Biology subjects

Gao, X.

Publications and source records attributed to Gao, X..

At least 253 records · Page 14Linked to original sources

bioRxiv2022

HiC-LDNet: A general and robust deep learning framework for accurate chromatin loop detection in genome-wide contact maps

MotivationIdentifying chromatin loops from genome-wide interaction matrices like Hi-C data is notoriously difficult. Such kinds of patterns can span through the genome from a hundred kilobases to thousands of kilobases. Most loop patterns are frequently related to biological functions, such as providing contacts between regulatory regions and promoters. They can also affect the cell-specific biological functions of different regulatory regions of DNA, thus leading to disease and tumorigenesis. While most statistical methods failed in the generalization to multiple cell types, recently proposed machine learning-based methods struggled when tested on sparse single-cell Hi-C (scHi-C) contact maps. We notice that there is an urgent need for an algorithm that can handle sparse scHi-C maps, and at the same time, can generate confident loop calls on regular cell lines. ResultsTherefore, we propose a novel deep learning-based framework for Hi-C chromatin loop detection (HiC-LDNet) and provide corresponding downstream analysis. HiC-LDNet can give relatively more accurate predictions in multiple tissue types and contact technologies. Compared to other loop calling algorithms, such as HiCCUPS, Peakachu, and Chromosight, HiC-LDNet recovers a higher number of loop calls in multiple experimental platforms (Hi-C, ChIA-PET, DNA-SPRITE, and HiChIP), and achieves higher confidence scores in multiple cell types (Human GM12878, K562, HAP1, and H1-hESC). For example, in genome-wide loop detection on the human GM12878 cell line, HiC-LDNet successfully recovered 82.5% of loops within only 5 pixels of 10k bp resolution. Furthermore, in the sparse scHi-C ODC tissue, HiC-LDNet achieves superior performance by recovering 93.5% of ground truth loops with high confidence scores, compared with that of Peakachu (31.5%), Chromosight(69.6%), and HiCCUPS(9.5%). Therefore, our method is a robust and general pipeline for genome-wide chromatin loop detection for both bulk Hi-C and scHi-C data. Availabilityhttps://github.com/frankchen121212/HiC-LDNet Contactliyu@cse.cuhk.edu.hk and xin.gao@kaust.edu.sa

bioinformatics↗

bioRxiv2022

Quantitative proteomics of the CDK9 interactome reveals a novel function of the HSP90-CDC37-P-TEFb complex for BETi-induced HIV-1 latency reactivation

Brd4 has been intensively investigated as a promising drug target because of its implicated functions in oncogenesis, inflammation and HIV-1 transcription. The formation of the Brd4-P-TEFb (CDK9/Cyclin T1) complex and its regulation of transcriptional elongation is critical for HIV latency reactivation and expression of many oncogenes. To further investigate the mechanism of the Brd4-P-TEFb complex in controlling elongation, mass spectrometry-based quantitative proteomics of the CDK9 interactome was performed. Upon treatment with the selective BET bromodomain inhibitor (BETi) JQ1, 535 proteins were successfully identified with high confidence as CDK9-interacting proteins. Among them, that increased bindings of HSP90 and CDC37 to CDK9 were particularly striking, and our data suggest that the HSP90-CDC37-P-TEFb complex is involved in controlling P-TEFbs dynamic equilibrium during BETi-induced HIV-1 latency reactivation. Furthermore, the HSP90-CDC37-P-TEFb complex directly regulates HIV-1 transcription and relies on the recruitment by heat shock factor 1 (HSF1) for binding to the HIV-1 promoter. These results advance the understanding of HSP90-CDC37-P-TEFb in HIV-1 latency reversal and enlighten the development of potential strategies to eradicate HIV-1 using a combination of targeted drugs.

molecular biology↗

bioRxiv2022

Encoding sensing functions into material interface for a rationally engineered integrated electrochemical liquid biopsy

Limited healthcare capacity highlights the needs of integrated and simple sensing systems for personalized health monitoring. However, only a limited set of sensors can be employed for point-of-care applications, emphasizing the lack of a generalizable engineering strategy for sensor construction. Here, we report a de novo rational engineering strategy for the construction of an integrated electrochemical liquid biopsy (ELB) platform capable of direct profiling cancer exosomes from blood. Using a bottom-up approach for sensor design, a series of critical sensing functions is considered and encoded into the material interface by programming the electrode material with different chemical and structure features. We present that the rationally engineered electrochemical liquid biopsy platform is able to achieve one-step sensor fabrication, target isolation, non-fouling and high-sensitivity sensing, direct signal transduction and multiplexed detection. Integrating the multiplexed sensing with principal component analysis, we demonstrate the capability of the programmed sensing system on differentiating cancerous groups from healthy controls by analyzing clinical samples from lung cancer patients.

