Telomeres are specialized structures at the ends of linear chromosomes that protect genome stability.The telomeric repeat-containing RNA(TERRA)that is transcribed from subtelomeric regions can invade into double-stran...Telomeres are specialized structures at the ends of linear chromosomes that protect genome stability.The telomeric repeat-containing RNA(TERRA)that is transcribed from subtelomeric regions can invade into double-stranded DNA regions and form RNA:DNA hybrid-containing structure called R-loop.In tumor cells,R-loop formation is closely linked to gene expression and the alternative lengthening of telomeres(ALT)pathway.Dysregulated R-loops can cause stalled replication forks and telomere instability.However,how R-loops are recognized and regulated,particularly at telomeres,is not well understood.We discovered that ILF3 selectively associates with telomeric R-loops and safeguards telomeres from abnormal homologous recombination.Knocking out ILF3 results in excessive R-loops at telomeres and triggers telomeric DNA damage responses.In addition,ILF3 deficiency disrupts telomere homeostasis and causes abnormalities in the ALT pathway.Using the proximity-dependent biotin identification(BioID)technology,we mapped the ILF3 interactome and discovered that ILF3 could interact with several DNA/RNA helicases,including DHX9.Importantly,ILF3 may aid in the resolution of telomeric R-loops through its interaction with DHX9.Our findings suggest that ILF3 may function as a reader of telomeric R-loops,helping to prevent abnormal homologous recombination and maintain telomere homeostasis.展开更多
Biomolecular condensates or membraneless organelles(MLOs)formed by liquid-liquid phase separation(LLPS)divide intracellular spaces into discrete compartments for specific functions.Dysregulation of LLPS or aberrant ph...Biomolecular condensates or membraneless organelles(MLOs)formed by liquid-liquid phase separation(LLPS)divide intracellular spaces into discrete compartments for specific functions.Dysregulation of LLPS or aberrant phase transition that disturbs the formation or material states of MLOs is closely correlated with neurodegeneration,tumorigenesis,and many other pathological processes.Herein,we summarize the recent progress in development of methods to monitor phase separation and we discuss the biogenesis and function of MLOs formed through phase separation.We then present emerging proof-of-concept examples regarding the disruption of phase separation homeostasis in a diverse array of clinical conditions including neurodegenerative disorders,hearing loss,cancers,and immunological diseases.Finally,we describe the emerging discovery of chemical modulators of phase separation.展开更多
Aging biomarkers are a combination of biological parameters to(i)assess age-related changes,(ii)track the physiological aging process,and(iii)predict the transition into a pathological status.Although a broad spectrum...Aging biomarkers are a combination of biological parameters to(i)assess age-related changes,(ii)track the physiological aging process,and(iii)predict the transition into a pathological status.Although a broad spectrum of aging biomarkers has been developed,their potential uses and limitations remain poorly characterized.An immediate goal of biomarkers is to help us answer the following three fundamental questions in aging research:How old are we?Why do we get old?And how can we age slower?This review aims to address this need.Here,we summarize our current knowledge of biomarkers developed for cellular,organ,and organismal levels of aging,comprising six pillars:physiological characteristics,medical imaging,histological features,cellular alterations,molecular changes,and secretory factors.To fulfill all these requisites,we propose that aging biomarkers should qualify for being specific,systemic,and clinically relevant.展开更多
The clustered regularly interspaced short palindromic repeats(CRISPR)-Cas9 system has been widely used for genome engineering and transcriptional regulation in many different organisms.Current CRISPR-activation(CRISPR...The clustered regularly interspaced short palindromic repeats(CRISPR)-Cas9 system has been widely used for genome engineering and transcriptional regulation in many different organisms.Current CRISPR-activation(CRISPRa)platforms often require multiple components because of inefficient transcriptional activation.Here,we fused different phase-separation proteins to dCas9-VPR(dCas9-VP64-P65-RTA)and observed robust increases in transcriptional activation efficiency.Notably,human NUP98(nucleoporin 98)and FUS(fused in sarcoma)IDR domains were best at enhancing dCas9-VPR activity,with dCas9-VPR-FUS IDR(VPRF)outperforming the other CRISPRa systems tested in this study in both activation efficiency and system simplicity.dCas9-VPRF overcomes the target strand bias and widens gRNA designing windows without affecting the off-target effect of dCas9-VPR.These findings demonstrate the feasibility of using phase-separation proteins to assist in the regulation of gene expression and support the broad appeal of the dCas9-VPRF system in basic and clinical applications.展开更多
DearEditor,The CRISPR-mediated genome editing tools,including nucleases,base editors(ABE/CBE),transposases/recombinases,and prime editor(PE),have been extensively applied in basic and clinical researches,although the ...DearEditor,The CRISPR-mediated genome editing tools,including nucleases,base editors(ABE/CBE),transposases/recombinases,and prime editor(PE),have been extensively applied in basic and clinical researches,although the off-target effect remains a major concern(Anzalone et al.,2020).Recently,various methods have been developed to assess the specificity and accuracy of different tools(Zhang et al.,2021),yet each method is designed for limited editing systems,and none of them can simultaneously detect off-target sites in vivo and in vitro.A versatile method for profiling genome-wide off-target effects of various tools remains lacking.展开更多
