Biology subjects

Jin, E.

Publications and source records attributed to Jin, E..

At least 19 recordsLinked to original sources

bioRxiv2026

Cellular context restricts a promiscuous m6A reader IDR to a single functional effector interface for mRNA decay

N6-methyladenosine (m6A) is a conserved mRNA modification that regulates transcript stability, yet how m6A readers engage effectors remains unknown. We show that during yeast meiosis, the YTH-domain protein Pho92 promotes the decay of m6A-modified transcripts through an uncharacterised, promiscuous intrinsically disordered region (IDR). In vitro, the Pho92 IDR makes multiple contacts with the Ccr4-NOT deadenylase complex and drives tethered reporter decay in the absence of any single subunit. Yet in meiosis, turnover of endogenous m6A-modified transcripts strictly depends on a single interface: direct binding of the Pho92 IDR to Caf40. A single hydrophobic residue substitution is sufficient to abolish Caf40 binding and halt transcript decay. Human YTHDF proteins can functionally substitute for Pho92, but require multiple hydrophobic patches within the IDR for decay activity. Thus, on endogenous m6A-modified transcripts during meiosis, the promiscuous Pho92 IDR is restricted to a single functional interface, revealing unappreciated specificity in m6A-directed mRNA decay.

molecular biology↗

bioRxiv2026

A multimodal interrogation of Broca's area in the pediatric and adult human brain

Language is a defining trait of our species, and disruptions in language acquisition can have profound consequences to the individuals affected. Uncovering the neurodevelopmental basis of this complex trait requires detailed molecular and cellular insights into the neocortical areas that support linguistic abilities. Here we performed joint gene expression and chromatin accessibility profiling at single-nucleus resolution (10x Genomics Single cell Multiome) and spatial transcriptomic profiling (Xenium high-plex in situ spatial transcriptomics) of Brocas area alongside adjacent motor cortical areas. We profiled individuals from different ancestries (European and African) and developmental stages (infancy, childhood, adolescence, and adulthood). We provide a high-resolution dissection of the cellular and molecular architecture of Brocas and motor cortical areas across early life stages and anchor the trajectories to the cellular states found in the adult human brain. We identify distinct area- and stage-specific cellular signatures, including a prominent role of glia populations and interneuron subtypes contributing to cytoarchitectonic specializations. Using longitudinal single cell spatial transcriptomic profiling, we orthogonally validate our consensus cell taxonomy and spatially resolve layer enrichment of neuronal and astrocyte subtypes that distinguish Brocas area and motor cortex. We also uncover cell type-specific molecular signatures that distinguish cell developmental trajectories in these cortical areas, including an early molecular code established by differential expression of cadherin genes that might contribute to area-specific intercellular communication. We also identify cell type-specific vulnerabilities to language- related neurodevelopmental and neuropsychiatric disorders, with selective susceptibility of particular somatostatin-positive interneuron subtypes to ASD/ADHD. Finally, evolutionary analysis of differentially accessible regions between Brocas area and motor cortex suggests that genetic mutations that might have contributed to the emergence of linguistic abilities accumulated over the course of million years following the divergence of human and chimpanzee lineages. Together, our study provides a comprehensive molecular, cellular and spatial definition of Brocas area and motor cortex, laying the groundwork for investigations into unique aspects of human cognition and related neurodevelopmental and neuropsychiatric disorders.

neuroscience↗

bioRxiv2025

Alanine dependence of trans-translation contributes to riboregulation of mycobacterial antibiotic recalcitrance genes

ASBTRACTAntibiotic recalcitrance refers to a slower rate of death for either a bacterial population or a subpopulation of cells upon antibiotic exposure. It complicates treatment of many bacterial infections by contributing to treatment length, treatment failure, disease recurrence, and the emergence of antimicrobial resistance (AMR). Thus, blocking antibiotic recalcitrance could be a powerful strategy for improving treatment outcomes and reducing AMR rates. Here, using a forward genetic method for the isolation of antibiotic-recalcitrant mutants, we isolated two Mycobacterium smegmatis strains with mutations in the tRNA-modifying enzyme adenine-N(1)-methyltransferase. Both mutants were recalcitrant to proteostasis-perturbing antibiotics. We linked these phenotypes to upregulation of the transcriptional regulator WhiB7, highlighting its role as a point of convergence in the regulation of multiple mechanisms of antibiotic recalcitrance and resistance. Further, we identified a mechanism by which the amino acid alanine couples trans-translation to ribosome regulation-dependent, WhiB7-mediated expression of antibiotic resistance and recalcitrance genes, allowing bacterial cells to engage seemingly mutually exclusive mechanisms of survival upon exposure to stress.

