Biology subjects

Wu, Y.

Publications and source records attributed to Wu, Y..

At least 847 records · Page 47Linked to original sources

bioRxiv2021

Locally restricted glucose availability in the embryonic hypocotyl determines seed germination under ABA treatment

O_LIAbiotic stresses directly affect seed germination, plant growth, and reproduction. Seed germination is a complex and energy-demanding process, involving diverse physical, metabolic and cellular events, and is controlled by intrinsic and environmental cues. Abiotic stresses involving abscisic acid (ABA) inhibit seed germination by suppressing physiological processes essential for completion of germination. It remains unclear whether the component tissues of an embryo respond to stress, and are suppressed differentially. C_LIO_LIHere we used a genetically engineered FRET sensor to show that ABA significantly affected the spatiotemporal distribution of glucose (Glc) in lower hypocotyl region. Transcriptome analysis and 14C-Glc uptake assay suggested that Glc limitation in the embryonic hypocotyl was largely due to suppressed sugar partitioning along with enhanced sugar metabolism. The loss-of-function mutants of ABA-induced sucrose-phosphate synthase (SPS) genes accumulated more Glc, leading to ABA insensitivity during germination. In addition, we identified molecular signatures that Glc antagonizes ABA by globally counteracting the ABA influence on gene expression, including expansin (EXP) family genes that are inhibited by ABA. C_LIO_LIThis study presents a new perspective on the interaction between ABA and Glc in response to external stimuli, which restricts Glc availability and thereby controls the transition from seed to seedling. C_LI

plant biology↗

bioRxiv2021

Screening of HLA-A restricted T cell epitopes of SARS-CoV-2 and induction of CD8+ T cell responses in HLA-A transgenic mice

While SARS-CoV-2-specific T cells have been characterized to play essential roles in host immune protection in COVID-19 patients, few researches focus on the functional validation of T cell epitopes and development of vaccines inducing specific T cell responses. In this study, 120 CD8+ T cell epitopes from E, M, N, S and RdRp proteins were validated. Among them, 110 epitopes have not been reported previously; 110, 15, 6, 14 and 12 epitopes were highly homologous with SARS-CoV, OC43, NL63, HKU1, and 229E, respectively; 4 epitopes from S protein displayed one amino acid distinct from the current variants of SARS-CoV-2. Thirty-one epitopes restricted by HLA-A2 molecule were used to generate peptide cocktail vaccines in combination with Poly(I:C), R848 or polylactic-co-glycolic acid nanoparticles, which elicited robust specific CD8+ T cell responses in wild-type and HLA-A2/DR1 transgenic mice. Seven of the 31 epitopes were found to be cross-presented by HLA-A2 and H-2K/Db molecules. Unlike previous researches, this study established a modified cell co-culture system of DC-peptide-PBL using healthy donors PBMCs to validate the CD8+ T cell epitope on-silicon predicted; provided a library of CD8+ T cell epitopes restricted by a series of high-frequency HLA-A allotypes which covering broad Asian populations; identified the HLA-A cross-restrictions of these CD8+ T cell epitopes using competitive binding experiments with HMy2.CIR cell lines expressing indicated HLA-A molecules; and initially confirmed the in vivo feasibility of 9 or 10-mer peptide cocktail vaccines of SARS-CoV2. These data will facilitate the development of vaccines inducing antiviral CD8+ T cell responses.

immunology↗

bioRxiv2021

The effect of histone deacetylase inhibitor Trichostatin A on IL-17A-induced transformation of MRC5 into myofibroblasts and its mechanism