bioengineering↗

bioRxiv2021

Identification of upstream transcription factor binding sites in orthologous genes using mixed Student's t-test statistics

BackgroundTranscription factor (TF) regulates the transcription of DNA to messenger RNA by binding to upstream sequence motifs. Identifying the locations of known motifs in whole genomes is computationally intensive. Methodology/Principal FindingsThis study presents a computational tool, named "Grit", for screening TF-binding sites (TFBS) by coordinating transcription factors to their promoter sequences in orthologous genes. This tool employs a newly developed mixed Students t-test statistical method that detects high-scoring conserved and non-conserved binding sites among species. The program performs sequence scanning at a rate of 3.2 Mb/s on a quad-core Amazon server and has been benchmarked by the well-established ChIP-Seq datasets, putting Grit amongst the top-ranked TFBS predictors. It marginally outperforms the well-known transcription factor motif scanning tools, Pscan (4.8%) and FIMO (17.8%), in analyzing well-documented ChIP-Atlas human genome Chip-Seq datasets. SignificanceGrit is a good alternative to current available motif scanning tools and is publicly available at http://www.thua45.cn/grit under an academic free license. Author SummaryLocating transcription factor-binding (TF-binding) site in the genome and identification their function is fundamental in understanding various biological processes. Improve the performance of the prediction tools is important because accurate TF-binding site prediction can save cost and time for wet-lab experiments. Also, genome wide TF-binding site prediction can provide new insights for transcriptome regulation in system biology perspective. This study developed a new TF-binding site prediction tool based on mixed Students t-test statistical method. The tool is amongst the top-ranked TF-binding site predictors, as such, it can help the researchers in TF-binding site identification and transcriptional regulation mechanism interpretation of genes.

bioinformatics↗

bioRxiv2021

Cell cycle arrest explained the observed bulk 3D genomic alterations in response to long term heat shock for mammalian cells

Heat shock is a common environmental stress, while the response of the nucleus to it remains controversial in mammalian cells. Acute reaction and chronic adaptation to environmental stress may have distinct internal rewiring in the gene regulation networks. However, this difference remains largely unexplored. Here, we report that chromatin conformation and chromatin accessibility respond differently in short- and long-term heat shock in human K562 cells. Interestingly, we found that chromatin conformation in K562 cells was largely stable in response to short heat shock, while showed clear and characteristic changes after long-term heat treatment with little alteration in chromatin accessibility during the whole process. We further showed in silico and experimental evidence strongly suggesting that changes in chromatin conformation may largely stem from an accumulation of cells in the M stage of cell cycle in response to heat shock. Our results represent a paradigm shift away from the controversial view of chromatin response to heat shock and emphasize the necessity of cell cycle analysis while when interpreting bulk Hi-C data.

genomics↗

bioRxiv2021

FastQTLmapping: an ultra-fast package for mQTL-like analysis

SummaryHere we describe fastQTLmapping, a C++ package that is computationally efficient not only for mQTL-like analysis but as a generic solver also for conducting exhaustive linear regressions involving extraordinarily large numbers of dependent and explanatory variables allowing for covariates. Compared to the state-of-the-art MatrixEQTL, fastQTLmapping was an order of magnitude faster with much lower peak memory usage. In a large dataset consisting of 3,500 individuals, 8 million SNPs, 0.8 million CpGs and 20 covariates, fastQTLmapping completed the mQTL analysis in 7 hours with 230GB peak memory usage. Availability and ImplementationFastQTLmapping is implemented in C++ and released under a GPL license. FastQTLmapping can be downloaded from https://github.com/TianTTL/xQTLmapping. Contactliufan@big.ac.cn

bioinformatics↗

bioRxiv2021

PD-L1-expressing astrocytes act as a gate-keeper for neuroinflammation in the central nervous system of mice with traumatic brain injury