microbiology↗

bioRxiv2025

Mechanism of MEK1 activation by phosphorylation

Phosphorylation is the most common post-translational protein modification, often acting as the activator of protein function. In the case of MEK1, a member of the MAP kinase family, phosphorylation of both S218 and S222 are necessary for activation. Yet the molecular activation mechanism and its cooperative nature are poorly understood, especially due to the lack of experimental phosphorylated MEK1 structures. We performed molecular dynamics simulations to investigate the structural and dynamical consequences of single and double phosphorylation in MEK1. We find that successive phosphorylation progressively unwinds the helix containing the phosphorylation sites, thereby rotating the phosphate groups to directly interact with the catalytic site. Consequently, the solvent accessible surface area of the catalytic residues increase with phosphorylation. Yet, only in the double-phosphorylated state do all four critical catalytic residues become solvent exposed. By calculating the conformational entropy, we find that only in the double-phosphorylated state do all four catalytic residues have mutual information with each other, suggesting that phosphorylation also induces correlated motion at the active site. To validate our approach, we show that our simulations predict the alignment of the R-spine motif in the double-phosphorylated state, in agreement with the other kinases for which this alignment has been experimentally observed. These results show that phosphorylation can, via a partial unfolding mechanism, increase the solvent exposure of and dynamical coupling within the active site, both of which are critical for enzymatic activity.

biophysics↗

bioRxiv2025

CP12 controls ribulose 1,5 bisphosphate recycling and carbon acquisition in Chlamydomonas reinhardtii

The small chloroplastic protein CP12 has multiple functions, including the regulation of enzymes in the Calvin-Benson-Bassham cycle. Here, we investigated its role in the acclimation of Chlamydomonas reinhardtii to varying CO2 availability. This alga has a CO2 concentrating mechanism that increases the supply of CO2 to ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) and involves hallmarks such as HCO3- transporters and carbonic anhydrases as well as the condensation of RuBisCO within the pyrenoid via its interaction with a scaffold protein named Essential Pyrenoid Component 1 (EPYC1). We showed that compared to the wild type, at high CO2, C. reinhardtii CP12 deletion mutants, or partially complemented mutants, have less phosphoribulokinase and ribulose-1,5-bisphosphate (RuBP) indicating that the regeneration of RuBP is regulated by CP12. In the absence of CP12, the expected relocation of RuBisCO towards the pyrenoid was not observed upon transition from high to very low CO2, contrary to WT cells. The CP12 deletion mutants are a unique example where the induction of CO2 concentrating mechanism hallmarks at very low CO2 was not accompanied by RuBisCO relocation. Altogether, these results suggest that CP12 contributes to the coordination between RuBP regeneration, RuBisCO location and CO2 acquisition. HighlightCP12 regulates phosphoribulokinase amount and its product RuBP. The CP12 deletion mutants are unique example where the RuBisCO location was not correlated with the induction of CO2 concentration mechanism. This reveals a novel link between Calvin-Benson-Bassham cycle regulation and CO2 concentrating mechanisms in Chlamydomonas reinhardtii. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=115 SRC="FIGDIR/small/659560v1_ufig1.gif" ALT="Figure 1"> View larger version (39K): org.highwire.dtl.DTLVardef@1cdadb2org.highwire.dtl.DTLVardef@46ae27org.highwire.dtl.DTLVardef@538295org.highwire.dtl.DTLVardef@a214c7_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2025

Amino acid sensing by the α-cell mitochondrial phosphoenolpyruvate cycle regulates intracellular Ca2+ levels without impacting glucagon secretion