β-Thalassemia is a global health issue, caused by mutations in the HBB gene. Among these mutations, HBB -28 （A〉G） mutations is one of the three most common mutations in China and Southeast Asia patients with β-th...β-Thalassemia is a global health issue, caused by mutations in the HBB gene. Among these mutations, HBB -28 （A〉G） mutations is one of the three most common mutations in China and Southeast Asia patients with β-thalassemia. Correcting this mutation in human embryos may prevent the disease being passed onto future generations and cure anemia. Here we report the first study using base editor （BE） system to correct disease mutant in human embryos. Firstly, we produced a 293T cell line with an exogenous HBB -28 （A〉G） mutant fragment for gRNAs and targeting efficiency evaluation. Then we collected primary skin fibroblast cells from a β-thalassemia patient with HBB -28 （A〉G） homozygous mutation. Data showed that base editor could precisely correct HBB -28 （A〉G） mutation in the patient＇s primary cells. To model homozygous mutation disease embryos, we consb＇ucted nuclear transfer embryos by fusing the lymphocyte or skin fibroblast cells with enucleated in vitro matured （IVM） oocytes.Notably, the gene correction efficiency was over 23.0% in these embryos by base editor. Although these embryos were still mosaic, the percentage of repaired blastomeres was over 20.0%. In addition, we found that base editor variants, with narrowed deamination window, could promote G-to-A conversion at HBB -28 site precisely in human embryos. Collectively, this study demonstrated the feasibility of curing genetic disease in human somatic cells and embryos by base editor system.展开更多
Targeted point mutagenesis through homologous recombination has been widely used in genetic studies and holds considerable promise for repairing disease- causing mutations in patients. However, problems such as mosaic...Targeted point mutagenesis through homologous recombination has been widely used in genetic studies and holds considerable promise for repairing disease- causing mutations in patients. However, problems such as mosaicism and low mutagenesis efficiency continue to pose challenges to clinical applicaUon of such approaches. Recently, a base editor （BE） system built on cytidine （C） deaminase and CRISPR/Cas9 technology was developed as an alternative method for targeted point mutagenesis in plant, yeast, and human cells. Base editors convert C in the deamination window to thymidine （T） efficiently, however, it remains unclear whether targeted base editing in mouse embryos is feasible. In this report, we generated a modified high- fidelity version of base editor 2 （HF2-BE2）, and investigated its base editing efficacy in mouse embryos. We found that HF2-BE2 could convert C to T efficiently, with up to 100% biallelic mutation efficiency in mouse embryos. Unlike BE3, HF2-BE2 could convert C to T on both the target and non-target strand, expanding the editing scope of base editors. Surprisingly, we found HF2-BE2 could also deaminate C that was proximal to the gRNA-binding region. Taken together, our work demonstrates the feasibility of generating point mutations in mouse by base editing, and underscores the need to carefully optimize base editing systems in order to eliminate proximal-site deamination.展开更多
Dear Editor,Lipid droplets(LDs)are dynamic lipid-storage organelles of storage depots and sources of essential substrates for myriad cellular processes and protect cells from lipotoxicity(Ohsaki et al.,2006).Disrupted...Dear Editor,Lipid droplets(LDs)are dynamic lipid-storage organelles of storage depots and sources of essential substrates for myriad cellular processes and protect cells from lipotoxicity(Ohsaki et al.,2006).Disrupted LD and fat storage homeostasis has been linked to metabolic diseases such as atherosclerosis,obesity,and type II diabetes(Levin et al.,2001).Structurally,the core of neutral lipids in LDs is surroun ded by a phospholipid mono layer and coated with specific proteins(Storey et al.,2011).Perilipin family of proteins are the predominant LD-associated proteins.展开更多
In mammalian cells,long noncoding RNAs(lncRNAs)form complexes with proteins to execute various biological functions such as gene transcription,RNA processing and other signaling activities.However,methods to track end...In mammalian cells,long noncoding RNAs(lncRNAs)form complexes with proteins to execute various biological functions such as gene transcription,RNA processing and other signaling activities.However,methods to track endogenous lncRNA dynamics in live cells and screen for lncRNA interacting proteins are limited.Here,we report the development of CERTIS(CRISPR-mediated Endogenous lncRNA Tracking and Immunoprecipitation System)to visualize and isolate endogenous lncRNA,by precisely inserting a 24-repeat MS2 tag into the distal end of lncRNA locus through the CRISPR7Cas9 technology.In this study,we show that CERTIS effectively labeled the paraspeckle lncRNA NEAT1 without disturbing its physiological properties and could monitor the endogenous expression variation of NEAT1.In addition,CERTIS displayed superior performance on both short-and long-term tracking of NEAT1 dynamics in live cells.We found that NEAT1 and paraspeckles were sensitive to topoisomerase I specific inhibitors.Moreover,RNA Immunoprecipitation(RIP)of the MS2-tagged NEAT1 lncRNA successfully revealed several new protein components of paraspeckle.Our results support CERTIS as a tool suitable to track both spatial and temporal lncRNA regulation in live cells as well as study the lncRNA-protein interactomes.展开更多
