativa) grown in field environments. We determined that trait canalization is heritable and can evolve separately from trait means. We identified the gene OsTGA5, part of a regulatory module shaping trade-offs between growth and stress responses, as impacting trait canalization. Plants with less noisy gene expression and evolving in warmer environments display greater developmental stability, contributing to the notion that canalization in rice may be adaptive.

evolutionary biology↗

Systematic bias in surface area asymmetry measurements from automatic cortical parcellations

Anatomical asymmetry is a hallmark of the human brain and may reflect hemispheric differences in its functional organization. Widely used software like FreeSurfer can automate neuroanatomical measurements and facilitate studies of hemispheric asymmetry. However, patterns of surface area lateralization measured using FreeSurfer are curiously consistent across diverse samples. Here, we demonstrate systematic biases in these measurements obtained from the default processing pipeline. We compared surface area asymmetry measured from reconstructions of original brains vs. the same scans after flipping their left-right orientation. The default pipeline returned implausible asymmetry patterns between the original and flipped brains: Many structures were always left- or right-lateralized. Notably, these biases occur prominently in key speech and language regions. In contrast, manual labeling and curvature-based parcellations of key structures both yielded the expected reversals of left/right lateralization in flipped brains. We determined that these biases result from discrepancies in how regional labels are defined in the left vs. right hemisphere in the default cortical parcellation atlases. These biases are carried into individual parcellations because the FreeSurfer parcellation algorithm prioritizes vertex correspondence to the template atlas relative to individual neuroanatomical variation. We further demonstrate several straightforward, bias-free approaches to measuring surface area asymmetry, including using symmetric registration templates and parcellation atlases, vertex-wise analyses, and within-subject curvature-based parcellations. These results highlight theoretical concerns about using only the default processing stream to make inferences about population-level brain asymmetry and underscore the need for validating bias-free neuroanatomical measurements, particularly when studying regions where structural lateralization may underlie functional lateralization.

neuroscience↗

Transposition, duplication, and divergence of the telomerase RNA underlies the Mimulus telomere evolution

Telomeres are nucleoprotein complexes with a crucial role of protecting chromosome ends. It consists of simple repeat sequences and dedicated telomere-binding proteins. Because of its vital functions, components of the telomere, for example its sequence, should be under strong evolutionary constraint. But across all plants, telomere sequences display a range of variation and the evolutionary mechanism driving this diversification is largely unknown. Here, we discovered in Monkeyflower (Mimulus) the telomere sequence is even variable between species. We investigated the basis of Mimulus telomere sequence evolution by studying the long noncoding telomerase RNA (TR), which is a core component of the telomere maintenance complex and determines the telomere sequence. We conducted total RNA-based de novo transcriptomics from 16 Mimulus species and analyzed reference genomes from 6 species, and discovered Mimulus species have evolved at least three different telomere sequences: (AAACCCT)n, (AAACCCG)n, and (AAACCG)n. Unexpectedly, we discovered several species with TR duplications and the paralogs had functional consequences that could influence telomere evolution. For instance, M. lewisii had two sequence-divergent TR paralogs and synthesized a telomere with sequence heterogeneity, consisting of AAACCG and AAACCCG repeats. Evolutionary analysis of the M. lewisii TR paralogs indicated it had arisen from a transposition-mediate duplication process. Further analysis of the TR from multiple Mimulus species showed the gene had frequently transposed and inserted into new chromosomal positions during Mimulus evolution. From our results, we propose the TR transposition, duplication, and divergence model to explain the evolutionary sequence turnovers in Mimulus and potentially all plant telomeres.

evolutionary biology↗

A primary culture method for the easy, efficient and effective acquisition of oligodendrocyte lineage cells

Oligodendrocytes (OL) are myelin forming glial cells in the central nervous system. In vitro primary OL culture models provide the benefit of a more readily controlled environment facilitating the evaluation of diverse OL stages and convoluted dynamics. Conventional methods of primary OL culture do exist, but their performance in terms of efficiency and simplicity has room for improvement. We present a novel method of primary OL culture, namely the E3 (Easy, efficient, and effective) method, which greatly improves cell yield and reduces time required to oligodendrocyte progenitor cell (OPC) acquisition and maturation into OLs. We also provide optimal media compositions for augmentation of OPC proliferation and a more robust maturation into myelin forming OLs. In vitro characteristics of the OL lineage discovered during the development of the E3 method present implications for further research on OL physiology and pathophysiology.

neuroscience↗

A Potent Kalihinol Analogue Disrupts Apicoplast Function and Vesicular Trafficking in P. falciparum Malaria.