BackgroundTissue damage and cellular destruction are the major events in traumatic brain injury (TBI), which trigger sterile neuroimmune and neuroinflammatory responses in the brain. While appropriate acute and transient neuroimmune and neuroinflammatory responses facilitate the repair and adaptation of injured brain tissues, prolonged and excessive neuroimmune and neuroinflammatory responses exacerbate brain damage. The mechanisms that control the intensity and duration of neuroimmune and neuroinflammatory responses in TBI largely remain elusive. MethodsWe used the controlled cortical impact (CCI) model of TBI to study the role of immune checkpoints (ICPs), key regulators of immune homeostasis, in the regulation of neuroimmune and neuroinflammatory responses in the brain in vivo. ResultsWe found that de novo expression of PD-L1, a potent inhibitory ICP, was robustly and transiently induced in reactive astrocytes, but not in microglial cells, neurons, or oligodendrocyte progenitor cells (OPCs). These PD-L1+ reactive astrocytes were highly enriched to form a dense zone around the TBI lesion. Blockade of PD-L1 signaling enlarged brain tissue cavity size, increased infiltration of inflammatory Ly-6CHigh monocytes/macrophages (M/M{phi}) but not tissue-repairing Ly-6CLow/F4/80+ M/M{phi}, and worsened TBI outcomes in mice. PD-L1 gene knockout enhanced production of CCL2 that interacted with its cognate receptor CCR2 on Ly-6CHigh M/M{phi} to chemotactically recruit these cells into inflammatory sites. Mechanically, PD-L1 signaling in astrocytes likely exhibits dual inhibitory activities for the prevention of excessive neuroimmune and neuroinflammatory responses to TBI through (1) the PD-1/PD-L1 axis to suppress the activity of brain-infiltrating PD-1+ immune cells such as PD-1+ T cells, and (2) PD-L1 reverse signaling to regulate the timing and intensity of astrocyte reactions to TBI. ConclusionsPD-L1+ astrocytes act as a gatekeeper to the brain to control TBI-related neuroimmune and neuroinflammatory responses, thereby opening a novel avenue to study the role of ICP-neuroimmune axes in the pathophysiology of TBI and other neurological disorders.

neuroscience↗

bioRxiv2021

Programmable large DNA deletion, replacement, integration, and inversion with twin prime editing and site-specific recombinases

The targeted deletion, replacement, integration, or inversion of DNA sequences at specified locations in the genome could be used to study or treat many human genetic diseases. Here, we describe twin prime editing (twinPE), a method for the programmable replacement or excision of DNA sequence at endogenous human genomic sites without requiring double-strand DNA breaks. TwinPE uses a prime editor (PE) protein and two prime editing guide RNAs (pegRNAs) that template the synthesis of complementary DNA flaps on opposing strands of genomic DNA, resulting in the replacement of endogenous DNA sequence between the PE-induced nick sites with pegRNA-encoded sequences. We show that twinPE in human cells can perform precise deletions of at least 780 bp and precise replacements of genomic DNA sequence with new sequences of at least 108 bp. By combining single or multiplexed twinPE with site-specific serine recombinases either in separate steps or in a single step, we demonstrate targeted integration of gene-sized DNA plasmids (>5,000 bp) into safe-harbor loci including AAVS1, CCR5, and ALB in human cells. To our knowledge, these results represent the first RNA-programmable insertion of gene-sized DNA sequences into targeted genomic sites of unmodified human cells without requiring double-strand breaks or homology-directed repair. Twin PE combined with recombinases also mediated a 40,167-bp inversion at IDS that corrects a common Hunter syndrome allele. TwinPE expands the capabilities of precision gene editing without requiring double-strand DNA breaks and synergizes with other tools to enable the correction or complementation of large or complex pathogenic alleles in human cells.

genomics↗

bioRxiv2021

A Potential Novel COVID-19 Vaccine With RBD-HR1/HR2 Hexamer Structure

The COVID-19 pandemic and the continued spreading of the SARS-CoV-2 variants have brought a grave public health consequence and severely devastated the global economy with recessions. Vaccination is considered as one of the most promising and efficient methods to end the COVID-19 pandemic and mitigate the disease conditions if infected. Although a few vaccines have been developed with an unprecedented speed, scientists around the world are continuing pursuing the best possible vaccines with innovations. Comparing to the expensive mRNA vaccines and attenuated/inactivated SARS-CoV-2 vaccines, recombinant protein vaccines have certain advantages, including their safety (non-virus components), potential stronger immunogenicity, broader protection, ease of scaling-up production, reduced cost, etc. In this study, we reported a novel COVID-19 vaccine generated with RBD-HR1/HR2 hexamer that was creatively fused with the RBD domain and heptad repeat 1 (HR1) or heptad repeat 2 (HR2) to form a dumbbell-shaped hexamer to target the spike S1 subunit. The novel hexamer COVID-19 vaccine induced high titers of neutralizing antibody in mouse studies (>100,000), and further experiments also showed that the vaccine also induced an alternative antibody to the HR1 region, which probably alleviated the drop of immunogenicity from the frequent mutations of SARS-CoV-2.

