【目的】基于猪极端饲料报酬表型,利用靶向切割标签技术(cleavage under targets and tagmentation,CUT&Tag)构建H3K27ac差异图谱,鉴定关联的启动子、增强子和关联候选基因,为猪饲料报酬解析提供基础数据。【方法】从209头杜洛克猪...【目的】基于猪极端饲料报酬表型,利用靶向切割标签技术(cleavage under targets and tagmentation,CUT&Tag)构建H3K27ac差异图谱,鉴定关联的启动子、增强子和关联候选基因,为猪饲料报酬解析提供基础数据。【方法】从209头杜洛克猪中筛选饲料报酬表型差异最大的4头个体分别组成低剩余采食量组(L组,n=2)和高剩余采食量组(H组,n=2)。利用CUT&Tag技术,以H3K27ac作为活性启动子和增强子的表观遗传标记对4头个体的肝脏组织进行全基因组扫描,鉴定关联启动子、增强子和候选基因,并进一步采用real-time quantitative PCR(RT-qPCR)对重要基因进行验证。【结果】共鉴定出47271个H3K27ac峰,包括15739个潜在启动子和31532个推定增强子,大部分的H3K27ac峰位于近端启动子区域。根据H3K27ac全基因的分布情况和作用特点,发现3087个差异峰(对应2188个基因),其中867个H3K27ac峰(对应664个基因)富集在H组,2220个H3K27ac峰(对应1575个基因)富集在L组。GO和KEGG结果发现H3K27ac增强子可能是通过影响胆汁酸代谢、淋巴细胞代谢和NF-κB通路来调节饲料报酬。RT-qPCR结果显示,与H组相比,DIAPH3、DPYD、FTO、TCF7L2、ABCC2、ABCC11、RXRA和ABCG8在L组中显著上调(P<0.05),而PAX5、GRHPR、NFATC1、CARD11、BLNK和LYN在L组中显著下调(P<0.05)。【结论】本研究成功生成了具有极端RFI差异的杜洛克猪肝脏组织中的H3K27ac差异图谱以及相关数据。基于该图谱鉴定和验证了关联候选基因,为进一步解析启动子和增强子调控饲料报酬的分子机制提供了基础数据。展开更多
新兴的染色质靶向切割和标签化(clevage under target and tagment,CUT&Tag)技术利用转座酶在目标蛋白结合的DNA附近进行切割并对切割下的DNA片段进行标签化,通过后续的二代测序可以快速鉴定蛋白质-DNA相互作用,极大的简化了染色质...新兴的染色质靶向切割和标签化(clevage under target and tagment,CUT&Tag)技术利用转座酶在目标蛋白结合的DNA附近进行切割并对切割下的DNA片段进行标签化,通过后续的二代测序可以快速鉴定蛋白质-DNA相互作用,极大的简化了染色质免疫共沉淀测序(chromatin immunoprecipitation sequencing,ChIP-seq)的实验过程。CUT&Tag中转座酶完成标签化后需要DNA回收或其他后处理才能进行建库PCR,不同的回收方法对CUT&Tag结果有着显著的影响。通过建立生物素化转座体-链霉亲和素磁珠体系(streptavidin beads recovery CUT&Tag,srCUT&Tag),可以快速便捷地完成CUT&Tag的产物回收。本文在K562细胞中展开H3K4me3、RNA聚合酶Ⅱ(RNA polymeraseⅡ,RNAPⅡ)、转录因子CTCF和HMGA1的CUT&Tag实验,并利用现有的乙醇沉淀、片段分选(solid-phase reversible immobilization,SPRI)磁珠回收和直接PCR法,以及本研究建立的srCUT&Tag方法对产物进行回收。结果表明,从整体上看,SPRI磁珠回收和srCUT&Tag方法着较高的回收效率,而乙醇沉淀法则回收效率低下。在全部4种CUT&Tag产物回收过程中,SPRI磁珠回收均会损失大部分小于150 bp的产物片段。在CTCF和HMGA1 CUT&Tag产物的回收中,直接PCR法则损失了大部分大于300 bp的片段并与其他回收方法的结果有较大的差别。因此,srCUT&Tag能够比其他三种回收方法提供更多更完整的测序信息。综上所述,新建立srCUT&Tag回收方法相比现有的CUT&Tag产物回收方法能提高建库效率并得到更好的数据质量,为表观遗传学研究提供了更好的技术选择。展开更多
染色体靶向切割和标签化(clevage under target and tagment,CUT&Tag)技术利用Tn5转座酶与Protein A/G的融合蛋白,引导Tn5酶至与靶蛋白结合的抗体附近,对靶蛋白结合的附近染色质区域进行切割,随后通过标签化处理对片段化染色质进行...染色体靶向切割和标签化(clevage under target and tagment,CUT&Tag)技术利用Tn5转座酶与Protein A/G的融合蛋白,引导Tn5酶至与靶蛋白结合的抗体附近,对靶蛋白结合的附近染色质区域进行切割,随后通过标签化处理对片段化染色质进行文库制备,并利用高通量测序技术获取特定位点或蛋白质结合位置的染色质信息。CUT&Tag技术在蛋白质和DNA相互作用的研究领域起到了重大作用,不仅可以了解组蛋白修饰发生的位置,而且可以明确转录因子结合的区域。相较于传统的染色质免疫沉淀高通量测序(chromatin immunoprecipitation-sequencing,ChIP-seq)技术,CUT&Tag技术具有信噪比高、可重复性好、实验周期短、细胞投入量低等优点,在早期胚胎发育、干细胞、肿瘤以及表观遗传学等研究领域体现出巨大优势。本文将针对CUT&Tag在代谢组织细胞(以小鼠原代胰岛细胞为例)的具体操作步骤进行描述,以提供一种研究代谢细胞的表观遗传学方法。展开更多
Tn5是一种细菌转座子。经改造的Tn5能够高效地切割DNA,同时连接上特定的接头序列,因而广泛应用于高通量二代测序文库构建中。CUT&Tag(Cleavage Under Target&Tagmentation)是一种改进的研究蛋白质与DNA互作的技术,具有重复性好...Tn5是一种细菌转座子。经改造的Tn5能够高效地切割DNA,同时连接上特定的接头序列,因而广泛应用于高通量二代测序文库构建中。CUT&Tag(Cleavage Under Target&Tagmentation)是一种改进的研究蛋白质与DNA互作的技术,具有重复性好、信噪比高及操作简便等优点。该技术采用pA(Protein A)或pG(Protein G)与Tn5形成融合蛋白,定位于特定抗体(用于识别目标蛋白),利用Tn5的特性,在目标位点附近打断DNA的同时引入测序接头,随后提取DNA,再进行PCR扩增即可获得测序文库。但不同类型的抗体与pA或pG的亲和力不同,因此限制了部分抗体在CUT&Tag技术中的应用。为克服这一局限,该文构建了pG与Tn5的融合蛋白表达载体,通过原核表达及亲和纯化的方式获得pG-Tn5重组蛋白;并以RNA聚合酶Ⅱ(PolⅡ)特异性抗体PolⅡSer5P(小鼠IgG1型抗体和兔IgG型抗体)为例,在模式植物拟南芥(Arabidopsis thaliana)中评估pA-Tn5与pG-Tn5在不同类型抗体的CUT&Tag测序文库构建中的效果。结果表明,IgG1型抗体与p G-Tn5的亲和力更高,构建的文库质量更好,而IgG型抗体与2种酶的亲和力相当;同时,较低起始量的植物材料也能获得较好的效果,证明了CUT&Tag的应用优势。该研究优化了CUT&Tag技术,可为后续CUT&Tag实验中针对不同抗体时Tn5融合蛋白的选择提供参考。展开更多