Pluripotent stem cells （PSCs） have the potential to pro- duce any types of cells from all three basic germ layers and the capacity to self-renew and proliferate indefinitely in vitro. The two main types of PSCs, emb...Pluripotent stem cells （PSCs） have the potential to pro- duce any types of cells from all three basic germ layers and the capacity to self-renew and proliferate indefinitely in vitro. The two main types of PSCs, embryonic stem cells （ESCs） and induced pluripotent stem cells （iPSCs）, share common features such as colony morphology, high expression of Oct4 and Nanog, and strong alkaline phosphatase activity. In recent years, increasing evi- dences suggest that telomere length represents another important internal factor in maintaining stem cell pluri- potency. Telomere length homeostasis and its structural integrity help to protect chromosome ends from recom- bination, end fusion, and DNA damage responses, ensuring the divisional ability of mammalian cells. PSCs generally exhibit high telomerase activity to maintain their extremely long and stable telomeres, and emerging data indicate the alternative lengthening of telomeres （ALT） pathway may play an important role in telomere functions too. Such characteristics are likely key to their abilities to differentiate into diverse cell types in v/vo. In this review, we will focus on the function and regulation of telomeres in ESCs and iPSCs, thereby shedding light on the importance of telomere length to pluripotency and the mechanisms that regulate telomeres in PSCs.展开更多
Understanding the regulatory networks for germ cell fate specification is necessary to developing strategies for improving the efficiency of germ cell production in vitro.In this study,we developed a coupled screening...Understanding the regulatory networks for germ cell fate specification is necessary to developing strategies for improving the efficiency of germ cell production in vitro.In this study,we developed a coupled screening strategy that took advantage of an arrayed bi-molecular fluorescence complementation(BiFC)platform for protein-protein interaction screens and epiblast-like cell(EpiLC)-induction assays using reporter mouse embryonic stem cells(mESCs).Investigation of candidate interaction partners of core human pluripotent factors OCT4,NANOG,KLF4 and SOX2 in EpiLC differentiation assays identified novel primordial germ cell(PGC)-inducing factors including BEN-domain(BEND/Bend)family members.Through RNA-seq,ChIP-seq,and ATAC-seq analyses,we showed that Bend5 worked together with Bend4 and helped mark chromatin boundaries to promote EpiLC induction in vitro.Our findings suggest that BEND/Bend proteins represent a new family of transcriptional modulators and chromatin boundary factors that participate in gene expression regulation during early germline development.展开更多
More than 32,000 pathogenic single nucleotide polymorphisms(SNPs)have been identified in the human genome(Gaudelli et al.,2017).Genetically modified mice with pathogenic SNPs are good models for studies of disease pat...More than 32,000 pathogenic single nucleotide polymorphisms(SNPs)have been identified in the human genome(Gaudelli et al.,2017).Genetically modified mice with pathogenic SNPs are good models for studies of disease pathogenesis and the development of new therapeutics.Accordingly,an efficient,high-throughput method for the generation of mouse models with SNPs is needed.展开更多
Mammalian spermatogenesis is maintained by a rare population of spermatogonial stem cells(SSCs),which are important for male fertility. SSCs remain a subset of undifferentiated spermatogonia, which can be isolated by ...Mammalian spermatogenesis is maintained by a rare population of spermatogonial stem cells(SSCs),which are important for male fertility. SSCs remain a subset of undifferentiated spermatogonia, which can be isolated by a combination of surface markers. Specific markers to identify and isolate undifferentiated spermatogonia are lacking. Ussp1, a transcript previously annotated as long noncoding RNA(RIKEN cDNA 4933427D06, Gene ID: 232217), virtually encodes a membrane protein, USSP1, in a highly testisspecific manner in mouse. We demonstrate its expression on the membrane of undifferentiated spermatogonia by a homemade polyclonal rabbit antibody against the protein. In vivo, USSP1^+ clusters consist mainly of As, Apr(GFRa1^+) and Aal(PLZF^+) cells. USSP1^+ cells exhibit enrichment of undifferentiated spermatogonia, as shown by increased expression of SSC self-renewal molecular markers and the potential to form SSC clones in vitro and in vivo. However, Ussp1 knockout did not affect the number of SSCs or spermatogenesis in mice. Thy1^+ cells from Ussp1 null mice did not show any defect in the SSC colony formation capacity, indicating that USSP1 is not essential for SSC self-renewal. Our data demonstrate that Ussp1 is specifically expressed in undifferentiated murine spermatogonia, indicating the potential to sort undifferentiated spermatogonia with USSP1 antibodies. Ussp1 might be a good maker for SSC enrichment in neonatal mice.展开更多
Dear Editor, Many human genetic diseases are caused by pathogenic single nucleotide mutations. Animal models are often used to study these diseases where the pathogenic point mutations are created and/or corrected thr...Dear Editor, Many human genetic diseases are caused by pathogenic single nucleotide mutations. Animal models are often used to study these diseases where the pathogenic point mutations are created and/or corrected through gene editing （e.g., the CRISPP-JCas9 system） （Komor et al., 2017; Liang et al., 2017）. CRISPR/Cas9-mediated gene editing depends on DNA double-strand breaks （DSBs）, which can be of low efficiency and lead to indels and off-target cleavage （Kim et al., 2016）. We and others have shown that base editors （BEs） may represent an attractive alternative for disease mouse model generation （Liang et al., 2017; Kim et al., 2017）. Compared to CRISPR/ Cas9, cytidine base editors （CBEs） can generate C·G to T·A mutations in mouse zygotes without activating DSB repair pathways （Liang et al., 2017; Kim et al., 2017; Komor et al., 2016）. In addition, CBEs showed much lower off-targets than CRISPR]Cas9 （Kim et al., 2017）, making the editing process potentially safer and more controllable. Recently, adenine base editors （ABEs） that were developed from the tRNA- specific adenosine deaminase （TADA） of Escherichia coli were also reported （Gaudelli et al., 2017）. As a RNA-guided programmable adenine deaminase, ABE can catalyze the conversion of A to I. Following DNA replication, base I is replaced by G, resulting in A·T to G·C conversion （Gaudelli et al., 2017; Hu et al., 2018）. The development of ABEs has clearly expanded the editing capacity and application of BEs. Here, we tested whether ABEs could effectively generate disease mouse models, and found high efficiency by ABEs in producing edited mouse zygotes and mice with single-nucleotide substitutions.展开更多