Pancreatic islet -cells are increasingly recognized as amino acid sensors for the organism. Building on our prior work in {beta}-cells, we sought to determine whether the mitochondrial phosphoenolpyruvate (PEP) cycle is involved in -cell amino acid sensing. Three different methods were used to probe the PEP cycle, including pyruvate kinase activators (TEPP-46), and mice with -cell specific deletion of pyruvate kinase (PKM1/2-KO) or mitochondrial PEP carboxykinase (PCK2-KO). The mitochondrial fuels glutamine/leucine antagonized alanine/arginine-stimulated Ca2+ influx and glucagon secretion under hypoglycemic conditions. Both PKM1/2 and PCK2 were required for glutamine/leucine to close KATP channels and limit amino acid-stimulated membrane depolarization. The Ca2+ response to amino acids was suppressed by pyruvate kinase activation with TEPP-46, and enhanced by -cell deletion of pyruvate kinase or PCK2 - all without changing glucagon secretion. Finally, using diazoxide/KCl to probe the pathways downstream of membrane depolarization, we identified an essential role of the PEP cycle in homeostatically restoring intracellular Ca2+ levels. In sum, the -cell mitochondrial PEP cycle senses glutamine/leucine and inhibits KATP channels similarly to {beta}-cells, while restricting amino acid-stimulated membrane depolarization and Ca2+ influx. However, defying expectations, none of the amino acids tested, including alanine/arginine, regulate glucagon secretion by modulating membrane depolarization or intracellular Ca2+. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=158 SRC="FIGDIR/small/656009v2_ufig1.gif" ALT="Figure 1"> View larger version (57K): org.highwire.dtl.DTLVardef@18a29f0org.highwire.dtl.DTLVardef@1c77041org.highwire.dtl.DTLVardef@9adc1dorg.highwire.dtl.DTLVardef@e91407_HPS_FORMAT_FIGEXP M_FIG Graphical abstract-cells as amino acids sensors. Arginine, alanine, and glutamine potentiate glucagon secretion, while leucine has a suppressive effect (left). Independently of glucagon secretion, glutamine and leucine suppress alanine and arginine-stimulated Ca2+ influx via the phosphoenolpyruvate (PEP) cycle, which closes KATP channels and suppresses Vm depolarization (right). C_FIG HighlightsO_LIOur studies identify a role for the -cell PEP cycle in sensing amino acids under hypoglycemic conditions. C_LIO_LIPyruvate kinase and PCK2 are required for glutamine/leucine to close -cell KATP channel and limit membrane depolarization and Ca2+ influx. C_LIO_LIGlutamine/leucine oppose alanine/arginine-stimulated Ca2+ influx and glucagon secretion. C_LIO_LIAll of the amino acids tested regulate glucagon secretion, but none do so by modulating membrane depolarization or intracellular Ca2+ levels. C_LI

cell biology↗

bioRxiv2025

The GSA Family in 2025: A Broadened Sharing Platform for Multi-Omics and Multimodal Data

The Genome Sequence Archive Family (GSA family) provides a suite of database resources for archiving, retrieving, and sharing multi-omics data for the global academic and industrial communities. It currently comprises four distinct database members: the Genome Sequence Archive (GSA, https://ngdc.cncb.ac.cn/gsa/), the Genome Sequence Archive for Human (GSA-Human, https://ngdc.cncb.ac.cn/gsa-human/), the open Archive for Miscellaneous Data (OMIX, https://ngdc.cncb.ac.cn/omix/), and the Open Biomedical Imaging Archive (OBIA, https://ngdc.cncb.ac.cn/obia). Compared to the 2021 version, the GSA family has significantly expanded by introducing a new database member, the OBIA, and through comprehensive upgrades to the existing ones. Notable enhancements to the existing members include broadening the range of accepted data types, enhancing the quality control systems, fine-tuning the data retrieval system, and refining the data-sharing management mechanisms.