Here we report the discovery of MED6-189, a new analogue of the kalihinol family of isocyanoterpene (ICT) natural products. MED6-189 is effective against drug-sensitive and-resistant P. falciparum strains blocking both intraerythrocytic asexual replication and sexual differentiation. This compound was also effective against P. knowlesi and P. cynomolgi. In vivo efficacy studies using a humanized mouse model of malaria confirms strong efficacy of the compound in animals with no apparent hemolytic activity or apparent toxicity. Complementary chemical biology, molecular biology, genomics and cell biological analyses revealed that MED6-189 primarily targets the parasite apicoplast and acts by inhibiting lipid biogenesis and cellular trafficking. Genetic analyses in P. falciparum revealed that a mutation in PfSec13, which encodes a component of the parasite secretory machinery, reduced susceptibility to the drug. The high potency of MED6-189 in vitro and in vivo, its broad range of efficacy, excellent therapeutic profile, and unique mode of action make it an excellent addition to the antimalarial drug pipeline. Editors SummaryHere we report the mode of action and mechanism of resistance of a pan-antimalarial agent, MED6-189, which disrupts apicoplast function and vesicular trafficking in P. falciparum.

microbiology↗

Hypothalamic neuronal activation in primates drives naturalistic goal-directed eating behavior

Eating addiction is the primary cause of modern obesity. Although the causal role of the lateral hypothalamic area (LHA) for eating is demonstrated in rodents, there is no evidence in primates regarding naturalistic eating behaviors. We investigated the role of LHA GABAergic (LHAGABA) neurons in eating by chemogenetics in three macaques. LHAGABA neuron activation significantly increased naturalistic goal-directed behaviors and food motivation, which was specific for palatable food. PET and MRS validated the chemogenetic activation. Rs-fMRI result revealed that functional connectivity (FC) between the LHA and frontal areas was increased, while the FC between the frontal cortices was decreased after the LHAGABA neuron activation. Thus, our study elucidates the role of LHAGABA neurons in eating and obesity therapeutics for primates and humans.

neuroscience↗

Nascent transcription and the associated cis-regulatory landscape in rice

BackgroundPlant genomes encode transcripts that require spatio-temporal regulation for proper cellular function, and a large fraction of the regulators can be found in intergenic regions. In animals, distal intergenic regions described as enhancer regions are actively transcribed as enhancer RNAs (eRNAs); the existence of eRNAs in plants has only been fairly recently documented. In this study, we evaluated with high sensitivity the synthesis of eRNAs that arise at genomic elements both distal and proximal to genes by combining PRO-seq with chromatin accessibility, histone modification, and methylation profiles in rice. ResultsWe found that regions defined as transcribed intergenic regions are widespread in the rice genome, and many likely harbor transcribed regulatory elements. In addition to displaying evidence of selective constraint, the presence of these transcribed regulatory elements are correlated with an increase in nearby gene expression. We further identified molecular interactions between genic regions and intergenic transcribed regulatory elements using 3D chromosomal contact data, and found that these interactions were both associated with eQTLs as well as promoting transcription. We also compared the profile of accessible chromatin regions to our identified transcribed regulatory elements, and found less overlap than expected. Finally, we also observed that transcribed intergenic regions that overlapped partially or entirely with repetitive elements had a propensity to be enriched for cytosine methylation, and were likely involved in TE silencing rather than promoting gene transcription. ConclusionThe characterization of eRNAs in the rice genome reveals that many share features of enhancers and are associated with transcription regulation, which could make them compelling candidate enhancer elements.

plant biology↗

Lysosomal dysfunction in Down Syndrome and Alzheimer mouse models is caused by selective v-ATPase inhibition by Tyr682 phosphorylated APP βCTF