ObjectiveTo elucidate potential IL-17A- and TSA-mediated regulation of fibroblasts transformation. MethodsMTT assay, HDAC1 activity assay, cell immunofluorescence and Western blot were employed to detect the expression of related indicators. ResultsMRC5 cells expressed only a small amount of Vimentin. IL-17A treatment upregulated MRC5 cell proliferation, in a concentration-dependent manner. TSA treatment, however, suppressed MRC5 cell proliferation. IL-17A treatment also upregulated HDAC1 activity in MRC5 cells, in a concentration-dependent manner. Using immunofluorescence, we demonstrated that IL-17A-treated MRC5 cells had markedly elevated Vimentin, Collagen-I and a-SMA levels, compared to controls. However, a combined treatment of IL-17A and TSA resulted in markedly reduced levels of the Vimentin, Collagen-I and a-SMA, compared to IL-17A alone, yet the amount was higher than controls. Using western blot analysis, we also revealed that the IL-17A-treated MRC5 cells had markedly elevated levels of Vimentin, a-SMA, HDAC1, p-Smad2, and p-Smad3, and markedly reduced level of Smad7, compared to controls. In TSA intervention group, the expression effect of the above protein was opposite. Moreover, no discernible difference was observed in the levels of Smad2 and Smad3 among the treated and un-treated groups. ConclusionIL-17A stimulates proliferation of MRC5 cells and increases HDAC1 activity and protein expression. It also transforms MRC5 cells into myofibroblasts via activation of the TGF -{beta}1/ Smads signaling network. TSA, on the other hand, strongly suppresses TGF -{beta}1/ Smads pathway-mediated fibrosis by ceasing HDAC1 activity and protein expression.

cell biology↗

bioRxiv2021

Control of osteocyte dendrite formation by Sp7 and its target gene osteocrin

Osteocytes use an elaborate network of dendritic connections to control bone remodeling. Some osteoblasts embed within mineralized bone matrix, change shape, and become osteocytes. The molecular circuitry that drives dendrite formation during "osteocytogenesis" is poorly understood. Here we show that deletion of Sp7, a gene linked to rare and common skeletal disease, in mature osteoblasts and osteocytes causes severe defects in osteocyte dendrites. Unbiased profiling of Sp7 target genes and binding sites reveals unexpected repurposing of this transcription factor to drive dendrite formation. Osteocrin is a Sp7 target gene that promotes osteocyte dendrite formation and rescues phenotypic and molecular defects in Sp7-deficient mice. Single-cell RNA-sequencing demonstrates overt defects in osteocyte maturation in vivo in the absence of Sp7. Sp7-dependent gene networks enriched in developing osteocytes are associated with rare and common human skeletal traits. Moreover, humans homozygous for the osteogenesis imperfecta-causing SP7R316C mutation show dramatic defects in osteocyte morphology. Genes that mark osteocytes in vivo and that are regulated by Sp7 in vitro are highly enriched in neurons, highlighting shared features between osteocytic and neuronal connectivity. Taken together, these findings reveal a crucial role for Sp7 and its target gene Osteocrin in osteocytogenesis, demonstrating that pathways that control osteocyte development influence human bone diseases.

molecular biology↗

bioRxiv2021

TMPRSS2 inhibitor discovery facilitated through an in silico and biochemical screening platform

The COVID-19 pandemic has highlighted the need for new antiviral targets, as many of the currently approved drugs have proven ineffective against mitigating SARS-CoV-2 infections. The host transmembrane serine protease TMPRSS2 is a highly promising antiviral target, as it plays a direct role in priming the spike protein before viral entry occurs. Further, unlike other targets such as ACE2, TMPRSS2 has no known biological role. Here we utilize virtual screening to curate large libraries into a focused collection of potential inhibitors. Optimization of a recombinant expression and purification protocol for the TMPRSS2 peptidase domain facilitates subsequent biochemical screening and characterization of selected compounds from the curated collection in a kinetic assay. In doing so, we demonstrate that serine protease inhibitors camostat, nafamostat, and gabexate inhibit through a covalent mechanism. We further identify new non-covalent compounds as TMPRSS2 protease inhibitors, demonstrating the utility of a combined virtual and experimental screening campaign in rapid drug discovery efforts.

biochemistry↗

bioRxiv2021

Distinct Hypoxia-induced Translational Profiles of Embryonic and Adult-derived Macrophages

