Biology subjects

Jin, C.

Publications and source records attributed to Jin, C..

At least 55 records · Page 3Linked to original sources

bioRxiv2025

Formaldehyde Exposure Induces Systemic Epigenetic Alterations in Histone Methylation and Acetylation

Formaldehyde (FA) is a pervasive environmental organic pollutant and a Group 1 human carcinogen. While FA has been implicated in various cancers, its genotoxic effects, including DNA damage and DNA-protein crosslinking, have proven insufficient to fully explain its role in carcinogenesis, suggesting the involvement of epigenetic mechanisms. Histone post-translational modifications (PTMs) on H3 and H4, critical for regulating gene expression, may contribute to FA-induced pathogenesis as lysine and arginine residues serve as targets for FA-protein adduct formation. This study aimed to elucidate the effects of FA on histone methylation and acetylation patterns. Human bronchial epithelial cells (BEAS-2B) were exposed to low-dose (100 M) and high-dose (500 M) FA for 1 hour, and their histone extracts were analyzed using high-resolution liquid chromatography-tandem mass spectrometry-based proteomics, followed by PTM-combined peptide analysis and single PTM site/type comparisons. We identified 40 peptides on histone H3 and 16 on histone H4 bearing epigenetic marks. Our findings revealed that FA exposure induced systemic alterations in H3 and H4 methylation and acetylation, including hypomethylation of H3K4 and H3K79 and changes in H3K9, H3K14, H3K18, H3K23, H3K27, H3K36, H3K37, and H3R40, as well as modifications in H4K5, H4K8, H4K12, and H4K16. These FA-induced histone modifications exhibited strong parallels with epigenetic alterations observed in cancers, leukemia, and Alzheimers disease. This study provides novel evidence of FA epigenetic toxicity, offering new insights into the potential mechanisms underlying FA-driven pathogenesis.

pharmacology and toxicology↗

bioRxiv2024

Development of a monoclonal antibody against duck IFN-γ protein and the application for Intracellular Cytokine Staining

ABSTRACTInterferon-{gamma} (IFN-{gamma}), a member of the type II IFN family, is a crucial cytokine in the immune system and serves as an important indicator of immune response. Intracellular Cytokine Staining (ICS) is a technique used to analyze the production of cytokines within individual cells, and it has a wide range of applications in the fields of immunological monitoring, vaccine trials, and the study of infectious diseases. This study aimed to prepare monoclonal antibodies against duck IFN-{gamma} protein and to establish an ICS protocol for detecting the duck IFN-{gamma} protein. The duIFN-{gamma}-His or duIFN-{gamma}-Fc gene was cloned into the pEE12.4 expression vector and expressed as a recombinant protein of size 20.2 KDa or 54.9 KDa in 293F cells. The purified recombinant proteins were inoculated into BALB/c mice to generate splenic lymphocytes capable of secreting anti-duIFN-{gamma} antibodies, and hybridoma cells were obtained after fusion with SP2/0 cells. A new hybridoma cell line named 24H4, which stably secreted IgG3 {kappa} subtype antibody against duck IFN-{gamma}. This monoclonal antibody (mAb) was identified by Western Blot to recognize duck IFN-{gamma} antibodies, and the indirect ELISA results showed that its ability to recognize IFN-{gamma} protein reached 0.001 g/ml. The established ICS method was used to stain PBMCs after ConA stimulation, and duck IFN-{gamma} protein was successfully detected by flow cytometry, indicating that the ICS method was successfully established. This study we use the monoclonal antibody, 24H4, provides a crucial tool for subsequent research on duck cellular immune responses.

immunology↗

bioRxiv2024

Structural ubiquitin contributes to K48 linkage-specificity of the HECT ligase Tom1