biochemistry↗

bioRxiv2021

Total parenteral nutrition drives glucose metabolism disorders by modulating gut microbiota and its metabolites

The occurrence of glucose metabolism disorders is a potentially fatal complication of total parenteral nutrition (TPN). However, the mechanisms of TPN-associated glucose metabolism disorders remain unclarified. Given that the glucose metabolism was related to gut microbiome and TPN could induce the gut microbiota dysbiosis, we hypothesized that gut microbiota and its metabolites played the important roles in TPN-associated glucose metabolism disorders. By performing a cohort study of 256 type 2 IF patients given PN, we found that H-PN (PN>80%) patients exhibited insulin resistance and a higher risk of complications. Then, TPN and microbiome transfer mice model showed that TPN promoted glucose metabolism disorders by inducing gut microbiota dysbiosis; 16S rRNA sequencing demonstrated that the abundance of Lactobacillaceae was decreased in mice model and negatively correlated with HOMA-IR and lipopolysaccharide level in TPN patients. Untargeted metabolomics found that indole-3-acetic acid (IAA) was decreased in TPN mice, and the serum level was also decreased in H-PN patients. Furthermore, GLP-1 secretion regulated by IAA and aryl hydrocarbon receptor was reduced in TPN mice and patients; IAA or liraglutide completely prevented glucose metabolism disorders in TPN mice. In conclusion, TPN drives glucose metabolism disorders by inducing alteration of gut microbiota and its metabolites.

microbiology↗

bioRxiv2021

The production of 4,182 mouse lines identifies experimental and biological variables impacting Cas9-mediated mutant mouse line production

The International Mouse Phenotyping Consortium (IMPC) systematically produces and phenotypes mouse lines with presumptive null mutations to provide insight into gene function. The IMPC now uses the programmable RNA-guided nuclease Cas9 for its increased capacity and flexibility to efficiently generate null alleles in the C57BL/6N strain. In addition to being a valuable novel and accessible research resource, the production of 3,313 knockout mouse lines using comparable protocols provides a rich dataset to analyze experimental and biological variables affecting in vivo gene engineering with Cas9. Mouse line production has two critical steps - generation of founders with the desired allele and germline transmission (GLT) of that allele from founders to offspring. A systematic evaluation of the variables impacting success rates identified gene essentiality as the primary factor influencing successful production of null alleles. Collectively, our findings provide best practice recommendations for using Cas9 to generate alleles in mouse essential genes, many of which are orthologs of genes linked to human disease.

genetics↗

bioRxiv2021

pcnaDeep: A Fast and Robust Single-Cell Tracking Method Using Deep-Learning Mediated Cell Cycle Profiling

MotivationComputational methods that track single-cells and quantify fluorescent biosensors in time-lapse microscopy images have revolutionised our approach in studying the molecular control of cellular decisions. One barrier that limits the adoption of single-cell analysis in biomedical research is the lack of efficient methods to robustly track single-cells over cell division events. ResultsHere, we developed an application that automatically tracks and assigns mother-daughter relationships of single-cells. By incorporating cell cycle information from a well-established fluorescent cell cycle reporter, we associate mitosis relationships enabling high fidelity long-term single-cell tracking. This was achieved by integrating a deep-learning based fluorescent PCNA signal instance segmentation module with a cell tracking and cell cycle resolving pipeline. The application offers a user-friendly interface and extensible APIs for customized cell cycle analysis and manual correction for various imaging configurations. Availability and ImplementationpcnaDeep is an open-source Python application under the Apache 2.0 licence. The source code, documentation and tutorials are available at https://github.com/chan-labsite/PCNAdeep. Supplementary InformationSupplementary data are available online.

bioinformatics↗

bioRxiv2021

Role of sleep quality in the acceleration of biological aging and its potential for preventive interaction on air pollution insults: findings from the UK Biobank cohort