Lysosome dysfunction arises early and propels Alzheimers Disease (AD). Herein, we show that amyloid precursor protein (APP), linked to early-onset AD in Down Syndrome (DS), acts directly via its {beta}-C-terminal fragment ({beta}CTF) to disrupt lysosomal v-ATPase and acidification. In human DS fibroblasts, the phosphorylated 682YENPTY internalization motif of APP-{beta}CTF binds selectively within a pocket of the v-ATPase V0a1 subunit cytoplasmic domain and competitively inhibits association of the V1 subcomplex of v-ATPase, thereby reducing its activity. Lowering APP-{beta}CTF Tyr682 phosphorylation restores v-ATPase and lysosome function in DS fibroblasts and in vivo in brains of DS model mice. Notably, lowering APP-{beta}CTF Tyr682 phosphorylation below normal constitutive levels boosts v-ATPase assembly and activity, suggesting that v-ATPase may also be modulated tonically by phospho-APP-{beta}CTF. Elevated APP-{beta}CTF Tyr682 phosphorylation in two mouse AD models similarly disrupts v-ATPase function. These findings offer new insight into the pathogenic mechanism underlying faulty lysosomes in all forms of AD.

neuroscience↗

Selection on ancient variations drives the adaptive radiation of Metrosideros across the Hawaiian archipelago

Some of the most spectacular adaptive radiations begin with founder populations on remote islands. How genetically limited founder populations give rise to the striking phenotypic and ecological diversity characteristic of adaptive radiations is a paradox of evolutionary biology. We conducted an evolutionary genomic analysis of genus Metrosideros, a landscape-dominant, incipient adaptive radiation of woody plants that spans a striking range of phenotypes and environments across the Hawaiian Islands. Using nanopore-sequencing, we created a chromosome-level genome assembly for M. polymorpha var. incana and analyzed wholegenome sequences of 131 individuals from 11 taxa sampled across the islands. We found evidence of population structure that grouped taxa by island. Demographic modeling showed concordance between the divergence times of island-specific lineages and the geological formation of individual islands. Gene flow was also detected within and between island taxa, suggesting a complex reticulated evolutionary history. We investigated genomic regions with increased differentiation as these regions may harbor variants involved in local adaptation or reproductive isolation, thus forming the genomic basis of adaptive radiation. We discovered differentiation outliers have arisen from balancing selection on ancient divergent haplotypes that formed before the initial colonization of the archipelago. These regions experienced recurrent divergent selection as lineages colonized and diversified on new islands, and hybridization likely facilitated the transfer of these ancient variants between taxa. Balancing selection on multiple ancient haplotypes-or time-tested variants-may help to explain how lineages with limited gene pools can rapidly diversify to fill myriad ecological niches on remote islands. Significance statementSome of the most spectacular adaptive radiations of plants and animals occur on remote oceanic islands, yet such radiations are preceded by founding events that severely limit genetic variation. How genetically depauperate founder populations give rise to the spectacular phenotypic and ecological diversity characteristic of island adaptive radiations is not known. We generated novel genomic resources for Hawaiian Metrosideros--a hyper-variable incipient adaptive radiation of woody taxa--for insights into the paradox of remote island radiations. We found that Metrosideros colonized each island shortly after formation and diversified within islands through recurrent selection on ancient variations that predate the radiation. Recurring use of ancient variants may explain how genetically depauperate lineages can diversify to fill countless niches on remote islands.

evolutionary biology↗

Nasal commensal, Staphylococcus epidermidis shapes the mucosal environment to prevent influenza virus invasion through Serpine1 induction