Tissue homeostasis and repair are orchestrated by resident and newly recruited macrophages that alter their gene expression program in response to changes in tissue microenvironment. Embryonic macrophages, such as fetal liver derived macrophages (FLDM) seed the organs, including heart and lung during embryonic development and persist throughout the adult lifetime, while bone marrow-derived macrophages (BMDM) are recruited following an acute perturbation. Transcriptome analyses of FLDM and BMDM identified differences between them at the level of RNA expression, which correlates imperfectly with protein levels. Post-transcriptional regulation by microRNAs (miRNAs) and RNA-binding proteins determines mRNA stability and translation rate and may override transcriptional cues in response to environmental changes, such as hypoxia. To identify distinct features of FLDM and BMDM response to hypoxia at the level of translation, we employed translating ribosome affinity purification (TRAP) to isolate polysomal RNA. RNA-seq profiling of translated RNA identified distinct hypoxia-induced translational signature of BMDM (Ly6e, vimentin and glycolysis-associated enzymes Pgk1, Tpi1, Aldoa, Ldha) and FLDM (chemokines Ccl7 and Ccl2). By translational profiling of BMDM and FLDM with deletion of the RNA-binding protein HuR, we identified transcripts that were dependent on HuR. These findings highlight the importance of HuR and identify its distinct targets for post-transcriptional regulation of gene expression in embryonic vs. adult-derived macrophages.

cell biology↗

bioRxiv2021

RENET2: High-Performance Full-text Gene-Disease Relation Extraction with Iterative Training Data Expansion

BackgroundRelation extraction is a fundamental task for extracting gene-disease associations from biomedical text. Existing tools have limited capacity, as they can extract gene-disease associations only from single sentences or abstract texts. ResultsIn this work, we propose RENET2, a deep learning-based relation extraction method, which implements section filtering and ambiguous relations modeling to extract gene-disease associations from full-text articles. We designed a novel iterative training data expansion strategy to build an annotated full-text dataset to resolve the scarcity of labels on full-text articles. In our experiments, RENET2 achieved an F1-score of 72.13% for extracting gene-disease associations from an annotated full-text dataset, which was 27.22%, 30.30% and 29.24% higher than the best existing tools BeFree, DTMiner and BioBERT, respectively. We applied RENET2 to (1) ~1.89M full-text articles from PMC and found ~3.72M gene-disease associations; and (2) the LitCovid articles set and ranked the top 15 proteins associated with COVID-19, supported by recent articles. ConclusionRENET2 is an efficient and accurate method for full-text gene-disease association extraction. The source-code, manually curated abstract/full-text training data, and results of RENET2 are available at https://github.com/sujunhao/RENET2.

bioinformatics↗

bioRxiv2021

Revealing the transcription factor regulatory context of human specific cortical development using single-cell multi-omics

Human behaviors are at least partially driven by genomic regions that influence human-specific neurodevelopment. This includes genomic regions undergoing human specific sequence acceleration (Human Accelerated Regions or HARs) and regions showing human-specific enhancer activity (Human Gained Enhancers or HGEs) not present in other primates. However, prior studies on HAR/HGE activities involved mixtures of brain cell types and focused only on putative downstream target genes. Here, we directly measured cell type specific HAR/HGE activity in the developing fetal human brain using two independent single-cell chromatin accessibility datasets with matching single-cell gene expression data. Transcription factor (TF) motif analyses identified upstream TFs binding to HARs/HGEs and identified LHX2, a key regulator of forebrain development, as an active HGE regulator in neuronal progenitors. We integrated our TF motif analyses with published chromatin interaction maps to build detailed regulatory networks where TFs are linked to downstream genes via HARs/HGEs. Through these networks, we identified a potential regulatory role for NFIC in human neuronal progenitor networks via modulating the Notch signaling and cell adhesion pathways. Therefore, by using a single cell multi-omics approach, we were able to capture both the upstream and downstream regulatory context of HARs/HGEs, which may provide a more comprehensive picture of the roles HARs/HGEs play amongst diverse fetal cell types of the developing human brain.

genomics↗

bioRxiv2021

Case study of a rhizosphere microbiome assay on a bamboo rhizome with excessive shoots

