Biology subjects

Yan, Y.

Publications and source records attributed to Yan, Y..

At least 145 records · Page 8Linked to original sources

bioRxiv2024

Carbohydrate-active enzyme annotation in microbiomes using dbCAN

CAZymes or carbohydrate-active enzymes are critically important for human gut health, lignocellulose degradation, global carbon recycling, soil health, and plant disease. We developed dbCAN as a web server in 2012 and actively maintain it for automated CAZyme annotation. Considering data privacy and scalability, we provide run_dbcan as a standalone software package since 2018 to allow users perform more secure and scalable CAZyme annotation on their local servers. Here, we offer a comprehensive computational protocol on automated CAZyme annotation of microbiome sequencing data, covering everything from short read pre-processing to data visualization of CAZyme and glycan substrate occurrence and abundance in multiple samples. Using a real-world metagenomic sequencing dataset, this protocol describes commands for dataset and software preparation, metagenome assembly, gene prediction, CAZyme prediction, CAZyme gene cluster (CGC) prediction, glycan substrate prediction, and data visualization. The expected results include publication-quality plots for the abundance of CAZymes, CGCs, and substrates from multiple CAZyme annotation routes (individual sample assembly, co-assembly, and assembly-free). For the individual sample assembly route, this protocol takes [~]33h on a Linux computer with 40 CPUs, while other routes will be faster. This protocol does not require programming experience from users, but it does assume a familiarity with the Linux command-line interface and the ability to run Python scripts in the terminal. The target audience includes the tens of thousands of microbiome researchers who routinely use our web server. This protocol will encourage them to perform more secure, rapid, and scalable CAZyme annotation on their local computer servers.

bioinformatics↗

bioRxiv2023

Integrated data models on Receptor-Like Kinases for novel domain discovery and functional inference in the plant kingdom

Receptor-like kinases (RLKs) are the largest signal transduction component in plants, determining how different plants adapt to their ecological environment, resulting in plant-specific ecological niches. Current research on RLKs has focused mainly on a small number of typical RLK members of a few model plants. There is an urgent need to study the composition, distribution, and evolution of RLKs at the holistic level to accelerate the understanding of how RLK assists in the ecological adaptation of different plants. In this study, we have collected 528 plant genomes and established an RLK data model, resulting in the discovery and characterization of 524,948 RLK members. Each member is subject to systematic topology classification and coherent gene ID assignment. Using this data model, we discovered two novel families (Xiao and Xiang) of RLKs. Evolutionary analysis of the RLK families indicates that RLCK-XVII and RLCK-XII-2 exist exclusively in dicots, suggesting that the diversification in RLKs between monocots and dicots could cause differences in downstream cytoplasmic responses. We also use interaction proteome to help empower the data mining of inferring new functions of RLK from a global perspective, with the ultimate goal of understanding how RLKs shape the adaptation of different plants to the environment/ecology. The RLK data model compiled herein, together with the annotations and analytic tools, form an integrated data foundation involving multi-omics data and is publicly accessible via the web portal (http://metaRLK.biocloud.top).

bioinformatics↗

bioRxiv2023

Structure and mechanism of Zorya anti-phage defense system

Zorya is a recently identified and widely distributed bacterial immune system, which protects against phage invasion. It consists of a predicted membrane-embedded complex (ZorAB) and soluble components that differ among Zorya subtypes, notably ZorC and ZorD, in type I Zorya systems. Here, we reveal the molecular basis of the Zorya defense system using cryo-electron microscopy, mutagenesis, fluorescence microscopy, proteomics, and functional studies. We demonstrate that ZorAB shares the stoichiometry of other 5:2 inner membrane ion-driven rotary motors. Additionally, ZorA5B2 features a dimeric ZorB peptidoglycan binding domain and a pentameric -helical coiled-coil tail made of ZorA that projects approximately 700 [A] into the cytoplasm. We further characterize the structure and function of the soluble Zorya components, ZorC and ZorD, and find that they harbour DNA binding and nuclease activity, respectively. Comprehensive functional and mutational analyses demonstrates that all Zorya components work in concert to protect bacterial cells against invading phages. We present evidence that ZorAB operates as an ion-driven motor that becomes activated and anchors to the cell wall upon sensing of cell envelope perturbations during phage invasion. Subsequently, ZorAB transfers the phage invasion signal through the ZorA cytoplasmic tail to the soluble effectors, which function to prevent phage propagation. In summary, our study elucidates the foundational mechanisms of Zorya function and reveals a novel triggering signal for the rapid activation of an anti-phage defense system.