Homologous to E6AP C-Terminus (HECT) ubiquitin ligases play key roles in essential pathways such as DNA repair, cell cycle control or protein quality control. Tom1 is one of five HECT ubiquitin E3 ligases encoded in the S. cerevisiae genome and prototypical for a ligase with pleiotropic functions such as ubiquitin chain amplification, orphan quality control and DNA damage response. Structures of full-length HECT ligases, including the Tom1 ortholog HUWE1, have been reported, but how domains beyond the conserved catalytic module contribute to catalysis remains largely elusive. Here, through cryogenic electron microscopy (cryo-EM) of Tom1 during an active ubiquitylation cycle, we demonstrate that the extended domain architecture directly contributes to activity. We identify a Tom1-ubiquitin architecture during ubiquitylation involving a non-canonical ubiquitin binding site in the solenoid shape of Tom1. We demonstrate that this ubiquitin binding site coordinates a structural ubiquitin contributing to the fidelity of K48 poly-ubiquitin chain assembly.

biochemistry↗

bioRxiv2024

Stacked Human Arterial Endothelial Cells Generate Atherosclerotic Fatty Streaks and Release Proinflammatory Cytokines

Fatty streaks are the first sign of atherosclerosis. They consist of lipid-containing foam cells, which were believed to be derived from the monocytes in the blood through the leaky endothelium, and from the vascular smooth muscle cells migrating into the intima from the media. Here, we showed that fatty streaks can also be formed by the stacked human arterial endothelial cells (HAECs) cultured in vitro. Via SEM we revealed a novel cell phenotype (coralthelial) that forms a streak/coral-like structure. We observed accumulation of lipids in the coralthelial cell and increased Golgi and coat protein II markers in its nucleus. Additionally, proinflammatory cytokines were upregulated in these cells, likely due to Golgi nuclear translocation and subsequently increased expression of the ribosomal protein RPL23 in the nucleus. We demonstrated, for the first time, that the atherosclerotic fatty streak-like structure can be generated from the stacked HAECs, which also create a proinflammatory microenvironment. Significance StatementOur work presents a novel perspective on atherosclerotic fatty streak formation, a critical early event in atherosclerosis development. We demonstrate, for the first time, that human arterial endothelial cells (HAECs) can transform into a novel phenotype, termed "coralthelial cells". These cells contribute to fatty streak formation, and produce proinflammatory cytokines through the relocation of RPL23 with the Golgi apparatus to the nucleus. This finding provides a new cellular mechanism by which endothelial cells initiate atherosclerosis, independent of traditional monocyte-derived foam cells. By enriching established paradigms, our research not only opens new avenues for therapeutic intervention targeting endothelial cells but also enhances understanding of vascular diseases and provides potential diagnostic and prognostic markers for atherosclerosis.

cell biology↗

bioRxiv2024

O-glycosylation contributes to mammalian glycoRNA biogenesis

There is an increasing appreciation for the role of cell surface glycans in modulating interactions with extracellular ligands and participating in intercellular communication. We recently reported the existence of sialoglycoRNAs, where mammalian small RNAs are covalently linked to N-glycans through the modified base acp3U and trafficked to the cell surface. However, little is currently known about the role for O-glycosylation, another major class of carbohydrate polymer modifications. Here, we use parallel genetic, enzymatic, and mass spectrometry approaches to demonstrate that O-linked glycan biosynthesis is responsible for the majority of sialoglycoRNA levels. By examining the O-glycans associated with RNA from cell lines and colon organoids we find known and previously unreported O-linked glycan structures. Further, we find that O-linked glycans released from small RNA from organoids derived from ulcerative colitis patients exhibit higher levels of sialylation than glycans from healthy organoids. Together, our work provides flexible tools to interrogate O-linked glycoRNAs (O-glycoRNA) and suggests that they may be modulated in human disease.

molecular biology↗

bioRxiv2024

Transcriptomic signatures of mouse ovarian aging and estropausal transition at single cell resolution