genomics↗

bioRxiv2024

CRISP: Correlation-Refined Image Segmentation Process

Calcium imaging enables real-time recording of cellular activity across various biological contexts. To assess the activity of individual cells, scientists typically manually outline the cells based on visual inspection. This manual cell masking introduces potential user error. To ameliorate this error, we developed the Correlation-Refined Image Segmentation Process (CRISP), a two-part automated algorithm designed to both enhance the accuracy of user-drawn cell masks and to automatically identify cell masks. We developed and tested CRISP on calcium images of densely packed {beta}-cells within the islet of Langerhans. Because these {beta}-cells are densely packed within the islet, traditional clustering-based image segmentation methods struggle to identify individual cell outlines. Using {beta}-cells isolated from two different mouse phenotypes and imaged on two different confocal microscopes, we show that CRISP is generalizable and accurate. To test the benefit of using CRISP in functional biological analyses, we show that CRISP improves accuracy of functional network analysis and utilize CRISP to characterize the distribution of {beta}-cell size.

bioengineering↗

bioRxiv2024

Glucokinase activity controls subpopulations of lower case Greek beta-cells that alternately lead islet Ca2+ oscillations

Oscillations in insulin secretion, driven by islet Ca2+ waves, are crucial for glycemic control. Prior studies, performed with single-plane imaging, suggest that subpopulations of electrically coupled {beta}-cells have privileged roles in leading and coordinating the propagation of Ca2+ waves. Here, we used 3D light- sheet imaging to analyze the location and Ca2+ activity of single {beta}-cells within the entire islet at >2 Hz. In contrast with single-plane studies, 3D network analysis indicates that the most highly synchronized {beta}-cells are located at the islet center, and remain regionally but not cellularly stable between oscillations. This subpopulation, which includes hub cells, is insensitive to changes in fuel metabolism induced by glucokinase and pyruvate kinase activation. {beta}-cells that initiate the Ca2+ wave ( leaders) are located at the islet periphery, and strikingly, change their identity over time via rotations in the wave axis. Glucokinase activation, which increased oscillation period, reinforced leader cells and stabilized the wave axis. Pyruvate kinase activation, despite increasing oscillation frequency, had no effect on leader cells, indicating the wave origin is patterned by fuel input. These findings emphasize the stochastic nature of the {beta}-cell subpopulations that control Ca2+ oscillations and identify a role for glucokinase in spatially patterning leader {beta}-cells. Highlights* Studies of islet Ca2+ oscillations by 3D light-sheet imaging provide a more complete picture of {beta}- cell subpopulations than prior 2D studies. * Highly synchronized {beta}-cells (including hub cells) are a regionally-stable subpopulation located at the islet center that is insensitive to metabolic perturbation. * Glucokinase activation patterns the Ca2+ wave axis, which originates from stochastic {beta}-cell subpopulations on the islet periphery that change between oscillations. * The stochasticity of leader {beta}-cells, and the stability of hubs, is geographically consistent with the peripheral location of /{delta}-cells in mouse islets.

biophysics↗

bioRxiv2023

Multiple transcription factors mediate acclimation of Chlamydomonas to light stress

Light as a substrate for photosynthesis may be a boon or a bane. To thrive, photosynthetic organisms must constantly respond to changing light and CO2 conditions by balancing energy harvest and consumption in a highly dynamic way. Two major safeguard measures of photoacclimation, that is photoprotection and carbon concentrating mechanism, underlie tight transcriptional control, leading to expression changes under high light and limited CO2 with different dynamics for both systems. Here, by using a consensus gene regulatory network inferred by employing a compendium of 1,869 RNA-seq datasets, we identified and validated in vivo eight candidate transcription factors (TFs) that contribute to photoacclimation in Chlamydomonas reinhardtii. Target gene analyses indicate that the TFs act individually in associated pathways but also influence each other in expression, and function as network parts with partial redundancy with respect to photoprotection. The analyses unveil that stress responses in Chlamydomonas are mediated by a complex, interconnected network of TFs rather than a hierarchical system where multiple regulators can influence each other and target gene expression and thereby mitigate the effects of loss.

plant biology↗

bioRxiv2023

RCoV19: A One-stop Hub for SARS-CoV-2 Genome Data Integration, Variants Monitoring, and Risk Pre-warning