Young Moso bamboo shoots are a very popular seasonal food. Bamboo is an important source of income for farmers and the value for cultivation has recently been estimated to $30,000 per hectare. A rare and valuable phenomenon has recently appeared where dozens of adjacent buds within a single Moso bamboo rhizome have grown into shoots. Due to its rarity, this phenomenon, which is of practical importance for the production of edible shoots, has not been scientifically studied. We report the occurrence of a rhizome with 18 shoots, of which the microbiome were analyzed, using rhizomes having one or no shoots as controls. The community of prokaryotes, but not fungi, correlated with the shoot numbers. Burkholderia was the most abundant genus, which negatively correlated with rhizome shoot number, while Clostridia and Ktedonobacteria positively correlated with many shoots. Two Burkholderia strains were isolated and their plant-growth promoting activity was tested. The isolated Burkholderia strains attenuated the growth of bamboo seedlings. Analysis of collected events of enhanced shoot production in China showed no evidence that enhanced shoot development was heritable. Overall, our data provides a firsthand study on excessive shoot development of bamboo.

plant biology↗

bioRxiv2021

Paratransgenic manipulation of tsetse miR275 alters the physiological homeostasis of the flys midgut environment

Tsetse flies are vectors of parasitic African trypanosomes (Trypanosoma spp.). Current disease control methods include fly-repelling pesticides, trapping flies, and chemotherapeutic treatment of infected people. Inhibiting tsetses ability to transmit trypanosomes by strengthening the flys natural barriers can serve as an alternative approach to reduce disease. The peritrophic matrix (PM) is a chitinous and proteinaceous barrier that lines tsetses midgut. It protects the epithelial cells from the gut lumen content such as food and invading trypanosomes, which have to overcome this physical barrier to establish an infection. Bloodstream form trypanosomes shed variant surface glycoproteins (VSG) into tsetses gut lumen early during the infection establishment. The VSG molecules are internalized by the flys PM-producing cardia, which results in a reduction in tsetse miR275 expression and a sequential molecular cascade that compromises the PM integrity. In the present study, we investigated the role(s) of miR275 in tsetses midgut physiology and trypanosome infection processes by developing a paratransgenic expression system. We used tsetses facultative bacterial endosymbiont Sodalis glossinidius to express tandem antagomir-275 repeats (or miR275 sponge) that constitutively reduce miR275 transcript abundance. This paratransgenic system successfully knocked down miR275 levels in the flys midgut, which consequently obstructed blood digestion and modulated infection outcomes with an entomopathogenic bacteria and with trypanosomes. RNA sequencing of cardia and midgut tissues from the paratransgenic tsetse confirmed that miR275 regulates processes related to the expression of PM-associated proteins and digestive enzymes as well as genes that encode abundant secretory proteins. Our study demonstrates that paratransgenesis can be employed to study microRNA-regulated pathways in arthropods housing symbiotic bacteria. Author SummaryTsetse flies transmit African trypanosomes, which are the parasites that cause sleeping sickness in human in sub-Saharan Africa. When tsetse ingests a blood meal containing trypanosomes, the expression level of a microRNA (miR275) decreases in the flys gut. This process results in a series of events that interrupt the physiological homeostasis of the gut environment. To further understand the function of miR275 in tsetse fly, we genetically modified a tsetses native bacterial symbiont, reintroduced the genetically modified bacterium back into the fly, and successfully knocked down the miR275 expression in tsetses midgut. These paratransgenic flies (which house genetically modified bacteria) presented impaired digestive processes and were highly susceptible to infection with trypanosomes. Lastly, we discovered that miR275 regulates tsetse secretory pathways. Our novel paratransgenic expression system can be applied to study the function of other microRNAs and how they regulate disease transmission in tsetse and other insect systems.

microbiology↗

bioRxiv2021

DeepLncLoc: a deep learning framework for long non-coding RNA subcellular localization prediction based on subsequence embedding