Female reproductive aging affects fertility and overall health. Functional decline in mouse ovary during reproductive aging is accompanied by estrous cycle prolongation and cessation. However, the molecular mechanism underlying reproductive aging concomitant with such cycle changes remains unclear. Using single-cell transcriptomics, we characterized aging signatures in mouse ovaries across the reproductive lifespan ranging from reproductively young (regular cycle) through peri-estropause (regular vs. irregular cycles) to post-estropause age (acyclic). Reproductive aging significantly remodeled cell compositions and increased transcriptional heterogeneity, with more pronounced changes post-estropause, exhibiting coordinated alterations across cell types in the ovary. Genes undergoing monotonic changes during reproductive aging across cell types were consistently enriched in the conserved pathways of aging, including oxidative phosphorylation, stress responses, and proteostasis. Additionally, cell type-specific changes were identified including dysregulation of hormone synthesis in granulosa cells, alterations in collagen and hyaluronan metabolism in stromal and early theca cells, and functional decline of a unique phagocytosis-associated macrophage. Aging also led to a significant decrease in cell-cell communications, particularly between stromal and granulosa cells, and an increase in extracellular vesicle secretion. Furthermore, we found increased expression of the senescence marker Cdkn1a and senescence-associated secretory phenotype (SASP) factors during ovarian aging, especially in granulosa cells. Notably, most of these aging-associated changes were more pronounced in irregular cycling ovaries compared to the regular cycling counterparts at the same age during the peri-estropause stage, suggesting that aging-related molecular changes in the ovary drive the estropausal transition in mice.

bioinformatics↗

bioRxiv2024

PD-1 controls differentiation, survival, and TCR affinity evolution of stem-like CD8+ T cells

Stem-like progenitors are a critical subset of cytotoxic T cells that self-renew and give rise to expanded populations of effector cells critical for successful checkpoint blockade immunotherapy. Emerging evidence suggests that the tumor-draining lymph nodes can support the continuous generation of these stem-like cells that replenish the tumor sites and act as a critical source of expanded effector populations, underlining the importance of understanding what factors promote and maintain activated T cells in the stem-like state. Using advanced 3D multiplex immunofluorescence imaging, here we identified antigen-presentation niches in tumor-draining lymph nodes that support the expansion, maintenance, and affinity evolution of a unique population of TCF-1+PD-1+SLAMF6hi stem-like CD8+ T cells. Our results show that contrary to the prevailing view that persistent TCR signaling drives terminal effector differentiation, prolonged antigen engagement well beyond the initial priming phase sustained the proliferation and self-renewal of these stem-like T cells in vivo. The inhibitory PD-1 pathway plays a central role in this process by mediating the fine-tuning of TCR and co-stimulatory signal input that enables selective expansion of high affinity TCR stem-like clones, enabling them to act as a renewable source of high affinity effector cells. PD-1 checkpoint blockade disrupts this fine tuning of input signaling, leading to terminal differentiation to the effector state or death of the most avid anti-tumor stem-like cells. Our results thus reveal an unexpected relationship between TCR ligand affinity recognition, a key negative feedback regulatory loop, and T cell stemness programming. Furthermore, these findings raise questions about whether anti-PD-1 checkpoint blockade during cancer immunotherapy provides a short-term anti-tumor effect that comes at the cost of diminishing efficacy due to progressive loss of these critical high affinity stem-like precursors.

immunology↗

bioRxiv2024

Restoration of locus coeruleus noradrenergic transmission during sleep

Sleep is indispensable for health and wellbeing, but its basic function remains elusive. The locus coeruleus (LC) powerfully promotes arousal by releasing noradrenaline. We found that noradrenaline transmission is reduced by prolonged wakefulness and restored during sleep. Fiber-photometry imaging of noradrenaline using its biosensor showed that its release evoked by optogenetic LC neuron activation was strongly attenuated by three hours of sleep deprivation and restored during subsequent sleep. This is accompanied by the reduction and recovery of the wake-promoting effect of the LC neurons. The reduction of both LC evoked noradrenaline release and wake-inducing potency is activity dependent, and the rate of noradrenaline transmission recovery depends on mammalian target of rapamycin (mTOR) signaling. The decline and recovery of noradrenaline transmission also occur in spontaneous sleep-wake cycles on a timescale of minutes. Together, these results reveal an essential role of sleep in restoring transmission of a key arousal-promoting neuromodulator.