molecular biology↗

bioRxiv2023

Integrated Hfq-interacting RNAome and transcriptomic analysis reveals complex regulatory networks of nitrogen fixation in root-associated Pseudomonas stutzeri A1501

The RNA chaperone Hfq acts as a global regulator of numerous biological processes, such as carbon/nitrogen metabolism and environmental adaptation in plant-associated diazotrophs; however, its target RNAs and the mechanisms underlying nitrogen fixation remain largely unknown. Here, we used enhanced UV cross-linking immunoprecipitation coupled with high-throughput sequencing (eCLIP-seq) to identify hundreds of Hfq-binding RNAs probably involved in nitrogen fixation, carbon substrate utilization, biofilm formation, and other functions. Collectively, these processes endow strain A1501 with the requisite capabilities to thrive in the highly competitive rhizosphere. Our findings revealed a previously uncharted landscape of Hfq target genes. Notable among these is nifM, encoding an isomerase necessary for nitrogenase reductase solubility; amtB, encoding an ammonium transporter; oprB, encoding a carbohydrate porin; and cheZ, encoding a chemotaxis protein. Furthermore, we identified more than one hundred genes of unknown function, which expands the potential direct regulatory targets of Hfq in diazotrophs. Our data showed that Hfq directly interacts with regulatory proteins (RsmA, AlgU, NifA), regulatory ncRNA RsmY, and other potential targets, thus revealing the mechanistic links in nitrogen fixation and other metabolic pathways. IMPORTANCENumerous experimental approaches often face challenges in distinguishing between direct and indirect effects of Hfq-mediated regulation. New technologies based on high-throughput sequencing are increasingly providing insight into the global regulation of Hfq in gene expression. Here, enhanced UV cross-linking immunoprecipitation coupled with high-throughput sequencing (eCLIP-seq) was employed to identify the Hfq-binding sites and potential targets in the root-associated P. stutzeri A1501, and identify hundreds of novel Hfq-binding RNAs that are predicted to be involved in metabolism, environmental adaptation, and nitrogen fixation. In particular, we have shown that Hfq interactions with various regulatory proteins and their potential targets at both the protein and RNA levels. This study not only enhances our understanding of Hfq regulation but, importantly, also provides a framework for addressing integrated regulatory network underlying root-associated nitrogen fixation.

microbiology↗

bioRxiv2023

Substrate recruitment via eIF2γ enhances catalytic efficiency of a holophosphatase that terminates the Integrated Stress Response

Dephosphorylation of pSer51 of the subunit of translation initiation factor 2 (eIF2P) terminates signalling in the integrated stress response (ISR). A trimeric mammalian holophosphatase comprised of a PP1 catalytic subunit, the conserved C-terminally located [~]70 amino acid core of a substrate-specific regulatory subunit (PPP1R15A/GADD34 or PPP1R15B/CReP) and G-actin (an essential co-factor) efficiently dephosphorylate eIF2P in vitro. Unlike their viral or invertebrate counterparts, with whom they share the conserved 70 residue core, the mammalian PPP1R15s are large proteins of more than 600 residues. Genetic and cellular observations point to a functional role for regions outside the conserved core of mammalian PPP1R15A in dephosphorylating its natural substrate, the eIF2 trimer. We have combined deep learning technology, all-atom molecular dynamics simulations, X-Ray crystallography and biochemistry to uncover binding of the {gamma} subunit of eIF2 to a short helical peptide repeated four times in the functionally-important N-terminus of human PPP1R15A that extends past its conserved core. Binding entails insertion of Phe and Trp residues that project from one face of an -helix formed by the conserved repeats of PPP1R15A into a hydrophobic groove exposed on the surface of eIF2{gamma} in the eIF2 trimer. Replacing these conserved Phe and Trp residues with Ala compromises PPP1R15A function in cells and in vitro. These findings suggest mechanisms by which contacts between a distant subunit of eIF2 and elements of PPP1R15A distant to the holophosphatase active site contribute to dephosphorylation of eIF2P by the core PPP1R15 holophosphatase and to efficient termination of the ISR in mammals.