Dear Editor： Gao et al. published data in Nature Biotechnology （Nat Biotechnol. 2016 May 2） showing that DNA-guided genome editing using the Natronobacterium gregoryi Argonaute （NgAgo） protein targeted 47 mammali...Dear Editor： Gao et al. published data in Nature Biotechnology （Nat Biotechnol. 2016 May 2） showing that DNA-guided genome editing using the Natronobacterium gregoryi Argonaute （NgAgo） protein targeted 47 mammalian genomic loci with a 100% success rate and an efficiency of 21.3%-41.3% at various targets. This report led us to test NgAgo＇s utility in various cells and organisms such as mouse and zebrafish for gene editing.展开更多
Pluripotent stem cells(PSCs)such as embryonic stem cells(ESCs),ESCs derived by somatic cell nuclear transfer(ntESCs),and induced pluripotent stem cells(iPSCs)have unlimited capacity for self-renewal and pluripotency a...Pluripotent stem cells(PSCs)such as embryonic stem cells(ESCs),ESCs derived by somatic cell nuclear transfer(ntESCs),and induced pluripotent stem cells(iPSCs)have unlimited capacity for self-renewal and pluripotency and can give rise to all types of somatic cells.In order to maintain their self-renewal and pluripotency,PSCs need to preserve their telomere length and homeostasis.In recent years,increasing studies have shown that telomere reprogramming is essential for stem cell pluripotency maintenance and its induced pluripotency process.Telomere-associated proteins are not only required for telomere maintenance in both stem cells,their extra-telomeric functions have also been found to be critical as well.Here,we will discuss how telomeres and telomere-associated factors participate and regulate the maintenance of stem cell pluripotency.展开更多
基金National Natural Science Foundation(Grant Nos.82271598,81871109,82071587,31930058,32330023 and 32170757)National Key Research and Development Program of China(2018YFA0107003)Guang Dong Basic and Applied Basic Research Foundation(2020A1515010462).
文摘Telomeres are specialized structures at the ends of linear chromosomes that protect genome stability.The telomeric repeat-containing RNA(TERRA)that is transcribed from subtelomeric regions can invade into double-stranded DNA regions and form RNA:DNA hybrid-containing structure called R-loop.In tumor cells,R-loop formation is closely linked to gene expression and the alternative lengthening of telomeres(ALT)pathway.Dysregulated R-loops can cause stalled replication forks and telomere instability.However,how R-loops are recognized and regulated,particularly at telomeres,is not well understood.We discovered that ILF3 selectively associates with telomeric R-loops and safeguards telomeres from abnormal homologous recombination.Knocking out ILF3 results in excessive R-loops at telomeres and triggers telomeric DNA damage responses.In addition,ILF3 deficiency disrupts telomere homeostasis and causes abnormalities in the ALT pathway.Using the proximity-dependent biotin identification(BioID)technology,we mapped the ILF3 interactome and discovered that ILF3 could interact with several DNA/RNA helicases,including DHX9.Importantly,ILF3 may aid in the resolution of telomeric R-loops through its interaction with DHX9.Our findings suggest that ILF3 may function as a reader of telomeric R-loops,helping to prevent abnormal homologous recombination and maintain telomere homeostasis.
基金supported by grants from the Strategic Priority Research Program of the Chinese Academy of Sciences(XDB0480000)the National Key Research and Development Program of China(2022YFA1103800,2022YFA1303100,2023YFE0210100)+10 种基金the National Natural Science Foundation of China(22337005,22377119,32025010,32241002,32270812,32270920,32325016,32350024,32261160376,82150003,82188101,82325016,92157202,92254301,T2325003)STI2030-Major Projects(2021ZD0202501)the Science and Technology Commission of Shanghai Municipality(2019SHZDZX02,20490712600)the Key Research Program CAS(ZDBS-ZRKJZ-TLC003)International Cooperation Program CAS(154144KYSB20200006)CAS Project for Young Scientists in Basic Research(YSBR-075)Guangdong Province Science and Technology Program(2023B1111050005,2023B1212060050)Natural Science Foundation of Anhui Province(2108085J12)Center for Advanced Interdisciplinary Science and Biomedicine of IHM(QYPY20220008)Shenzhen Talent Program(KQTD20210811090115021)Guangdong Innovative and Entrepreneurial Research Team Program(2021ZT09Y104)。
文摘Biomolecular condensates or membraneless organelles(MLOs)formed by liquid-liquid phase separation(LLPS)divide intracellular spaces into discrete compartments for specific functions.Dysregulation of LLPS or aberrant phase transition that disturbs the formation or material states of MLOs is closely correlated with neurodegeneration,tumorigenesis,and many other pathological processes.Herein,we summarize the recent progress in development of methods to monitor phase separation and we discuss the biogenesis and function of MLOs formed through phase separation.We then present emerging proof-of-concept examples regarding the disruption of phase separation homeostasis in a diverse array of clinical conditions including neurodegenerative disorders,hearing loss,cancers,and immunological diseases.Finally,we describe the emerging discovery of chemical modulators of phase separation.