BackgroundSleep has been associated with aging and relevant health outcomes, but their causal relationship remains inconclusive. MethodsIn this study, we investigated the associations of sleep behaviors with biological ages (BAs) among 363,886 middle and elderly-aged adults from UK Biobank. Sleep index (0 [worst]-6 [best]) of each participant was retrieved from six sleep behaviors: snoring, chronotype, daytime sleepiness, sleep duration, insomnia, and difficulties in getting up. Two BAs, the KDM-biological age and PhenoAge, were estimated by corresponding algorithms based on clinical traits, and their discrepancies with chronological age were defined as the age accelerations (AAs). ResultsWe first observed negative associations between the sleep index and the two AAs, and demonstrated that the change of AAs could be the consequence of sleep quality using Mendelian randomization with genetic risk scores of sleep index and BAs. Particularly, one unit increase in sleep index was associated with 0.105- and 0.125-year decreases in KDM-biological age acceleration and PhenoAge acceleration, respectively. Furthermore, we observed significant independent and joint effects of sleep and air pollution (i.e. PM2.5 and NO2), another key driver of aging, on BAs. Sleep quality also showed modifying effect on the associations of elevated PM2.5 and NO2 levels with accelerated aging. For instance, an interquartile range increase in PM2.5 level was associated with 0.011-, 0.047-, and 0.078-year increase in PhenoAge acceleration among people with high (5-6), medium (3-4), and low (0-2) sleep index, respectively. ConclusionsOur findings elucidate that better sleep quality could lessen accelerated biological aging resulting from exogenous exposures including air pollution. FundingPeking University Start-up Grant (BMU2021YJ044)

genetics↗

bioRxiv2021

Stem cell-derived macrophages as a new platform for studying host-pathogen interactions in livestock

Infectious diseases of farmed and wild animals pose a recurrent threat to food security and human health. The macrophage, a key component of the innate immune system, is the first line of defence against many infectious agents and plays a major role in shaping the adaptive immune response. However, this phagocyte is a target and host for many pathogens. Understanding the molecular basis of interactions between macrophages and pathogens is therefore crucial for the development of effective strategies to combat important infectious diseases. We explored how pluripotent stem cells (PSCs) can provide a limitless in vitro supply of genetically and experimentally tractable macrophages from livestock. Porcine and bovine PSC-derived macrophages (PSCdMs) exhibited molecular and functional characteristics of ex vivo primary macrophages. Pig PSCdMs were productively infected by Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) and African Swine Fever Virus (ASFV), two of the most economically important and devastating viruses in pig farming. Moreover, Pig PSCdMs were readily amenable to genetic modification by CRISPR/Cas9 gene editing applied in parental stem cells, or directly by lentiviral vector transduction. PSCs and differentiated derivatives therefore provide a useful and ethical experimental platform to investigate the genetic and molecular basis of host-pathogen interactions in livestock.

immunology↗

bioRxiv2021

ASFV pD345L protein negatively regulates NF-kB signaling through inhibiting IKK kinase activity

NF-{kappa}B is a critical transcription factor in immediate early viral infection, including African swine fever virus (ASFV), playing an important role in inflammation response and expression of antiviral genes. ASFV encodes for more than 151 proteins by its own transcription machinery and possesses a great capacity to evade or subvert antiviral innate immune responses. A couple of such viral proteins have been reported, but many remain unknown. Here, we showed that pD345L, an ASFV-encoded lambda-like exonuclease, is an inhibitor of cGAS/STING mediated NF-{kappa}B signaling by blocking IKK/{beta} kinase activity. Specifically, we showed that overexpression of pD345L suppresses cGAS/STING induced IFN{beta} and NF-{kappa}B activation, resulting in decreased transcription of IFN{beta} and several pro-inflammatory cytokines, including IL-1, IL-6, IL-8, and TNF. In addition, we showed that pD345L targeted at or downstream of IKK and upstream of p65. Importantly, we found that pD345L associates with KD and HLH domains of IKK and LZ domain of IKK{beta}, and thus interrupts their kinase activity on downstream substrate I{kappa}B. Finally, we showed that pD345L inhibition of NF-{kappa}B signaling was independent of its exonuclease activity. Taken together, we concluded that pD345L blocks IKK /{beta} kinase activity by protein-protein interaction and thus disrupts cGAS/STING mediated NF-{kappa}B signaling. ImportanceAfrican Swine Fever (ASF) is one of the most devastating and economically significant swine diseases caused by African swine fever virus (ASFV). Since expanding of ASFV affected areas into Asian countries, especially China, an effective vaccine is urgently needed more than ever. Therefore, it is of great significance to understand the interaction between ASFV infection and host immune responses. The NF-{kappa}B signaling plays a central role in innate and acquired immune responses. Activation of I{kappa}B kinase (IKK) complex is a key step of both canonical and non-canonical NF-{kappa}B pathways, and is commonly targeted by different viruses. But no ASFV protein has been shown to regulate IKK yet. In this study, we demonstrated that pD345L blocks IKK/{beta} kinase activity by protein-protein interaction and thus disrupts cGAS/STING mediated NF-{kappa}B signaling. It has been shown that conventional vaccine development approaches are proven to be inapplicable to ASFV. Neither subunit nor DNA vaccine provides efficient protection. Gene deleted live-attenuated vaccine candidates render adequate protection, but establishment of chronic or persistent infection in vaccinated animals and risk of recombination with filed strains are key challenges. To overcome these, one potential strategy would be generation of replication-defective viruses. As a lambda-like exonuclease, pD345L plays a critical role in ASFV replication and ASFV deficient in D345L cannot be rescued. Given the dual role of pD345L in virus replication and immune evasion, it may serve as a potential target for replication-defective virus vaccine development.