biochemistry↗

bioRxiv2023

DNA-terminus-dependent transcription by T7 RNA polymerase and its C-helix mutants

The remarkable success of mRNA-based vaccines has underscored their potential as a novel biotechnology platform for vaccine development and therapeutic protein delivery. However, the single-subunit RNA polymerase from bacteriophage T7 widely used for in vitro transcription is well known to generate double-stranded RNA (dsRNA) byproducts that strongly stimulate the mammalian innate immune response. The dsRNA was reported to be originated from self-templated RNA extension or promoter-independent transcription. Here, we identified that the primary source of the full-length dsRNA during in vitro transcription is the DNA-terminus-initiated transcription by T7 RNA polymerase. Guanosines or cytosines at the end of DNA templates enhance the DNA-terminus-initiated transcription. Moreover, we found that aromatic residues located at position 47 in the C-helix interfere with the binding of T7 RNA polymerase to DNA termini, leading to a significant reduction in the production of full-length dsRNA. As a result, the mRNA synthesized using the T7 RNA polymerase G47W mutant exhibits higher expression efficiency and lower immunogenicity compared to the mRNA produced using the wild-type T7 RNA polymerase.

molecular biology↗

bioRxiv2023

Cryptic endogenous retrovirus subfamilies in the primate lineage

Many endogenous retroviruses (ERVs) in the human genome are primate-specific and have contributed novel cis-regulatory elements and transcripts. However, current approaches for classifying and annotating ERVs and their long terminal repeats (LTRs) have limited resolution and are inaccurate. Here, we developed a new annotation based on phylogenetic analysis and cross-species conservation. Focusing on the evolutionary young MER11A/B/C subfamilies, we revealed the presence of 4 new subfamilies, that better explained the epigenetic heterogeneity observed within the MER11 instances, suggesting a new annotation for 412 (19.8%) of these repeat elements. Furthermore, we functionally validated the regulatory potential of these four new subfamilies using a massively parallel reporter assay (MPRA), which also identified motifs associated with their differential activities. Combining MPRA with new annotations across primates revealed an apes-specific gain of SOX related motifs through a single-nucleotide deletion. Lastly, by applying our approach across 53 simian-enriched LTR subfamilies, we defined a total of 75 new subfamilies and found that 3,807 (30.0%) instances from 26 LTR subfamilies could be categorized into a novel annotation, many of which with a distinct epigenetic profile. Thus, with our refined annotation of simian-enriched LTRs, it will be possible to better understand the evolution in primate genomes and potentially identify new roles for ERVs and their LTRs in the hosts.

genomics↗

bioRxiv2023

Dorsal hippocampal oxytocin receptor regulates adult peer bonding in rats

Healthy social relationships are beneficial whereas their breakdown is often linked to psychiatric disorders. Parental care and bonding between sexual partners have been well studied both at the level of behavioral analysis and underlying neuronal mechanisms. By contrast, little is known about the neural and molecular basis of peer bonding, defined as social bonds formed between unrelated individuals of the same sex, due to the lack of a suitable experimental paradigm. We found that adult Sprague Dawley (SD) rats of the same sex form strong peer bonds with each other following co-housing. Peer bonded rats exhibit affiliative displays toward their cagemates who are distressed whereas they exhibit agonistic behaviors toward strangers in these situations. Using innovative, genetic strategies in rats, we show that both oxytocin receptor (OXTR) bearing neurons and Oxtr signaling in the dorsal hippocampus are essential for peer bonds to form. Together, we have developed a new platform for studying peer bonding and demonstrate a neural pathway that governs this behavior.