基金supported by the National Natural Science Foundation of China(31730036,31871380,31871382,31930055,31930058,32000500,32022034,32030033,32070730,32130046,3217050247,32150005,32200595,32222024,81730019,81730022,81830014,81921006,81925005,81970426,81971301,81971312,82030041,82061160495,82070805,82071595,82090020,82100841,82120108009,82122024,82125002,82125011,82125012,82130045,82171284,82173061,82173398,82225007,82225015,82225017,82225018,82230047,82230088,82271600,91949106,91949201,92049116,92049302,92049304,92149303,92149306,92157202,92168201,92169102,92249301,92268201)the National Key Research and Development Program of China(2018YFA0800700,2018YFC2000100,2018YFC2000102,2018YFC2002003,2019YFA0110900,2019YFA0801703,2019YFA0801903,2019YFA0802202,2019YFA0904800,2020YFA0113400,2020YFA0803401,2020YFA0804000,2020YFC2002900,2020YFC2008000,2020YFE0202200,2021YFA0804900,2021YFA1100103,2021YFA1100900,2021YFE0114200,2021ZD0202400,2022YFA0806001,2022YFA0806002,2022YFA0806600,2022YFA1103200,2022YFA1103601,2022YFA1103701,2022YFA1103800,2022YFA1103801,2022YFA1104100,2022YFA1104904,2022YFA1303000,2022YFC2009900,2022YFC2502401,2022YFC3602400,2022YFE0118000,2022ZD0213200)+14 种基金the Strategic Priority Research Program of the Chinese Academy of Sciences(XDA16030302,XDB39000000,XDB39030600)the Youth Innovation Promotion Association of Chinese Academy of Sciences(2020085,2021080)CAS Project for Young Scientists in Basic Research(YSBR-076)the Program of the Beijing Natural Science Foundation(JQ20031)Clinical Research Operating Fund of Central High level hospitals(2022-PUMCHE-001)CAMS Innovation Fund for Medical Sciences(CIFMS)(2022-I2M1-004)Talent Program of the Chinese Academy of Medical Science(2022RC310-10)Research Funds from Health@Inno HK Program launched by Innovation Technology Commission of the Hong Kong Special Administrative Region,Guangdong Basic and Applied Basic Research Foundation(2020B1515020044)Guangzhou Planned Project of Science and Technology(202002020039)the Major Technology Innovation of Hubei Province(2019ACA141)the Science and Technology Major Project of Hunan Provincial Science and Technology Department(2021SK1010)Shanghai Municipal Science and Technology Major Project(2017SHZDZX01)the Natural Science Foundation of Sichuan Province(2023NSFSC0003)Yunnan Fundamental Research Project(202201AS070080)the State Key Laboratory of Membrane Biology。
文摘Aging biomarkers are a combination of biological parameters to(i)assess age-related changes,(ii)track the physiological aging process,and(iii)predict the transition into a pathological status.Although a broad spectrum of aging biomarkers has been developed,their potential uses and limitations remain poorly characterized.An immediate goal of biomarkers is to help us answer the following three fundamental questions in aging research:How old are we?Why do we get old?And how can we age slower?This review aims to address this need.Here,we summarize our current knowledge of biomarkers developed for cellular,organ,and organismal levels of aging,comprising six pillars:physiological characteristics,medical imaging,histological features,cellular alterations,molecular changes,and secretory factors.To fulfill all these requisites,we propose that aging biomarkers should qualify for being specific,systemic,and clinically relevant.
基金supported by the National Key Research and Development Program of China(2017YFA0102801)the National Natural Science Foundation of China(91640119,81330055,and 32001063)+2 种基金the Guangdong Special Support Program(2019BT02Y276)the Natural Science Foundation of Guangdong Province(2023A1515010176)the Guangzhou Science and Technology Program key projects(2023A04J1952)。
文摘The clustered regularly interspaced short palindromic repeats(CRISPR)-Cas9 system has been widely used for genome engineering and transcriptional regulation in many different organisms.Current CRISPR-activation(CRISPRa)platforms often require multiple components because of inefficient transcriptional activation.Here,we fused different phase-separation proteins to dCas9-VPR(dCas9-VP64-P65-RTA)and observed robust increases in transcriptional activation efficiency.Notably,human NUP98(nucleoporin 98)and FUS(fused in sarcoma)IDR domains were best at enhancing dCas9-VPR activity,with dCas9-VPR-FUS IDR(VPRF)outperforming the other CRISPRa systems tested in this study in both activation efficiency and system simplicity.dCas9-VPRF overcomes the target strand bias and widens gRNA designing windows without affecting the off-target effect of dCas9-VPR.These findings demonstrate the feasibility of using phase-separation proteins to assist in the regulation of gene expression and support the broad appeal of the dCas9-VPRF system in basic and clinical applications.