Maize ear development determines the crop yield,and many important transcription factors(TFs)have been identified to function in this process.However,their transcriptional regulation mechanisms are still elusive.In th...Maize ear development determines the crop yield,and many important transcription factors(TFs)have been identified to function in this process.However,their transcriptional regulation mechanisms are still elusive.In this study,we generated the genome-wide DNA binding sites for 8 TFs which are known to function or highly expressed in inflorescence by applying the ts CUT&Tag method in maize leaf protoplast.We exposed a regulatory grid of 4 WUSCHEL-related homeobox(WOX)genes and revealed their potential regulatory mechanisms.In addition,a hierarchical regulation network for the determinacy and specification of maize inflorescence meristems were also constructed using the binding profiles of a floral development gene INDETERMINATE FLORAL APEX1(IFA1)and 3 MADS-box genes.Our study provides an in-depth understanding and new insights of the regulatory mechanisms during maize inflorescence development.展开更多
Efficient and reliable profiling methods are essential to study epigenetics.Tn5,one of the first identified prokaryotic transposases with high DNA-binding and tagmentation efficiency,is widely adopted in different gen...Efficient and reliable profiling methods are essential to study epigenetics.Tn5,one of the first identified prokaryotic transposases with high DNA-binding and tagmentation efficiency,is widely adopted in different genomic and epigenomic protocols for high-throughputly exploring the genome and epigenome.Based on Tn5,the Assay for Transposase-Accessible Chromatin using sequencing(ATAC-seq)and the Cleavage Under Targets and Tagmentation(CUT&Tag)were developed to measure chromatin accessibility and detect DNA–protein interactions.These methodologies can be applied to large amounts of biological samples with low-input levels,such as rare tissues,embryos,and sorted single cells.However,fast and proper processing of these epigenomic data has become a bottleneck because massive data production continues to increase quickly.Furthermore,inappropriate data analysis can generate biased or misleading conclusions.Therefore,it is essential to evaluate the performance of Tn5-based ATAC-seq and CUT&Tag data processing bioinformatics tools,many of which were developed mostly for analyzing chromatin immunoprecipitation followed by sequencing(ChIP-seq)data.Here,we conducted a comprehensive benchmarking analysis to evaluate the performance of eight popular software for processing ATAC-seq and CUT&Tag data.We compared the sensitivity,specificity,and peak width distribution for both narrow-type and broad-type peak calling.We also tested the influence of the availability of control IgG input in CUT&Tag data analysis.Finally,we evaluated the differential analysis strategies commonly used for analyzing the CUT&Tag data.Our study provided comprehensive guidance for selecting bioinformatics tools and recommended analysis strategies,which were implemented into Docker/Singularity images for streamlined data analysis.展开更多
Knowledge of the transcription factor binding landscape(TFBL)is necessary to analyze gene regulatory networks for important agronomic traits.However,a low-cost and high-throughput in vivo chromatin profiling method is...Knowledge of the transcription factor binding landscape(TFBL)is necessary to analyze gene regulatory networks for important agronomic traits.However,a low-cost and high-throughput in vivo chromatin profiling method is still lacking in plants.Here,we developed a transient and simplified cleavage under targets and tagmentation(tsCUT&Tag)that combines transient expression of transcription factor proteins in protoplasts with a simplified CUT&Tag without nucleus extraction.Our tsCUT&Tag method provided higher data quality and signal resolution with lower sequencing depth compared with traditional ChIP-seq.Furthermore,we developed a strategy combining tsCUT&Tag with machine learning,which has great potential for profiling the TFBL across plant development.展开更多