neuroscience↗

bioRxiv2023

Combined Partial-Nitrification and Phosphorus Removal with the co-existence of Nitrite-resistant phosphorous accumulating organisms (PAOs) and nitrifiers in the treatment of high-strength manure digestate

Concurrent biological phosphorus (P) recovery and nitrogen (N) removal in treating high-strength wastewater (such as anaerobic digestate) has been considered incompatible due to presumed conflicts in the conflicting optimum conditions required by phosphorous accumulating organisms (PAO) and nitrifiers. However, this study achieved a stable nitrite accumulation while still maintained PAO activities in one sequencing batch reactor for treating the manure digestate under two aeration schemes (continuous versus intermittent aeration). Nitrite accumulated up to 80.5 {+/-} 21.1 mg-N/L under continuous aeration (6 h) mode. Switching to intermittent aeration (equivalent to 3 h) halved nitrite accumulation but increased total nitrogen removal efficiency from 53.5 {+/-} 12.2% to 84.7 {+/-} 9.4%. Mass balance analysis indicates that nearly all ammonia was removed as N2O. Both Enhanced Biological Phosphorus Removal (EBPR) activity assessment and phenotypic trait detection via single cell Raman spectrum (SCRS) confirmed the existence of yet to be identified PAOs that are resistant to high nitrite inhibition in our system. Visual Minteq calculation indicates that high concentrations of Ca in manure digestate may form precipitates and influence the bioavailability of P forms. Therefore, both biotic and abiotic pathways lead to a total P removal rate around 61.0 {+/-} 6.8%. This study highlights new opportunities to combine short-cut nitrogen removal via partial nitrification, nitrous oxide (N2O) collection, and EBPR in commercial farm-collected digested manure wastewater. Higher N and P removal efficiency could potentially be achieved by tuning aeration schemes in combination with down-stream anammox process. SynopsisConcurrent partial nitrification, N2O accumulation, and EBPR activity were found, leading to the exploration of novel nitrite-resistant PAOs, simultaneously N/P recovery, and waste-energy conversion in treating high strength wastewater.

microbiology↗

bioRxiv2023

Nitrite deteriorates bioreactor performance by reducing growth of Ca. Brocadia sapporoensis instead of inhibiting the anammox activity

Effects of nitrite on anammox activities have been of widespread concern. However, the molecular mechanisms of specific microorganisms in anammox systems responding to nitrite remain unexplored. This study investigated the effects of excess nitrite on core metabolism of AnAOB and symbiotic bacteria, and further elucidated the response mechanism of these effects on microbial growth and nitrogen removal performance. Specifically, nitrogen removal process in a continuous-flow anaerobic ammonia oxidation membrane bioreactor completely collapsed when the nitrite concentration reached 243 mg N/L. Integrated meta-omics analyses demonstrated that excess nitrite disrupted the energy metabolism of Ca. Brocadia sapporoensis (AMXB1), reducing the energy available for establishing tolerance. It disrupted cell replication by impairing biosynthesis process of AMXB1, especially DNA replication and the formation of vital cell structures, e.g., cell membrane and cell wall, as well as the cellular protection system, leading to the collapse of the anammox system. In addition, the cross-feeding of glycogen, lipopolysaccharide and amino acid between AMXB1 and symbiotic bacteria was hindered by excess nitrite, which also contributed to the anomalous cell proliferation and metabolism of AMXB1. These findings contribute to our understanding of the ability of anammox consortia to respond to nitrite stress and process stability in engineered ecosystems. HighlightsO_LINO --N concentration of 243 mg N/L caused the performance collapse of a continuous-flow anammox MBR. C_LIO_LIExcess nitrite likely disrupted the energy metabolism of AMXB1, reducing the energy availability for mitigating nitrite toxicity. C_LIO_LIThe cross-feeding between AMXB1 and symbiotic bacteria was hindered by excess nitrite. C_LIO_LIThe hindrance of cross-feeding was reversed as the concentration of nitrite decreased. C_LI Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=132 SRC="FIGDIR/small/568540v1_ufig1.gif" ALT="Figure 1"> View larger version (45K): org.highwire.dtl.DTLVardef@6b199forg.highwire.dtl.DTLVardef@15f2a74org.highwire.dtl.DTLVardef@dc2d8eorg.highwire.dtl.DTLVardef@132deb1_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2023