基金supported by the Ministry of Science and Technology of China to G.Z.L.(National Science and Technology Major Project,grant nos.2018YFA0109100,2019YFA0802203)National Natural Science Foundation of China to G.z.L.(Grant Nos.31922015,31870808,91753129)+1 种基金Natural Science Foundation of Guangdong Province to G.Z.L.(Grant No.2018B030306044)Guangdong Special Support Program to P.L.(2019BT02Y276).
文摘DearEditor,The CRISPR-mediated genome editing tools,including nucleases,base editors(ABE/CBE),transposases/recombinases,and prime editor(PE),have been extensively applied in basic and clinical researches,although the off-target effect remains a major concern(Anzalone et al.,2020).Recently,various methods have been developed to assess the specificity and accuracy of different tools(Zhang et al.,2021),yet each method is designed for limited editing systems,and none of them can simultaneously detect off-target sites in vivo and in vitro.A versatile method for profiling genome-wide off-target effects of various tools remains lacking.
基金We are grateful to Dr. Qi Zhou for helpful suggestions. This work was supported by National Key R＆D Program of China （2017YFC1001901 and 2017YFC1001600）, the Science and Technology Planning Project of Guangdong Province （2015B020228002）, the Guangzhou Science and Technology Project （201707010085） and the National Natural Science Foundation of China （Grant No. 81771579）.
文摘β-Thalassemia is a global health issue, caused by mutations in the HBB gene. Among these mutations, HBB -28 （A〉G） mutations is one of the three most common mutations in China and Southeast Asia patients with β-thalassemia. Correcting this mutation in human embryos may prevent the disease being passed onto future generations and cure anemia. Here we report the first study using base editor （BE） system to correct disease mutant in human embryos. Firstly, we produced a 293T cell line with an exogenous HBB -28 （A〉G） mutant fragment for gRNAs and targeting efficiency evaluation. Then we collected primary skin fibroblast cells from a β-thalassemia patient with HBB -28 （A〉G） homozygous mutation. Data showed that base editor could precisely correct HBB -28 （A〉G） mutation in the patient＇s primary cells. To model homozygous mutation disease embryos, we consb＇ucted nuclear transfer embryos by fusing the lymphocyte or skin fibroblast cells with enucleated in vitro matured （IVM） oocytes.Notably, the gene correction efficiency was over 23.0% in these embryos by base editor. Although these embryos were still mosaic, the percentage of repaired blastomeres was over 20.0%. In addition, we found that base editor variants, with narrowed deamination window, could promote G-to-A conversion at HBB -28 site precisely in human embryos. Collectively, this study demonstrated the feasibility of curing genetic disease in human somatic cells and embryos by base editor system.
基金This work was supported by the National Natural Science Foundation of China （Grant Nos. 91640119, 31601196, 81330055, 31371508, and 31671540）, the Natural Science Foundation of Guangdong Province （2016A030310206 and 2014A030312011）, the Science and Technology Planning Project of Guangdong Province （2015B020228002 and 2015A020212005）, the Guangzhou Science and Technology Project （201605030012 and 201707010085）, and the Fundamental Research Funds for the Central Universities （161gzd13 and 161gpy31）. We would also like to acknowledge the support of CA211653, CPRIT RP160462, the Welch Foundation Q-1673, and the C-BASS Shared Resource at the Dan L. Duncan Cancer Center （DLDCC） of Baylor College of Medicine （P30CA125123）.
文摘Targeted point mutagenesis through homologous recombination has been widely used in genetic studies and holds considerable promise for repairing disease- causing mutations in patients. However, problems such as mosaicism and low mutagenesis efficiency continue to pose challenges to clinical applicaUon of such approaches. Recently, a base editor （BE） system built on cytidine （C） deaminase and CRISPR/Cas9 technology was developed as an alternative method for targeted point mutagenesis in plant, yeast, and human cells. Base editors convert C in the deamination window to thymidine （T） efficiently, however, it remains unclear whether targeted base editing in mouse embryos is feasible. In this report, we generated a modified high- fidelity version of base editor 2 （HF2-BE2）, and investigated its base editing efficacy in mouse embryos. We found that HF2-BE2 could convert C to T efficiently, with up to 100% biallelic mutation efficiency in mouse embryos. Unlike BE3, HF2-BE2 could convert C to T on both the target and non-target strand, expanding the editing scope of base editors. Surprisingly, we found HF2-BE2 could also deaminate C that was proximal to the gRNA-binding region. Taken together, our work demonstrates the feasibility of generating point mutations in mouse by base editing, and underscores the need to carefully optimize base editing systems in order to eliminate proximal-site deamination.
基金the National Key Research and Development Program of China(2017YFA0102801,2018YFA0107 003)National Natural Science Foundation of China(Grant Nos.91640119,91749113,81330055,31570827 and 31871479)+6 种基金Guangzhou Science and Technology Project(201605030012)Natural Science Foundation of Guangdong Province(2017A03031 3116)Guangdong Science and Technology Department Planning Project(2015B020228002)the NIH(HL131744 and CA211653)the Welch Foundation(Q-1673 and I-1441)CPRITRP160462the C-BASS Shared Resource at the Dan L.Duncan Cancer Center(DLDCC)of Baylor College of Medicine(P30CA125123).