The Resource for Coronavirus 2019 (RCoV19, https://ngdc.cncb.ac.cn/ncov/) is an open-access information resource dedicated to providing valuable data on the genomes, mutations, and variants of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In this updated implementation of RCoV19, we have made significant improvements and advancements over the previous version. Firstly, we have implemented a highly refined genome data curation model. This model now features an automated integration pipeline and optimized curation rules, enabling efficient daily updates of data in RCoV19. Secondly, we have developed a global and regional lineage evolution monitoring platform, alongside an outbreak risk pre-warning system. These additions provide a comprehensive understanding of SARS-CoV-2 evolution and transmission patterns, enabling better preparedness and response strategies. Thirdly, we have developed a powerful interactive mutation spectrum comparison module. This module allows users to compare and analyze mutation patterns, assisting in the detection of potential new lineages. Furthermore, we have incorporated a comprehensive knowledgebase on mutation effects. This knowledgebase serves as a valuable resource for retrieving information on the functional implications of specific mutations. In summary, RCoV19 serves as a vital scientific resource, providing access to valuable data, relevant information, and technical support in the global fight against COVID-19.

bioinformatics↗

bioRxiv2023

OBIA: An Open Biomedical Imaging Archive

With the development of artificial intelligence (AI) technologies, biomedical imaging data play an important role in scientific research and clinical application, but the available resources are limited. Here we present Open Biomedical Imaging Archive (OBIA), a repository for archiving biomedical imaging and related clinical data. OBIA adopts five data objects (Collection, Individual, Study, Series, and Image) for data organization, accepts the submission of biomedical images of multiple modalities, organs, and diseases. In order to protect personal privacy, OBIA has formulated a unified de-identification and quality control process. In addition, OBIA provides friendly and intuitive web interface for data submission, browsing and retrieval, as well as image retrieval. As of September 2023, OBIA has housed data for a total of 937 individuals, 4136 studies, 24,701 series, and 1,938,309 images covering 9 modalities and 30 anatomical sites. Collectively, OBIA provides a reliable platform for biomedical imaging data management and offers free open access to all publicly available data to support research activities throughout the world. OBIA can be accessed at https://ngdc.cncb.ac.cn/obia.

bioinformatics↗

bioRxiv2023

Leucine suppresses glucagon secretion from pancreatic islets by directly modulating alpha-cell cAMP

ObjectivePancreatic islets are nutrient sensors that regulate organismal blood glucose homeostasis. Glucagon release from the pancreatic -cell is important under fasted, fed, and hypoglycemic conditions, yet metabolic regulation of -cells remains poorly understood. Here, we identified a previously unexplored role for physiological levels of leucine, which is classically regarded as a {beta}-cell fuel, in the intrinsic regulation of -cell glucagon release. MethodsGcgCreERT:CAMPER and GcgCreERT:GCaMP6s mice were generated to perform dynamic, high-throughput functional measurements of -cell cAMP and Ca2+ within the intact islet. Islet perifusion assays were used for simultaneous, time-resolved measurements of glucagon and insulin release from mouse and human islets. The effects of leucine were compared with glucose and the mitochondrial fuels 2-aminobicyclo(2,2,1)heptane-2-carboxylic acid (BCH, non-metabolized leucine analog that activates glutamate dehydrogenase), -ketoisocaproate (KIC, leucine metabolite), and methyl-succinate (complex II fuel). CYN154806 (Sstr2 antagonist), diazoxide (KATP activator, which prevents Ca2+-dependent exocytosis from , {beta}, and {delta}-cells), and dispersed -cells were used to inhibit islet paracrine signaling and identify -cell intrinsic effects. ResultsMimicking the effect of glucose, leucine strongly suppressed amino acid-stimulated glucagon secretion. Mechanistically, leucine dose-dependently reduced -cell cAMP at physiological concentrations, with an IC50 of 57, 440, and 1162 M at 2, 6, and 10 mM glucose, without affecting -cell Ca2+. Leucine also reduced -cell cAMP in islets treated with Sstr2 antagonist or diazoxide, as well as dispersed -cells, indicating an -cell intrinsic effect. The effect of leucine was matched by KIC and the glutamate dehydrogenase activator BCH, but not methyl-succinate, indicating a dependence on mitochondrial anaplerosis. Glucose, which stimulates anaplerosis via pyruvate carboxylase, had the same suppressive effect on -cell cAMP but with lower potency. Similarly to mouse islets, leucine suppressed glucagon secretion from human islets under hypoglycemic conditions. ConclusionsThese findings highlight an important role for physiological levels of leucine in the metabolic regulation of -cell cAMP and glucagon secretion. Leucine functions primarily through an -cell intrinsic effect that is dependent on glutamate dehydrogenase, in addition to the well-established -cell regulation by {beta}/{delta}-cell paracrine signaling. Our results suggest that mitochondrial anaplerosis-cataplerosis facilitates the glucagonostatic effect of both leucine and glucose, which cooperatively suppress -cell tone by reducing cAMP. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=173 SRC="FIGDIR/small/551113v2_ufig1.gif" ALT="Figure 1"> View larger version (44K): org.highwire.dtl.DTLVardef@1af2865org.highwire.dtl.DTLVardef@8508fborg.highwire.dtl.DTLVardef@10c009org.highwire.dtl.DTLVardef@1afb6e9_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LILeucine inhibits glucagon secretion from mouse and human islets C_LIO_LILeucine suppresses -cell cAMP via both direct and paracrine effects C_LIO_LIAnaplerosis via glutamate dehydrogenase is sufficient to suppress -cell cAMP C_LIO_LILeucine suppresses -cell cAMP and glucagon secretion more potently than glucose C_LI