Bivalve mollusks represent a taxonomically and economically significant clade within Mollusca.However,the regulatory mechanisms governing their embryonic development remain poorly characterized.The dwarf surf clam(Mul...Bivalve mollusks represent a taxonomically and economically significant clade within Mollusca.However,the regulatory mechanisms governing their embryonic development remain poorly characterized.The dwarf surf clam(Mulinia lateralis),characterized by a short generation time and high fecundity,has recently gained recognition as an ideal model system for bivalve embryological research.This study explored the epigenetic mechanisms driving embryogenesis in M.lateralis,with a particular focus on the maternal-to-zygotic transition(MZT),by integrating chromatin-state profiling and transcriptomic analysis.For the first time in this species,CUT&Tag was employed to generate high-resolution landscapes of histone modifications H3K4me1,H3K4me3,H3K27me3,and H3K27ac across key developmental stages.The resulting data revealed extensive reprogramming of histone marks,indicating dynamic shifts in chromatin architecture during early embryonic development.Integration with transcriptomic data identified the timing of MZT in M.lateralis between the morula and gastrula stages and highlighted a suite of candidate genes essential for embryogenesis.These findings provide mechanistic insight into chromatin-mediated control of bivalve embryogenesis and establish M.lateralis as a robust platform for epigenomic research in marine invertebrates,with implications for functional gene studies and aquaculture advancement.展开更多
Hair follicle stem cell(HFSC),capable of self-renewal and differentiation in hair follicle,represents an emerging stem cell model for regenerative medicine.The interaction between HFSC and dermal papilla cell(DPC)gove...Hair follicle stem cell(HFSC),capable of self-renewal and differentiation in hair follicle,represents an emerging stem cell model for regenerative medicine.The interaction between HFSC and dermal papilla cell(DPC)governs hair follicle development.FGF7 functions as a paracrine protein regulating epithelial proliferation,differentiation and migration.The single-cell transcriptome profling and immunofuorescence analysis demonstrated that FGF7 localizes at DPC,while FGF7 receptor(FGFR2)expresses in both DPC and HFSC.Through co-culture experiments of HFSC and DPC,the results indicated that FGF7 secreted from DPC promotes the proliferation of DPC and HFSC via Wnt signaling pathway and induces HFSC differentiation.Furthermore,CUT&Tag assay revealed genomic colocalization between FGF7 and pluripotency-related genes and GSK3β.Electrophoretic mobility shift assay(EMSA)demonstrated that FGF7 interacts with the promoter region of CISH and PRKX.This research provides valuable insights into the molecular mechanisms underlying the hair cycle.Understanding the interaction between HFSC and DPC,as well as the role of FGF7,may advance regenerative medicine and hair loss treatment.展开更多