Our recent study presented evidence that Staphylococcus epidermidis (S. epidermidis) was the most frequently encountered microbiome component in healthy human nasal mucus and that S. epidermidis could induce interferon (IFN)-dependent innate immunity to control acute viral lung infection. The serine protease inhibitor Serpine1 was identified to inhibit influenza A virus (IAV) spread by inhibiting glycoprotein cleavage, and the current study supports an additional mechanism of Serpine1 induction in the nasal mucosa, which can be regulated through S. epidermidis and IFN signaling. The exposure of in vivo mice to human S. epidermidis increased IFN-{lambda} secretion in nasal mucosa and prevented an increase in the burden of IAV in the lung. S. epidermidis-inoculated mice exhibited the significant induction of Serpine1 in vivo in the nasal mucosa, and by targeting airway protease, S. epidermidis-induced Serpine1 inhibited the intracellular invasion of IAV to the nasal epithelium and led to restriction of IAV spreading to the lung. Furthermore, IFN-{lambda} secretion was involved in the regulation of Serpine1 in S. epidermidis-inoculated nasal epithelial cells and in vivo nasal mucosa, and this was biologically relevant for the role of Serpine1 as an interferon-stimulated gene in the upper airway. Together, our findings reveal that human nasal commensal S. epidermidis manipulates the suppression of serine protease in in vivo nasal mucosa through Serpine1 induction and protects the nasal mucosa from IAV invasion through IFN-{lambda} signaling. IMPORTANCEPreviously, we proved that nasal microbiome could enhance IFN-related innate immune responses to protect the respiratory tract against influenza virus infection. The present study shows a great understanding of the intimate association of S. epidermidis-regulated IFN-lambda induction and serine protease inhibitor in nasal mucosa. Our data demonstrate that S. epidermidis-regulated Serpine1 suppresses the invasion of influenza virus through suppression of airway serine protease at the level of nasal mucosa and impedes IAV spread to the respiratory tract. Thus, human nasal commensal S. epidermidis represents a therapeutic potential for treating respiratory viral infections via the change of cellular environment in respiratory tract. O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY

immunology↗

A comparison of dopaminergic and cholinergic populations reveals unique contributions of VTA dopamine neurons to short-term memory

We systematically compared the contribution of two dopaminergic and two cholinergic ascending populations to a spatial short-term memory task in rats. In ventral tegmental area dopamine (VTA-DA) and nucleus basalis cholinergic (NB-ChAT) populations, trial-by-trial fluctuations in activity during the delay period related to performance with an inverted-U, despite the fact that both populations had low activity during that time. Transient manipulations revealed that only VTA-DA neurons, and not the other three populations we examined, contributed causally and selectively to short-term memory. This contribution was most significant during the delay period, when both increases or decreases in VTA-DA activity impaired short-term memory. Our results reveal a surprising dissociation between when VTA-DA neurons are most active and when they have the biggest causal contribution to short-term memory, while also providing new types of support for classic ideas about an inverted-U relationship between neuromodulation and cognition.

neuroscience↗

A Small interfering RNA lead targeting RNA-dependent RNA-polymerase effectively inhibit the SARS-CoV-2 infection in Golden Syrian hamster and Rhesus macaque

A small interfering RNA (siRNA) inhibitors have demonstrated the novel modality for suppressing infectious diseases. Sixty-one siRNA molecules, predicted by the bioinformatics programs, were screened for the possibility of treating severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) using an in vitro plaque assay. Among six siRNA leads with the efficacy of reducing plaque number, the siRNA targeting RNA-dependent RNA polymerase (RdRp) showed a reduction in SARS-CoV-2 infection-induced fever and virus titer in the Golden Syrian hamster and rhesus macaque. These results suggest the potential for RdRp targeting siRNA as a new treatment for the coronavirus disease 2019 (COVID-19).Competing Interest StatementThe authors have declared no competing interest.View Full Text

microbiology↗

Telomere lengths in plants are correlated with flowering time variation

Telomeres are highly repetitive tandemly repeating DNA sequences found at chromosomal ends that protect chromosomes from deterioration during cell division. Using whole genome re-sequencing data, we found substantial natural intraspecific variation in telomere lengths in Arabidopsis thaliana, Oryza sativa (rice) and Zea mays (maize). Genome-wide association mapping in A. thaliana identifies a region that includes the telomerase reverse transcriptase (TERT) gene as underlying telomere length variation. TERT appears to exist in two haplotype groups (L and S), of which the L haplogroup allele shows evidence of a selective sweep in Arabidopsis. We find that telomere length is negatively correlated with flowering time variation not only in A. thaliana, but also in maize and rice, indicating a link between life history traits and chromosome integrity. We suggest that longer telomeres may be more adaptive in plants that have faster developmental rates (and therefore flower earlier), and that chromosomal structure itself is an adaptive trait associated with plant life history strategies.Competing Interest StatementThe authors have declared no competing interest.View Full Text

plant biology↗