molecular biology↗

bioRxiv2023

Fetally-encoded GDF15 and maternal GDF15 sensitivity are major determinants of nausea and vomiting in human pregnancy

Human pregnancy is frequently accompanied by nausea and vomiting that may become severe and life-threatening, as in hyperemesis gravidarum (HG), the cause of which is unknown. Growth Differentiation Factor-15 (GDF15), a hormone known to act on the hindbrain to cause emesis, is highly expressed in the placenta and its levels in maternal blood rise rapidly in pregnancy. Variants in the maternal GDF15 gene are associated with HG. Here we report that fetal production of GDF15, and maternal sensitivity to it, both contribute substantially to the risk of HG. We found that the great majority of GDF15 in maternal circulation is derived from the feto-placental unit and that higher GDF15 levels in maternal blood are associated with vomiting and are further elevated in patients with HG. Conversely, we found that lower levels of GDF15 in the non-pregnant state predispose women to HG. A rare C211G variant in GDF15 which strongly predisposes mothers to HG, particularly when the fetus is wild-type, was found to markedly impair cellular secretion of GDF15 and associate with low circulating levels of GDF15 in the non-pregnant state. Consistent with this, two common GDF15 haplotypes which predispose to HG were associated with lower circulating levels outside pregnancy. The administration of a long-acting form of GDF15 to wild-type mice markedly reduced subsequent responses to an acute dose, establishing that desensitisation is a feature of this system. GDF15 levels are known to be highly and chronically elevated in patients with beta thalassemia. In women with this disorder, reports of symptoms of nausea or vomiting in pregnancy were strikingly diminished. Our findings support a causal role for fetal derived GDF15 in the nausea and vomiting of human pregnancy, with maternal sensitivity, at least partly determined by pre-pregnancy exposure to GDF15, being a major influence on its severity. They also suggest mechanism-based approaches to the treatment and prevention of HG.

genetics↗

bioRxiv2022

DepLink: an R Shiny app to systematically link genetic and pharmacologic dependencies of cancer

Large-scale genetic and pharmacologic dependency maps are generated to reveal genetic vulnerabilities and drug sensitivities of cancer. However, user-friendly software is needed to systematically link such maps. Here we present DepLink, an R Shiny server to identify genetic and pharmacologic perturbations that induce similar effects on cell viability or molecular changes. DepLink integrates heterogeneous datasets of genome-wide CRISPR loss-of-function screens, high-throughput pharmacologic screens, and perturbation expression signatures. The datasets are systematically connected by four complementary modules tailored for different query scenarios. In summary, DepLink enables easy navigation, visualization, and linkage of rapidly evolving cancer dependency maps.