MotivationLong non-coding RNAs (IncRNAs) are a class of RNA molecules with more than 200 nucleotides. A growing amount of evidence reveals that subcellular localization of lncRNAs can provide valuable insights into their biological functions. Existing computational methods for predicting lncRNA subcellular localization use k-mer features to encode lncRNA sequences. However, the sequence order information is lost by using only k-mer features. ResultsWe proposed a deep learning framework, DeepLncLoc, to predict lncRNA subcellular localization. In DeepLncLoc, we introduced a new subsequence embedding method that keeps the order information of lncRNA sequences. The subsequence embedding method first divides a sequence into some consecutive subsequences, and then extracts the patterns of each subsequence, last combines these patterns to obtain a complete representation of the lncRNA sequence. After that, a text convolutional neural network is employed to learn high-level features and perform the prediction task. Compared to traditional machine learning models with k-mer features and existing predictors, DeepLncLoc achieved better performance, which shows that DeepLncLoc could effectively predict lncRNA subcellular localization. Our study not only presented a novel computational model for predicting lncRNA subcellular localization but also provided a new subsequence embedding method which is expected to be applied in other sequence-based prediction tasks. AvailabilityThe DeepLncLoc web server, source code and datasets are freely available at http://bioinformatics.csu.edu.cn/DeepLncLoc/, and https://github.com/CSUBioGroup/DeepLncLoc. Contactlimin@mail.csu.edu.cn

bioinformatics↗

bioRxiv2021

Charting oncogenicity of genes and variants across lineages via multiplexed screens in teratomas

Deconstructing tissue-specific effects of genes and variants on proliferative advantage is critical to understanding cellular transformation and to systematic selection of cancer therapeutics. Dissecting these specificities at scale requires integrated methods for multiplexed genetic screens tracking fitness across time, across human cell types, and in a suitable cellular niche since functional differences also depend on physiological cues. Towards this, we present a novel approach, harnessing single-cell cancer driver screens in teratomas coupled with hit enrichment by serial teratoma reinjection, to simultaneously screen drivers across multiple lineages in vivo. Using this system, we analyzed population shifts and lineage-specific enrichment for 51 cancer associated genes and gene variants, profiling over 100,000 cells spanning over 20 lineages, across two rounds of serially injected teratomas. We confirmed that c-MYC alone or combined with myristoylated AKT1 potently drives proliferation in progenitor neural lineages, demonstrating signatures of malignancy. These drivers directed teratoma development to lineages representative of pediatric tumors such as medulloblastoma and rhabdomyosarcoma. Additionally, mutant MEK1S218D/S222D provides a proliferative advantage in mesenchymal lineages like fibroblasts. Our method provides a powerful new platform for multi-lineage longitudinal study of oncogenesis.

systems biology↗

bioRxiv2021

Recovery of high-qualitied Genomes from a deep-inland Salt Lake Using BASALT

Metagenomic binning enables the in-depth characterization of microorganisms. To improve the resolution and efficiency of metagenomic binning, BASALT (Binning Across a Series of AssembLies Toolkit), a novel binning toolkit was present in this study, which recovers, compares and optimizes metagenomic assembled genomes (MAGs) across a series of assemblies from short-read, long-read or hybrid strategies. BASALT incorporates self-designed algorithms which automates the separation of redundant bins, elongate and refine best bins and improve contiguity. Evaluation using mock communities revealed that BASALT auto-binning obtained up to 51% more number of MAGs with up to 10 times better MAG quality from microbial community at low (132 genomes) and medium (596 genomes) complexity, compared to other binners such as DASTool, VAMB and metaWRAP. Using BASALT, a case-study analysis of a Salt Lake sediment microbial community from northwest arid region of China was performed, resulting in 426 non-redundant MAGs, including 352 and 69 bacterial and archaeal MAGs which could not be assigned to any known species from GTDB (ANI < 95%), respectively. In addition, two Lokiarchaeotal MAGs that belong to superphylum Asgardarchaeota were observed from Salt Lake sediment samples. This is the first time that candidate species from phylum Lokiarchaeota was found in the arid and deep-inland environment, filling the current knowledge gap of earth microbiome. Overall, BASALT is proven to be a robust toolkit for metagenomic binning, and more importantly, expand the Tree of Life.

bioinformatics↗

bioRxiv2021

Emergence of a Hypervirulent Carbapenem-Resistant Klebsiella pneumoniae Co-harbouring a blaNDM-1-carrying Virulent Plasmid and a blaKPC-2-carrying Plasmid in an Egyptian Hospital