neuroscience↗

bioRxiv2024

Elucidating the kinetic and thermodynamic insight into regulation of glycolysis by lactate dehydrogenase and its impact on tricarboxylic acid cycle and oxidative phosphorylation in cancer cells

Lactate dehydrogenase (LDH) stands at the intersection of pyruvate metabolism. While it is believed that inhibition of LDH redirects pyruvate to mitochondrial metabolism, suppressing glycolysis and boosting oxidative phosphorylation, the mechanism remains largely unexplored. We found that individual LDH A or B knockouts had minimal impact on glycolysis, tricarboxylic acid cycle (TCA cycle), or oxidative phosphorylation (OXPHOS). However, combining LDH knockout with LDH inhibitor GNE-140 significantly suppressed these processes. Inhibition of LDH led to an increase in free NADH concentration and a decrease in free NAD+ concentration, the reduced free NAD+ concentration inhibited GAPDH, disrupting the balance of glycolytic intermediates, which were linked with thermodynamic shift of the Gibbs free energy of reactions between phosphofructokinase 1 (PFK1) and phosphoglycerate mutase (PGAM) in the glycolytic pathway, favoring their reverse direction. This disrupted glycolysis led to impaired TCA cycle and mitochondrial respiration due to reduced pyruvate and glutamine carbon influx into TCA cycle. Under hypoxia, LDH inhibition had a stronger effect, inducing energy crisis, redox imbalance, and cancer cell death. Our study reveals LDHs intricate control over glycolysis, TCA cycle, and mitochondrial respiration, highlighting the interplay of enzyme kinetics and thermodynamics in metabolic pathways, a crucial aspect for understanding metabolic regulation. Impact statementThis study elucidates a biochemical mechanism by which lactate dehydrogenase influences glycolytic flux in cancer cells, revealing a kinetic- thermodynamic interplay that contributes to metabolic regulation.

biochemistry↗

bioRxiv2024

Two retrotransposon-derived capsid genes PNMA1 and PNMA4 maintain reproductive capacity

The human genome contains 24 gag-like capsid genes derived from deactivated retrotransposons conserved among eutherians. Although some of their encoded proteins retain the ability to form capsids and even transfer cargo, their fitness benefit has remained elusive. Here we show that the gag-like genes PNMA1 and PNMA4 support reproductive capacity. Six-week-old mice lacking either Pnma1 or Pnma4 are indistinguishable from wild-type littermates, but by six months the mutant mice become prematurely subfertile, with precipitous drops in sex hormone levels, gonadal atrophy, and abdominal obesity; overall they produce markedly fewer offspring than controls. Analysis of donated human ovaries shows that expression of both genes declines normally with aging, while several PNMA1 and PNMA4 variants identified in genome-wide association studies are causally associated with low testosterone, altered puberty onset, or obesity. These findings expand our understanding of factors that maintain human reproductive health and lend insight into the domestication of retrotransposon-derived genes.

genetics↗

bioRxiv2024

Ribosome biogenesis factor AtRRB1 confers pollen heat stress tolerance in Arabidopsis