染色体免疫共沉淀测序(Chromatin immunoprecipitation followed by sequencing,ChIP-seq)是研究DNA-蛋白质互作的有力工具,被广泛用于RNA聚合酶、转录因子和组蛋白修饰等在基因组上的精确定位。近年来,在ChIP-seq技术的基础上,科学家...染色体免疫共沉淀测序(Chromatin immunoprecipitation followed by sequencing,ChIP-seq)是研究DNA-蛋白质互作的有力工具,被广泛用于RNA聚合酶、转录因子和组蛋白修饰等在基因组上的精确定位。近年来,在ChIP-seq技术的基础上,科学家提出了一系列研究DNA-蛋白质互作的技术方法,提高了测序分辨率,降低了实验成本,极大推动了表观基因组学的发展。本文综述了多种DNA-蛋白质互作研究技术的原理及其应用场景,介绍了在单细胞水平上研究DNA-蛋白质互作的实现方法,并展望其未来发展的方向。展开更多
Despite therapy with potent antiviral agents,chronic hepatitis B(CHB)patients remain at high risk of hepatocellular carcinoma(HCC).While metabolites have been rediscovered as active drivers of biological processes inc...Despite therapy with potent antiviral agents,chronic hepatitis B(CHB)patients remain at high risk of hepatocellular carcinoma(HCC).While metabolites have been rediscovered as active drivers of biological processes including carcinogenesis,the specific metabolites modulating HCC risk in CHB patients are largely unknown.Here,we demonstrate that baseline plasma from CHB patients who later developed HCC during follow-up exhibits growth-promoting properties in a case-control design nested within a large-scale,prospective cohort.Metabolomics analysis reveals a reduction in long-chain acylcarnitines(LCACs)in the baseline plasma of patients with HCC development.LCACs preferentially inhibit the proliferation of HCC cells in vitro at a physiological concentration and prevent the occurrence of HCC in vivo without hepatorenal toxicity.Uptake and metabolism of circulating LCACs increase the intracellular level of acetyl coenzyme A,which upregulates histone H3 Lys14 acetylation at the promoter region of KLF6 gene and thereby activates KLF6/p21 pathway.Indeed,blocking LCAC metabolism attenuates the difference in KLF6/p21 expression induced by baseline plasma of HCC/non-HCC patients.The deficiency of circulating LCACs represents a driver of HCC in CHB patients with viral control.These insights provide a promising direction for developing therapeutic strategies to reduce HCC risk further in the antiviral era.展开更多
文摘【目的】基于猪极端饲料报酬表型,利用靶向切割标签技术(cleavage under targets and tagmentation,CUT&Tag)构建H3K27ac差异图谱,鉴定关联的启动子、增强子和关联候选基因,为猪饲料报酬解析提供基础数据。【方法】从209头杜洛克猪中筛选饲料报酬表型差异最大的4头个体分别组成低剩余采食量组(L组,n=2)和高剩余采食量组(H组,n=2)。利用CUT&Tag技术,以H3K27ac作为活性启动子和增强子的表观遗传标记对4头个体的肝脏组织进行全基因组扫描,鉴定关联启动子、增强子和候选基因,并进一步采用real-time quantitative PCR(RT-qPCR)对重要基因进行验证。【结果】共鉴定出47271个H3K27ac峰,包括15739个潜在启动子和31532个推定增强子,大部分的H3K27ac峰位于近端启动子区域。根据H3K27ac全基因的分布情况和作用特点,发现3087个差异峰(对应2188个基因),其中867个H3K27ac峰(对应664个基因)富集在H组,2220个H3K27ac峰(对应1575个基因)富集在L组。GO和KEGG结果发现H3K27ac增强子可能是通过影响胆汁酸代谢、淋巴细胞代谢和NF-κB通路来调节饲料报酬。RT-qPCR结果显示,与H组相比,DIAPH3、DPYD、FTO、TCF7L2、ABCC2、ABCC11、RXRA和ABCG8在L组中显著上调(P<0.05),而PAX5、GRHPR、NFATC1、CARD11、BLNK和LYN在L组中显著下调(P<0.05)。【结论】本研究成功生成了具有极端RFI差异的杜洛克猪肝脏组织中的H3K27ac差异图谱以及相关数据。基于该图谱鉴定和验证了关联候选基因,为进一步解析启动子和增强子调控饲料报酬的分子机制提供了基础数据。
文摘染色体靶向切割和标签化(clevage under target and tagment,CUT&Tag)技术利用Tn5转座酶与Protein A/G的融合蛋白,引导Tn5酶至与靶蛋白结合的抗体附近,对靶蛋白结合的附近染色质区域进行切割,随后通过标签化处理对片段化染色质进行文库制备,并利用高通量测序技术获取特定位点或蛋白质结合位置的染色质信息。CUT&Tag技术在蛋白质和DNA相互作用的研究领域起到了重大作用,不仅可以了解组蛋白修饰发生的位置,而且可以明确转录因子结合的区域。相较于传统的染色质免疫沉淀高通量测序(chromatin immunoprecipitation-sequencing,ChIP-seq)技术,CUT&Tag技术具有信噪比高、可重复性好、实验周期短、细胞投入量低等优点,在早期胚胎发育、干细胞、肿瘤以及表观遗传学等研究领域体现出巨大优势。本文将针对CUT&Tag在代谢组织细胞(以小鼠原代胰岛细胞为例)的具体操作步骤进行描述,以提供一种研究代谢细胞的表观遗传学方法。
基金financially supported by the National Natural Science Foundation of China(32172026)the 111 Project Crop Genomics and Molecular Breeding(B20051)。