The hidden function of nonspecifically DNA-bound RNA polymerases: a buffer of resource competition in bacteria

RNA polymerase (RNAP) is the workhorse of bacterial gene expression, transcribing rRNA and mRNA. Experiments found that a significant fraction of RNAPs in bacteria are nonspecifically bound to DNA, which is puzzling as these idle RNAPs could have produced more RNAs. Whether nonspecifically DNA-bound RNAPs have any function or are merely a consequence of passive interaction between RNAP and DNA is unclear. In this work, we propose that nonspecifically DNA-bound RNAPs buffer the free RNAP concentration and mitigate the crosstalk between rRNA and mRNA transcription. We verify our theory using mean-field models and an agent-based model of transcription, showing that the buffering effects are robust against the interaction between RNAPs and sigma factors and the spatial fluctuation and temporal noise of RNAP concentration. We analyze the relevant parameters of Escherichia coli and find that the buffering effects are significant across different growth rates at a low cost, suggesting that nonspecifically DNA-bound RNAPs are evolutionarily advantageous.

microbiology↗

bioRxiv2023

OPUS-Rota5: A Highly Accurate Protein Side-chain Modeling Method with 3D-Unet and RotaFormer

Accurate protein side-chain modeling is crucial for protein folding and design. This is particularly true for molecular docking as ligands primarily interact with side chains. A protein structure with large errors in side chains has limited usage such as in drug design. Previous research on AlphaFold2 (AF2) predictions of GPCR targets indicates that the docking of natural ligands back on AF2-predicted structures has limited successful rate presumably due to large errors in side chains. Here, we introduce a two-stage side-chain modeling approach called OPUS-Rota5. It leverages a modified 3D-Unet to capture the local environmental features including ligand information of each residue, and then employs RotaFormer module to aggregate various types of feature. Evaluation on three test sets, including recently released targets from CAMEO and CASP15, reveals that side chains modeled by OPUS-Rota5 are significantly more accurate than those predicted by other methods. We also employ OPUS-Rota5 to refine the side chains of 25 GPCR targets predicted by AF2 and then performed docking of their natural ligands back with a significantly improved successful rate. Such results suggest that OPUS-Rota5 could be a valuable tool for molecular docking, particularly for targets with relatively accurate predicted backbones, but not side chains.

bioinformatics↗

bioRxiv2023

Resident memory T cell development is associated with AP-1 transcription factor upregulation across anatomical niches.