The plant male reproductive system is very sensitive to high temperature stress leading to a reduction in fertility. Damage caused by heat stress is restored by the activation of transcription and the synthesis of chaperones that regulate the heat stress response. Here we report that AtRRB1 is a homolog of the yeast ribosome chaperone protein Rrb1p. AtRRB1 is an essential gene and a T-DNA insertion in the coding region impairs male and female gametogenesis. The heterozygous rrb1-1 mutant shows decreased expression of AtRRB1 and increased transcription of the 60S ribosome proteins RPL3B and RPL4, in line with a chaperone role of AtRRB1 in ribosome biogenesis. Embryo sac development across ovules of a single pistil occurs uncoordinated and about half of the ovules abort. Half of rrb1-1 pollen is substantially smaller and produce shorter pollen tubes than WT pollen. In contrast to the Col-0 pollen, smaller pollen is overly sensitivity to high temperature (24h at 32{degrees}C) treatment, specifically during the early bicellular microspore development stage. Heat stressed rrb1-1 bicellular microspores accumulated excessively rough endoplasmic reticulum stacks, suggesting that loss of AtRRB1 activity causes an arrest in ER associated protein biosynthesis. These findings support a critical requirement for ribosome biogenesis and protein synthesis in bicellular microspores to recover from high temperature stress.

plant biology↗

bioRxiv2024

Dynamics of RNA localization to nuclear speckles are connected to splicing efficiency

Nuclear speckles, a type of membraneless nuclear organelle in higher eukaryotic cells, play a vital role in gene expression regulation. Using the reverse transcription-based RNA-binding protein binding sites sequencing (ARTR-seq) method, we study human transcripts associated with nuclear speckles. We identify three gene groups whose transcripts demonstrate different speckle localization properties and dynamics: stably enriched in nuclear speckles, transiently enriched in speckles at the pre-mRNA stage, and not enriched in speckles. Specifically, we find that stably-enriched transcripts contain inefficiently spliced introns. We show that nuclear speckles specifically facilitate splicing of speckle-enriched transcripts. We further reveal RNA sequence features contributing to transcript speckle localization, underscoring a tight interplay between genome organization, RNA cis-elements, and transcript speckle enrichment, and connecting transcript speckle localization with splicing efficiency. Finally, we show that speckles can act as hubs for the regulated retention of introns during cellular stress. Collectively, our data highlight a role of nuclear speckles in both co- and post-transcriptional splicing regulation. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=189 SRC="FIGDIR/small/581881v1_ufig1.gif" ALT="Figure 1"> View larger version (53K): org.highwire.dtl.DTLVardef@1a55b13org.highwire.dtl.DTLVardef@fe50baorg.highwire.dtl.DTLVardef@6610fborg.highwire.dtl.DTLVardef@e4df5b_HPS_FORMAT_FIGEXP M_FIG GRAPHICAL ABSTRACT C_FIG

cell biology↗

bioRxiv2024

Visualizing the M2 muscarinic acetylcholine receptor activation regulated by aromatic ring dynamics

A detailed molecular understanding of the G-protein coupled receptor (GPCR) activation mechanism is crucial for rational drug design. Despite the growing number of GPCR structures being resolved in the inactive and activated states, the detailed molecular mechanism of how receptors transits from the inactive towards the active one upon agonist binding remains to be further understood. Herein, we performed comprehensive atomic-level simulations of the M2 muscarinic receptor (M2R) to determine how ligand binding modulates the receptor conformational dynamics. The results reveal that aromatic residue dynamics are closely associated with receptor activation. Binding of antagonists or agonists differentially alters the interacting patterns of critical aromatic residues, stabilizing them into distinct conformations. In addition, we found that the change of interaction and dynamics of the W4006.48-F3966.44 pair at the transmembrane core plays an essential role in the structural transition of M2R from the inactive state into an active-like state induced by binding of the supra-physiological agonist iperoxo. Moreover, we found that the sidechain dynamics of Y2065.58 is important in modulating the conformation of the intracellular cavity. Our work highlights the role of protein conformational dynamics in M2R activation, and provides new insights for future drug designs.

biochemistry↗

bioRxiv2024

Ruminococcus torques is a keystone degrader of intestinal mucin glycoprotein, releasing oligosaccharides used by Bacteroides thetaiotaomicron