microbiology↗

bioRxiv2021

Investigating the active substance and mechanism of Jing-Fu-Kang granules via mass spectrometry technology and network pharmacology method

Jing-Fu-Kang granules (JFKG) is a famous Chinese patent medicine for the treatment of cervical spondylosis around the China, whereas the active substance and mechanism are not completely investigated clearly. In the current study, a rapid separation and identification method using UPLC-QE-Orbitrap-MS was established, 97 chemical constituents from JFKG were identified, and 16 prototype components from plasma samples after administration of JFKG were observed within 16 min. The structures of typical compounds were preliminarily speculated by comparing the retention time and fragmentation pattern. Furthermore, multiple databases were used to integrate the compound targets of JFKG, and the disease targets related to cervical spondylosis. After the intersection of the two sets of targets, a protein-protein interaction (PPI) network and a TCM-component-target-pathway-disease network were established, then using the DAVID database to perform gene ontology analysis and Kyoto Encyclopedia of Genes and Genomes analysis on the common targets to find related pathways. Finally, a total of 531 common targets and 136 pathways were found to participate in the mechanism. Our findings will help to further confirm the mechanism of JFKG for relieving cervical spondylosis, which will improve the scientific rationality of JFKG in clinical use, and can also assist in guiding doctors.

pharmacology and toxicology↗

bioRxiv2021

ChemPLAN-Net: A deep learning framework to find novel inhibitor fragments for proteins

Fragment-based drug design plays an important role in the drug discovery process by reducing the complex small-molecule space into a more manageable fragment space. We leverage the power of deep learning to design ChemPLAN-Net; a model that incorporates the pairwise association of physicochemical features of both the protein drug targets and the inhibitor and learns from thousands of protein co-crystal structures in the PDB database to predict previously unseen inhibitor fragments. Our novel protocol handles the computationally challenging multi-label, multi-class problem, by defining a fragment database and using an iterative featurepair binary classification approach. By training ChemPLAN-Net on available co-crystal structures of the protease protein family, excluding HIV-1 protease as a target, we are able to outperform fragment docking and recover the targets inhibitor fragments found in co-crystal structures or identified by in-vitro cell assays.

bioinformatics↗

bioRxiv2021

Knockout of circRNAs by base editing back-splice sites of circularized exons

A large number of circular RNAs (circRNAs) are produced from back-splicing of exon(s) of precursor mRNAs and generally co-expressed with their cognate linear RNAs from the same gene loci. Methods for circRNA-specific knockout are lacking, largely due to complete sequence-overlaps between circular and cognate linear RNAs. Here, we report to use base editors (BEs) for circRNA depletion. By targeting splice sites involved in both back-splicing and canonical splicing, BEs can repress both circular and linear RNAs expression, which confirms the requirement of canonical splice site signals for back-splice. Importantly, by targeting back-splice sites predominantly for circRNA biogenesis, BEs could efficiently repress the production of circular, but not linear cognate RNAs. As hundreds of exons were found to be predominantly back-spliced to produce circRNAs, this study provides an efficient method to deplete circRNAs for function study.

bioinformatics↗