Tissue-resident memory T (TRM) cells play a central role in immune responses to pathogens across all barrier tissues after infection. However, the underlying mechanisms that drive TRM differentiation and priming for their recall effector function remains unclear. In this study, we leveraged both newly generated and publicly available single-cell RNA-sequencing (scRNAseq) data generated across 10 developmental time points to define features of CD8 TRM across both skin and small-intestine intraepithelial lymphocytes (siIEL). We employed linear modeling to capture temporally-associated gene programs that increase their expression levels in T cell subsets transitioning from an effector to a memory T cell state. In addition to capturing tissue-specific gene programs, we defined a consensus TRM signature of 60 genes across skin and siIEL that can effectively distinguish TRM from circulating T cell populations, providing a more specific TRM signature than what was previously generated by comparing bulk TRM to naive or non-tissue resident memory populations. This updated TRM signature included the AP-1 transcription factor family members Fos, Fosb and Fosl2. Moreover, ATACseq analysis detected an enrichment of AP-1-specific motifs at open chromatin sites in mature TRM. CyCIF tissue imaging detected nuclear co-localization of AP-1 members Fosb and Junb in resting CD8 TRM >100 days post-infection. Taken together, these results reveal a critical role of AP-1 transcription factor members in TRM biology and suggests a novel mechanism for rapid reactivation of resting TRM in tissue upon antigen encounter.

immunology↗

bioRxiv2023

ONECUT2 Activates Diverse Resistance Drivers of Androgen Receptor-Independent Heterogeneity in Prostate Cancer

Significance StatementONECUT2 (OC2) is a master transcription factor that alters lineage identity by activating gene networks associated with both neuroendocrine prostate cancer and prostate adenocarcinoma. A small molecule inhibitor of OC2 represses the lineage plasticity program activated by enzalutamide, suggesting OC2 inhibition as a novel therapeutic strategy to prevent emergence of treatment-resistant variants. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=135 SRC="FIGDIR/small/560025v2_ufig1.gif" ALT="Figure 1"> View larger version (41K): org.highwire.dtl.DTLVardef@13278a4org.highwire.dtl.DTLVardef@8e82aeorg.highwire.dtl.DTLVardef@25a115org.highwire.dtl.DTLVardef@728eb4_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphic AbstractC_FLOATNO C_FIG Androgen receptor-(AR-) indifference is a mechanism of resistance to hormonal therapy in prostate cancer (PC). Here we demonstrate that the HOX/CUT transcription factor ONECUT2 (OC2) activates resistance through multiple drivers associated with adenocarcinoma, stem-like and neuroendocrine (NE) variants. Direct OC2 targets include the glucocorticoid receptor and the NE splicing factor SRRM4, among others. OC2 regulates gene expression by promoter binding, enhancement of chromatin accessibility, and formation of novel super-enhancers. OC2 also activates glucuronidation genes that irreversibly disable androgen, thereby evoking phenotypic heterogeneity indirectly by hormone depletion. Pharmacologic inhibition of OC2 suppresses lineage plasticity reprogramming induced by the AR signaling inhibitor enzalutamide. These results demonstrate that OC2 activation promotes a range of drug resistance mechanisms associated with treatment-emergent lineage variation in PC. Our findings support enhanced efforts to therapeutically target this protein as a means of suppressing treatment-resistant disease.

cancer biology↗

bioRxiv2023

Alveolar differentiation drives resistance to KRAS inhibition in lung adenocarcinoma

Lung adenocarcinoma (LUAD), commonly driven by KRAS mutations, is responsible for 7% of all cancer mortality. The first allele-specific KRAS inhibitors were recently approved in LUAD, but clinical benefit is limited by intrinsic and acquired resistance. LUAD predominantly arises from alveolar type 2 (AT2) cells, which function as facultative alveolar stem cells by self-renewing and replacing alveolar type 1 (AT1) cells. Using genetically engineered mouse models, patient-derived xenografts, and patient samples we found inhibition of KRAS promotes transition to a quiescent AT1-like cancer cell state in LUAD tumors. Similarly, suppressing Kras induced AT1 differentiation of wild-type AT2 cells upon lung injury. The AT1-like LUAD cells exhibited high growth and differentiation potential upon treatment cessation, whereas ablation of the AT1-like cells robustly improved treatment response to KRAS inhibitors. Our results uncover an unexpected role for KRAS in promoting intra-tumoral heterogeneity and suggest targeting alveolar differentiation may augment KRAS-targeted therapies in LUAD. SignificanceTreatment resistance limits response to KRAS inhibitors in LUAD patients. We find LUAD residual disease following KRAS targeting is composed of AT1-like cancer cells with the capacity to reignite tumorigenesis. Targeting the AT1-like cells augments responses to KRAS inhibition, elucidating a therapeutic strategy to overcome resistance to KRAS-targeted therapy.