Symbiotic interactions between humans and our communities of resident gut microbes (microbiota) play many roles in health and disease. Some gut bacteria utilize mucus as a nutrient source and can under certain conditions damage the protective barrier it forms, increasing disease susceptibility. We investigated how Ruminococcus torques--a known mucin-degrader that remains poorly studied despite its implication in inflammatory bowel diseases (IBDs)-- degrades mucin glycoproteins or their component O-linked glycans to understand its effects on the availability of mucin-derived nutrients for other bacteria. We found that R. torques utilizes both mucin glycoproteins and released oligosaccharides from gastric and colonic mucins, degrading these substrates with a panoply of mostly constitutively expressed, secreted enzymes. Investigation of mucin oligosaccharide degradation by R. torques revealed strong fucosidase, sialidase and {beta}1,4-galactosidase activities. There was a lack of detectable sulfatase and weak {beta}1,3-galactosidase degradation, resulting in accumulation of glycans containing these structures on mucin polypeptides. While the Gram-negative symbiont, Bacteroides thetaiotaomicron grows poorly on mucin glycoproteins, we demonstrate a clear ability of R. torques to liberate products from mucins, making them accessible to B. thetaiotaomicron. This work underscores the diversity of mucin-degrading mechanisms in different bacterial species and the probability that some species are contingent on others for the ability to more fully access mucin-derived nutrients. The ability of R. torques to directly degrade a variety of mucin and mucin glycan structures and unlock released glycans for other species suggests that it is a keystone mucin degrader, which may contribute to its association with IBD. ImportanceAn important facet of maintaining healthy symbiosis between host and intestinal microbes is the mucus layer, the first defense protecting the epithelium from lumenal bacteria. Some gut bacteria degrade different components of intestinal mucins, but detailed mechanisms used by different species are still emerging. It is imperative to understand these mechanisms as they likely dictate interspecies interactions and may illuminate particular species associated with bacterial mucus destruction and subsequent disease susceptibility. Ruminococcus torques is positively associated with IBD in multiple studies. We identified mucin glycan-degrading enzymes in R. torques and found that it shares mucin degradation products with another gut bacterium implicated in IBD, Bacteroides thetaiotaomicron. Our findings underscore the importance of understanding the mucin degradation mechanisms of different gut bacteria and their consequences on interspecies interactions, which may identify keystone bacteria that disproportionately contribute to defects in mucus protection and could therefore be targets to prevent or treat IBD.

microbiology↗

bioRxiv2023

Integration of multi-source gene interaction networks and omics data with graph attention networks to identify novel disease genes

The pathogenesis of diseases is closely associated with genes, and the discovery of disease genes holds significant importance for understanding disease mechanisms and designing targeted therapeutics. However, biological validation of all genes for diseases is expensive and challenging. In this study, we propose DGP-AMIO, a computational method based on graph attention networks, to rank all unknown genes and identify potential novel disease genes by integrating multi-omics and gene interaction networks from multiple data sources. DGP-AMIO outperforms other methods significantly on 20 disease datasets, with an average AUROC and AUPR exceeding 0.9. The superior performance of DGP-AMIO is attributed to the integration of multiomics and gene interaction networks from multiple databases, as well as triGAT, a proposed GAT-based method that enables precise identification of disease genes in directed gene networks. Enrichment analysis conducted on the top 100 genes predicted by DGP-AMIO and literature research revealed that a majority of enriched GO terms, KEGG pathways and top genes were associated with diseases supported by relevant studies. We believe that our method can serve as an effective tool for identifying disease genes and guiding subsequent experimental validation efforts.