文摘Dear Editor,Lipid droplets(LDs)are dynamic lipid-storage organelles of storage depots and sources of essential substrates for myriad cellular processes and protect cells from lipotoxicity(Ohsaki et al.,2006).Disrupted LD and fat storage homeostasis has been linked to metabolic diseases such as atherosclerosis,obesity,and type II diabetes(Levin et al.,2001).Structurally,the core of neutral lipids in LDs is surroun ded by a phospholipid mono layer and coated with specific proteins(Storey et al.,2011).Perilipin family of proteins are the predominant LD-associated proteins.
基金This work was supported by the National Key Research and Development Program of China(2017YFA0102801,2018YFA0107003)National Natural Science Foundation of China(91640119,91749113,31570827,31871479 and 31930058)+1 种基金Natural Science Foundation of Guangdong Province(2017A030313116)the China Postdoctoral Science Foundation(2018M631021).
文摘In mammalian cells,long noncoding RNAs(lncRNAs)form complexes with proteins to execute various biological functions such as gene transcription,RNA processing and other signaling activities.However,methods to track endogenous lncRNA dynamics in live cells and screen for lncRNA interacting proteins are limited.Here,we report the development of CERTIS(CRISPR-mediated Endogenous lncRNA Tracking and Immunoprecipitation System)to visualize and isolate endogenous lncRNA,by precisely inserting a 24-repeat MS2 tag into the distal end of lncRNA locus through the CRISPR7Cas9 technology.In this study,we show that CERTIS effectively labeled the paraspeckle lncRNA NEAT1 without disturbing its physiological properties and could monitor the endogenous expression variation of NEAT1.In addition,CERTIS displayed superior performance on both short-and long-term tracking of NEAT1 dynamics in live cells.We found that NEAT1 and paraspeckles were sensitive to topoisomerase I specific inhibitors.Moreover,RNA Immunoprecipitation(RIP)of the MS2-tagged NEAT1 lncRNA successfully revealed several new protein components of paraspeckle.Our results support CERTIS as a tool suitable to track both spatial and temporal lncRNA regulation in live cells as well as study the lncRNA-protein interactomes.
文摘Pluripotent stem cells （PSCs） have the potential to pro- duce any types of cells from all three basic germ layers and the capacity to self-renew and proliferate indefinitely in vitro. The two main types of PSCs, embryonic stem cells （ESCs） and induced pluripotent stem cells （iPSCs）, share common features such as colony morphology, high expression of Oct4 and Nanog, and strong alkaline phosphatase activity. In recent years, increasing evi- dences suggest that telomere length represents another important internal factor in maintaining stem cell pluri- potency. Telomere length homeostasis and its structural integrity help to protect chromosome ends from recom- bination, end fusion, and DNA damage responses, ensuring the divisional ability of mammalian cells. PSCs generally exhibit high telomerase activity to maintain their extremely long and stable telomeres, and emerging data indicate the alternative lengthening of telomeres （ALT） pathway may play an important role in telomere functions too. Such characteristics are likely key to their abilities to differentiate into diverse cell types in v/vo. In this review, we will focus on the function and regulation of telomeres in ESCs and iPSCs, thereby shedding light on the importance of telomere length to pluripotency and the mechanisms that regulate telomeres in PSCs.
基金the National Key R&D Program of China(2017YFA0102801)The National Natural Science Foundation of China(Grant Nos.31930058,31671540,32170802,and 31301082)+1 种基金Natural Science Foundation of Guangdong Province(2015B020228002,2017A030313093)Guangdong Basic and Applied Basic Research Foundation(2019A1515011422,2021A1515010759).
文摘Understanding the regulatory networks for germ cell fate specification is necessary to developing strategies for improving the efficiency of germ cell production in vitro.In this study,we developed a coupled screening strategy that took advantage of an arrayed bi-molecular fluorescence complementation(BiFC)platform for protein-protein interaction screens and epiblast-like cell(EpiLC)-induction assays using reporter mouse embryonic stem cells(mESCs).Investigation of candidate interaction partners of core human pluripotent factors OCT4,NANOG,KLF4 and SOX2 in EpiLC differentiation assays identified novel primordial germ cell(PGC)-inducing factors including BEN-domain(BEND/Bend)family members.Through RNA-seq,ChIP-seq,and ATAC-seq analyses,we showed that Bend5 worked together with Bend4 and helped mark chromatin boundaries to promote EpiLC induction in vitro.Our findings suggest that BEND/Bend proteins represent a new family of transcriptional modulators and chromatin boundary factors that participate in gene expression regulation during early germline development.
基金supported by the National Key R&D Program of China(2017YFC1001901,2017YFA0102801 and 2017YFC1001603)the National Natural Science Foundation of China(91640119,31671540,81330055 and 31601196)+3 种基金the Guangdong Special Support Program(2019BT02Y276)the Natural Science Foundation of Guangdong Province(2016A030310206 and 2014A030312011)the Science and Technology Planning Project of Guangdong Province(2015B020228002)the Guangzhou Science and Technology Project(201707010085 and 201803010020)。
文摘More than 32,000 pathogenic single nucleotide polymorphisms(SNPs)have been identified in the human genome(Gaudelli et al.,2017).Genetically modified mice with pathogenic SNPs are good models for studies of disease pathogenesis and the development of new therapeutics.Accordingly,an efficient,high-throughput method for the generation of mouse models with SNPs is needed.