cancer biology↗

bioRxiv2023

A resource for probing influences of perinatal factors on neurodevelopment in 3-10-years-old Chinese children

Adverse perinatal factors can disrupt the normal development of the brain, with potential long-term impacts on childrens overall development. Currently, the neuropathological mechanisms by which these factors lead to various neurodevelopmental disorders (NDDs) remain largely unknown. An open resource that integrate perinatal factors with brain and mental health development is essential for investigating NDD-related aetiology. In this Data Descriptor, we introduce a multicentre database containing information on perinatal factors that influence childrens brain-mind development, namely, periCBD, that combines neuroimaging and behavioural phenotypes with perinatal factors associated with a high incidence of NDDs at county/region/central district hospitals. PeriCBD was designed to establish a platform for the investigation of individual differences in brain-mind development among children aged 3-10 years are associated with perinatal factors. Ultimately, our goal was to develop an early prediction and screening model for NDDs that leverages normative data to facilitate NDD aetiology research. Herein, we provide a systematic overview of the data acquisition/cleaning/quality control/sharing, processes of periCBD and present preliminary brain-mind associations.

neuroscience↗

bioRxiv2023

Adaptive immunity: from CRISPR to CRIHSP?

Clustered regularly interspaced short palindromic repeats (CRISPR) confer adaptive immunity in prokaryotes against viral infection and plasmid transformation. Here, we identified abundant clustered regularly interspaced homologous stem-loop pairs (CRIHSP) within human adaptive immunity-related genes, such as antigen receptor germline genes. By examining genomic stability under activation-induced cytidine deaminase (AID) overexpression, we found that CRIHSP structures are preferred targets for AID. Through collecting and analyzing cancer cell genomic mutation databases, we discovered that these mutation sites tend to cluster toward stem-loop structures. Importantly, the frequency of stem-loop sequences within immunoglobulin heavy chain variable (IGHV) gene segments was over 3-fold higher compared to that within other regions. We concurrently observed stem-loop structures frequently flanking RSS motifs. Conservative estimates indicate a 74.07% probability of immunoglobulin heavy chain diversity (IGHD) gene segment enclosure within stem-loop. These RSS-proximal stem-loops may assemble into homologous stem-loop pair (HSP)-like intermediates and subsequent CRIHSP arrays. Our results implicate CRIHSP architectures as critical enhancer of antigen receptor gene recombination and diversification. Further molecular dissection of these processes could potentially elucidate mechanisms underlying cancer cell genomic instability, chromatin folding and dynamic regulation, gene expression control, etc.

immunology↗

bioRxiv2023

Guided Diffusion for molecular generation with interaction prompt

Molecular generative models have demonstrated their potential in designing molecules from scratch with high binding affinities in a pre-determined protein pocket and could be combined with traditional structural based drug design strategy. However, the generative processes of such models are random and the atomic interaction information between ligand and protein are ignored. On the other hand, the ligand has high propensity to bind with residues called hotspots. Hotspot residues contribute to the majority of the binding free energies and have been recognized as appealing targets for designed molecules. In this work, we develop an interaction prompt guided diffusion model-InterDiff to deal with the challenges. Four kinds of atomic interactions are involved in our model and represented as learnable vector embeddings. These embeddings serve as conditions for each residue to guide the molecular generative process. Comprehensive in-silico experiments evince that our model could generate molecules with desired ligand-protein interactions in a guidable way. Furthermore, we validate InterDiff on two realistic protein-based therapeutic agents. Results show that InterDiff could generate molecules with better or similar binding mode compared to known targeted drugs.

bioinformatics↗