bioinformatics↗

bioRxiv2023

Structural basis of anticancer drug recognition and amino acid transport by LAT1

LAT1 (SLC7A5) transports large neutral amino acids and their derivatives across the plasma membrane and plays pivotal roles in cancer cell proliferation, immune response and drug delivery across the blood-brain barrier. Despite recent advances in structural understanding of LAT1, how it discriminates substrates and inhibitors including the clinically relevant anticancer drugs remains elusive. Here we report six structures of LAT1, captured in three different conformations and bound with diverse bioactive ligands, elucidating its substrate transport and inhibitory mechanisms. JPH203, also known as nanvuranlat or KYT-0353 and currently in clinical trials as an anticancer drug, binds to the wide-open substrate-binding pocket of LAT1. It adopts a U-shaped conformer, with its amino-phenylbenzoxazol moiety pushing against transmembrane helix 3 (TM3), bending TM10 and arresting the transporter in the outward-facing conformation. In contrast, the physiological substrate L-Phe does not exhibit such inhibitory interactions, whereas melphalan, a slow substrate, poses steric hindrance in the pocket, explaining its inhibitory activity. Unexpectedly, the "classical" system L inhibitor BCH induces an occluded state, a key structural intermediate required for substrate transport. Trans stimulation assays show that BCH facilitates transporter turnover and is therefore a transportable substrate. These findings provide a structural framework for the intricate mechanisms of substrate recognition and inhibition of LAT1, paving the way for developing more specific and effective drugs against it.

biochemistry↗

bioRxiv2023

AttSiOff: A self-attention-based approach on siRNA de-sign with inhibition and off-target effect prediction

MotivationSmall interfering RNA (siRNA) is often used for function study and expression regulation of specific genes, as well as the development of small molecule drugs. Selecting siRNAs with high inhibition and low off-target effects from massive candidates is always a great challenge. Increasing experimentally validated samples prompt the development of machine-learning-based algorithms, including Support Vector Machine (SVM), Convolutional Neural Network (CNN), and Graph Neural Network (GNN). However, these methods still suffer from limited accuracy and poor generalization to design both potent and specific siRNAs. ResultsIn this study, we propose a novel approach for siRNA inhibition and off-target effect prediction, named AttSiOff. It combines self-attention-based siRNA inhibition predictor with an mRNA searching package and an off-target filter. The predictor gives the inhibition score via analyzing the embedding of siRNA and local mRNA sequences, generated from pre-trained RNA-FM model, as well as other meaningful prior-knowledge-based features. Self-attention mechanism can detect potentially decisive features, which may determine the inhibition of siRNA. It captures global and local dependencies more efficiently than normal convolutions. The 10-fold cross-validation results indicate that our model achieves a significant improvement of correlation between prediction and label, compared with all existing methods. And it reaches better performance of generalization and robustness on cross-dataset validation. In addition, the mRNA searching package could find all mature mRNAs for given gene name from GENOMES database, and the off-target filter can calculate the amount of unwanted off-target binding sites, which affects the specificity of siRNA. Experiments on mature siRNA drugs show that our entire framework, AttSioff, have excellent convenience and operability in practical applications. Contactyuanye_auto@sjtu.edu.cn or chengjin520@sjtu.edu.cn.

bioinformatics↗

bioRxiv2023

DeepSipred: A deep-learning-based approach on siRNA inhibition prediction

MotivationThe use of exogenous small interfering RNAs (siRNAs) for gene silencing has become a widespread molecular tool for gene function study and new drug identification. Although the pathway of RNAi to mediate gene expression has been widely investigated, the selection of hyperfunctional siRNA with high inhibition remains challenging. ResultsIn this study, we build a deep-learning-based approach on siRNA inhibition prediction, named DeepSipred. It combines features from sequence context, thermodynamic property, and other expert knowledge together to predict the inhibition more accurately than existing methods. The sequence features from siRNA and local target mRNA are generated via one-hot encoding and pretrained RNA-FM encoding. The convolution layers with multiple kernels in DeepSipred can detect various decisive motifs, which will determine the actual inhibition of siRNA. The thermodynamic features are calculated from Gibbs Free Energy. In addition, the expert knowledge includes those design criteria from previous studies. Benchmarked on large available public datasets, the 10-fold cross-validation results indicate that our predictor achieving the state-of-the-art performance. Contactyuanye_auto@sjtu.edu.cn or chengjin520@sjtu.edu.cn.

bioinformatics↗