The emergence of carbapenem-resistant Klebsiella pneumoniae (CRKP) isolates in Egyptian hospitals has been reported. However, the genetic basis and the analysis of the plasmids associated with CR-hypervirulent-KP (CR-HvKP) in Egypt are not presented. Therefore, we attempt to decipher the plasmids sequences, which are responsible for transferring the determinants of carbapenem-resistance, particularly the blaNDM-1 and blaKPC-2. Out of 34 K. pneumoniae isolates collected from two tertiary hospitals in Egypt, 31 were CRKP. Whole-genome sequencing revealed that our isolates were related to 13 different sequence types (STs). The most prevalent ST was ST101, followed by ST383, and ST11. Among the CRKP isolates, one isolate named EBSI036 has been reassessed using Nanopore sequencing. Genetic environment analysis showed that EBSI036 carried 20 antibiotic resistance genes and was identified as CR-HvKP strain, it harboured four plasmids, namely; pEBSI036-1-NDM-VIR, pEBSI036-2-KPC, pEBSI036-3, and pEBSI036-4. The two carbapenemase genes, blaNDM-1 and blaKPC-2, were located on plasmids pEBSI036-1-NDM-VIR and pEBSI036-2-KPC, respectively. The IncFIB:IncHI1B hybrid plasmid pEBSI036-1-NDM-VIR also carried some virulence factors, including regulator of the mucoid phenotype (rmpA), the regulator of mucoid phenotype 2 (rmpA2), and aerobactin (iucABCD, iutA). Thus, we set out this study to analyse in-depth the genetic basis of pEBSI036-1-NDM-VIR and pEBSI036-2-KPC plasmids. We reported for the first time a high-risk clone ST11 KL47 serotype of CR-HvKP strain isolated from the blood of a 60-year-old hospitalised female patient from the ICU in a tertiary-care hospital in Egypt, which showed the cohabitation of a novel hybrid plasmid coharbouring the blaNDM-1 and virulence genes, besides a blaKPC-2-carrying plasmid. IMPORTANCECRKP had been registered in the critical priority tier by the World Health Organization and became a significant menace to public health. Therefore, we set out this study to analyse in-depth the genetic basis of pEBSI036-1-NDM-VIR and pEBSI036-2-KPC plasmids. Herein, we reported for the first time (to the best of our knowledge) a high-risk clone ST11 KL47 serotype of CR-HvKP strain isolated from the blood of a 60-year-old hospitalised female patient in a tertiary-care hospital from the ICU in Egypt, which showed the cohabitation of a novel hybrid plasmid co-harbouring the blaNDM-1 and virulence genes, besides a blaKPC-2-carrying plasmid. Herein, the high rate of CRKP might be due to the continuous usage of carbapenems as empirical therapy, besides the failure to implement an antibiotic stewardship program in Egyptian hospitals. Thus, this study serves to alert the contagious disease clinicians to the presence of hypervirulence in CRKP isolates in Egyptian hospitals.

microbiology↗

bioRxiv2021

A massive 7T fMRI dataset to bridge cognitive and computational neuroscience

Extensive sampling of neural activity during rich cognitive phenomena is critical for robust understanding of brain function. We present the Natural Scenes Dataset (NSD), in which high-resolution fMRI responses to tens of thousands of richly annotated natural scenes are measured while participants perform a continuous recognition task. To optimize data quality, we develop and apply novel estimation and denoising techniques. Simple visual inspections of the NSD data reveal clear representational transformations along the ventral visual pathway. Further exemplifying the inferential power of the dataset, we use NSD to build and train deep neural network models that predict brain activity more accurately than state-of-the-art models from computer vision. NSD also includes substantial resting-state and diffusion data, enabling network neuroscience perspectives to constrain and enhance models of perception and memory. Given its unprecedented scale, quality, and breadth, NSD opens new avenues of inquiry in cognitive and computational neuroscience.

neuroscience↗

bioRxiv2021

BREVIPEDICELLUS and ERECTA mediate expression of AtPRX17 in preventing Arabidopsis callus retardation and browning