基金supported by the National Key Research and Development Program of China (2017YFA0102801 and 2017YFC1001901)the Science and Technology Planning Project of Guangdong Province (2015B020228002)+2 种基金the National Natural Science Foundation of China (31671540)the Natural Science Foundation of Guangdong Province (2015A020212005 and 2014A030312011)the Guangzhou Science and Technology Project (201803010020)
文摘Mammalian spermatogenesis is maintained by a rare population of spermatogonial stem cells(SSCs),which are important for male fertility. SSCs remain a subset of undifferentiated spermatogonia, which can be isolated by a combination of surface markers. Specific markers to identify and isolate undifferentiated spermatogonia are lacking. Ussp1, a transcript previously annotated as long noncoding RNA(RIKEN cDNA 4933427D06, Gene ID: 232217), virtually encodes a membrane protein, USSP1, in a highly testisspecific manner in mouse. We demonstrate its expression on the membrane of undifferentiated spermatogonia by a homemade polyclonal rabbit antibody against the protein. In vivo, USSP1^+ clusters consist mainly of As, Apr(GFRa1^+) and Aal(PLZF^+) cells. USSP1^+ cells exhibit enrichment of undifferentiated spermatogonia, as shown by increased expression of SSC self-renewal molecular markers and the potential to form SSC clones in vitro and in vivo. However, Ussp1 knockout did not affect the number of SSCs or spermatogenesis in mice. Thy1^+ cells from Ussp1 null mice did not show any defect in the SSC colony formation capacity, indicating that USSP1 is not essential for SSC self-renewal. Our data demonstrate that Ussp1 is specifically expressed in undifferentiated murine spermatogonia, indicating the potential to sort undifferentiated spermatogonia with USSP1 antibodies. Ussp1 might be a good maker for SSC enrichment in neonatal mice.
文摘Dear Editor, Many human genetic diseases are caused by pathogenic single nucleotide mutations. Animal models are often used to study these diseases where the pathogenic point mutations are created and/or corrected through gene editing （e.g., the CRISPP-JCas9 system） （Komor et al., 2017; Liang et al., 2017）. CRISPR/Cas9-mediated gene editing depends on DNA double-strand breaks （DSBs）, which can be of low efficiency and lead to indels and off-target cleavage （Kim et al., 2016）. We and others have shown that base editors （BEs） may represent an attractive alternative for disease mouse model generation （Liang et al., 2017; Kim et al., 2017）. Compared to CRISPR/ Cas9, cytidine base editors （CBEs） can generate C·G to T·A mutations in mouse zygotes without activating DSB repair pathways （Liang et al., 2017; Kim et al., 2017; Komor et al., 2016）. In addition, CBEs showed much lower off-targets than CRISPR]Cas9 （Kim et al., 2017）, making the editing process potentially safer and more controllable. Recently, adenine base editors （ABEs） that were developed from the tRNA- specific adenosine deaminase （TADA） of Escherichia coli were also reported （Gaudelli et al., 2017）. As a RNA-guided programmable adenine deaminase, ABE can catalyze the conversion of A to I. Following DNA replication, base I is replaced by G, resulting in A·T to G·C conversion （Gaudelli et al., 2017; Hu et al., 2018）. The development of ABEs has clearly expanded the editing capacity and application of BEs. Here, we tested whether ABEs could effectively generate disease mouse models, and found high efficiency by ABEs in producing edited mouse zygotes and mice with single-nucleotide substitutions.
文摘Dear Editor： Gao et al. published data in Nature Biotechnology （Nat Biotechnol. 2016 May 2） showing that DNA-guided genome editing using the Natronobacterium gregoryi Argonaute （NgAgo） protein targeted 47 mammalian genomic loci with a 100% success rate and an efficiency of 21.3%-41.3% at various targets. This report led us to test NgAgo＇s utility in various cells and organisms such as mouse and zebrafish for gene editing.
基金supported by National Natural Science Foundation of China(Grant Nos.81871109,31401223,81330055,31570827,91749113,91640119 and 31871479)National Key Research and Development Program of China(2017YFA0102801,2018YFA0107003)Natural Science Foundation of Guangdong Province(2017A030313116).
文摘Pluripotent stem cells(PSCs)such as embryonic stem cells(ESCs),ESCs derived by somatic cell nuclear transfer(ntESCs),and induced pluripotent stem cells(iPSCs)have unlimited capacity for self-renewal and pluripotency and can give rise to all types of somatic cells.In order to maintain their self-renewal and pluripotency,PSCs need to preserve their telomere length and homeostasis.In recent years,increasing studies have shown that telomere reprogramming is essential for stem cell pluripotency maintenance and its induced pluripotency process.Telomere-associated proteins are not only required for telomere maintenance in both stem cells,their extra-telomeric functions have also been found to be critical as well.Here,we will discuss how telomeres and telomere-associated factors participate and regulate the maintenance of stem cell pluripotency.