bioinformatics↗

bioRxiv2022

Photosystem II monomeric antenna CP26 has a key role in Non-Photochemical Quenching in Chlamydomonas reinhardtii

O_LIThermal dissipation of the excitation energy harvested in excess, named non-photochemical quenching (NPQ), is one of the main photoprotective mechanisms evolved in oxygenic photosynthetic organisms. Here, the specific function in photoprotection and light harvesting of the monomeric Photosystem II antenna CP26, was investigated in Chlamydomonas, model organism for green algae C_LIO_LICRISPR/Cas9 genome editing and complementation strategies were applied to generate new cp26 knock-out mutants (named k6#) that differently from previous findings, did not negatively affected CP29 accumulation, allowing to compare mutants specifically deprived of CP26, CP29 or both C_LIO_LIThe absence of CP26 partially affected Photosystem II activity causing a reduced growth at low or medium light but not at high irradiances. However, the main phenotype observed in k6# mutants was a more than 70% reduction of NPQ compared to wild-type. This NPQ phenotype could be fully rescued by genetic complementation demonstrating that [~]50% of CP26 content compared to wild-type was sufficient to restore the NPQ capacity. C_LIO_LIOur findings demonstrate a pivotal role for CP26 in NPQ induction while CP29 has a crucial function for Photosystem II activity. The genetic engineering of these two proteins could be a promising strategy to regulate photosynthetic efficiency of microalgae under different light regimes. C_LI

plant biology↗

bioRxiv2021

Predicting localized affinity of RNA binding proteins to transcripts with convolutional neural networks

RNA binding proteins (RBPs) are important regulators of transcriptional and post-transcriptional processes. Computational prediction of localized RBP binding affinity with transcripts is important for interpretation of genetic variation, especially variants outside of protein coding region. Here we describe POLARIS (Prediction Of Localized Affinity for RBPs In Sequence), a new deep-learning method for achieving fast, site-specific binding affinity predictions of RNA-binding proteins (RBPs) to the transcribed genome. POLARIS has two modules: 1. a convolutional neural network (CNN) to predict overall RBP binding within a region based on transcript sequence content and expression level; 2. a Gradient-weighted Class Activation Mapping (GradCAM) implementation for efficient signal backpropagation to individual sequence positions. We trained the model using enhanced crosslinking and immunoprecipitation (eCLIP) data from ENCODE. POLARIS has good performance with a median AUC ~ 0.96 for 160 RBPs across three different cell lines, substantially higher than selected popular published methods trained and tested on the same data sets. When tested on data from a different cell line with the same RBPs, the overall performance is maintained, supporting the ability of cell-type specific affinity prediction. Finally, the GradCAM module allows the model to identify the informative sites in a region that drive prediction. The localized prediction facilitates interpretation of the results and provides basis for inference of functional impact of noncoding variants.

bioinformatics↗

bioRxiv2020

Ubiquitin ligase component LRS1 and transcription factor CrHy5 act as a light switch for photoprotection in Chlamydomonas

Survival under excess light conditions requires the light-induced accumulation of protein LHCSR3 and other photoprotection factors, to enable efficient energy-dependent quenching in the green microalga Chlamydomonas reinhardtii. Here, we demonstrate that the high light-tolerant phenotype of mutant hit1 is caused by a de-repression of promoters belonging to photoprotection genes, which in turn results from an inactivation of the E3 ubiquitin ligase substrate adaptor LRS1. Transcriptome analyses of hit1 revealed massive alterations of gene expression modulation as a consequence of perturbed LRS1 function, indicating its role as a crown regulator. In conjunction with random forest-based network modeling, these transcriptome analyses predicted that LRS1 controls photoprotection gene expression via an algal HY5 homolog as its prime transcription factor target. CrHY5 binds to T-box elements present in the promoters of these genes and its inactivation in the hit1 mutant via CRISPR-Cas9 genome editing, confirmed the regulatory connection between LRS1 and CrHY5, predicted by the network analysis.

plant biology↗