Efficient in vitro callus generation is fundamental to tissue culture propagation, a process required for plant regeneration and transgenic breeding for desired phenotypes. Identifying genes and regulatory elements that prevent callus retardation and browning is essential to facilitate the development of vitro callus systems. Here we show that BREVIPEDICELLUS (BP) and ERECTA (ER) pathways in Arabidopsis callus are converged to prevent callus browning and positively regulate an isoperoxidase gene AtPRX17 expression in the rapid growth callus. Loss of functions in both BP and ER resulted in markedly increasing callus browning. Transgenic lines with pro35S::AtPRX17 in the bp-5 er105 double mutant background fully rescued this phenotypic abnormality. Using plant in vitro DNA-binding assays, we observed that BP protein bound directly to the upstream sequence of AtPRX17 to promote its transcription during callus growth. ER is a universally presenting factor required for cell proliferation and growth, we show that ER positively regulates expression of a transcription factor WRKY6, which also directly binds to an additional site of the AtPRX17 promoter for its high expression. Our data reveals an important molecular mechanism in regulating expression of peroxidase isozyme to reduce Arabidopsis callus browning. HighlightBREVIPEDICELLUS and ERECTA are involved in regulating Arabidopsis callus browning by controlling expression of AtPRX17.

plant biology↗

bioRxiv2021

A draft genome of Alliaria petiolata (garlic mustard) as a model system for invasion genetics

The emerging field of invasion genetics examines the genetic causes and consequences of biological invasions, but few study systems are available that integrate deep ecological knowledge with genomic tools. Here we report on the de novo assembly and annotation of a genome for the biennial herb Alliaria petiolata (M. Bieb.) Cavara & Grande (Brassicaceae), which is widespread in Eurasia and invasive across much of temperate North America. Our goal was to sequence and annotate a genome to complement resources available from hundreds of published ecological studies, a global field survey, and hundreds of genetic lines maintained in Germany and Canada. We sequenced a genotype (EFCC-3-20) collected from the native range near Venice, Italy and sequenced paired-end and mate pair libraries at ~70 x coverage. A de novo assembly resulted in a highly continuous draft genome (N50 = 121 Mb; L50 = 2) with 99.7 % of the 1.1 Gb genome mapping to scaffolds of at least 50 Kb in length. A total of 64,770 predicted genes in the annotated genome include 99 % of plant BUSCO genes and 98 % of transcriptome reads. Consistent with previous reports of (auto)hexaploidy in western Europe, we found that almost one third of BUSCO genes (390/1440) mapped to two or more scaffolds despite < 2 % genome-wide average heterozygosity. The continuity and gene space quality of our draft assembly will enable molecular and functional genomic studies of A. petiolata to address questions relevant to invasion genetics and conservation strategies.

genomics↗

bioRxiv2021

Spatially Interacting Phosphorylation Sites and Mutations in Cancer

Advances in mass-spectrometry have generated increasingly large-scale proteomics datasets containing tens of thousands of phosphorylation sites (phosphosites) that require prioritization. We develop a bioinformatics tool called HotPho and systematically discover 3D co-clustering of phosphosites and cancer mutations on protein structures. HotPho identifies 474 such hybrid clusters containing 1,255 co-clustering phosphosites, including RET p.S904/Y928, the conserved HRAS/KRAS p.Y96, and IDH1 p.Y139/IDH2 p.Y179 that are adjacent to recurrent mutations on protein structures not found by linear proximity approaches. Hybrid clusters, enriched in histone and kinase domains, frequently include expression-associated mutations experimentally shown as activating and conferring genetic dependency. Approximately 300 co-clustering phosphosites are verified in patient samples of 5 cancer types or previously implicated in cancer, including CTNNB1 p.S29/Y30, EGFR p.S720, MAPK1 p.S142, and PTPN12 p.S275. In summary, systematic 3D clustering analysis highlights nearly 3,000 likely functional mutations and over 1,000 cancer phosphosites for downstream investigation and evaluation of potential clinical relevance.

bioinformatics↗