文摘Maize ear development determines the crop yield,and many important transcription factors(TFs)have been identified to function in this process.However,their transcriptional regulation mechanisms are still elusive.In this study,we generated the genome-wide DNA binding sites for 8 TFs which are known to function or highly expressed in inflorescence by applying the ts CUT&Tag method in maize leaf protoplast.We exposed a regulatory grid of 4 WUSCHEL-related homeobox(WOX)genes and revealed their potential regulatory mechanisms.In addition,a hierarchical regulation network for the determinacy and specification of maize inflorescence meristems were also constructed using the binding profiles of a floral development gene INDETERMINATE FLORAL APEX1(IFA1)and 3 MADS-box genes.Our study provides an in-depth understanding and new insights of the regulatory mechanisms during maize inflorescence development.
基金supported by the National Institutes of Health,USA(Grant Nos.R35GM142917 to Bo Zhang,U24ES026699 to Bo Zhang,R25DA027995 to Bo Zhang,R03AG070474 to Guoyan Zhao,R01NS123571 to Guoyan Zhao,U19NS130607 to Guoyan Zhao,and U24HG012070 to Bo Zhang and Guoyan Zhao)National Institutes of Health,USA.
文摘Efficient and reliable profiling methods are essential to study epigenetics.Tn5,one of the first identified prokaryotic transposases with high DNA-binding and tagmentation efficiency,is widely adopted in different genomic and epigenomic protocols for high-throughputly exploring the genome and epigenome.Based on Tn5,the Assay for Transposase-Accessible Chromatin using sequencing(ATAC-seq)and the Cleavage Under Targets and Tagmentation(CUT&Tag)were developed to measure chromatin accessibility and detect DNA–protein interactions.These methodologies can be applied to large amounts of biological samples with low-input levels,such as rare tissues,embryos,and sorted single cells.However,fast and proper processing of these epigenomic data has become a bottleneck because massive data production continues to increase quickly.Furthermore,inappropriate data analysis can generate biased or misleading conclusions.Therefore,it is essential to evaluate the performance of Tn5-based ATAC-seq and CUT&Tag data processing bioinformatics tools,many of which were developed mostly for analyzing chromatin immunoprecipitation followed by sequencing(ChIP-seq)data.Here,we conducted a comprehensive benchmarking analysis to evaluate the performance of eight popular software for processing ATAC-seq and CUT&Tag data.We compared the sensitivity,specificity,and peak width distribution for both narrow-type and broad-type peak calling.We also tested the influence of the availability of control IgG input in CUT&Tag data analysis.Finally,we evaluated the differential analysis strategies commonly used for analyzing the CUT&Tag data.Our study provided comprehensive guidance for selecting bioinformatics tools and recommended analysis strategies,which were implemented into Docker/Singularity images for streamlined data analysis.
基金supported by the National Natural Science Foundation of China(31922068)the Fundamental Research Funds for the Central Universities(ZK202101)the China Postdoctoral Science Foundation(2019M662666)。
文摘Knowledge of the transcription factor binding landscape(TFBL)is necessary to analyze gene regulatory networks for important agronomic traits.However,a low-cost and high-throughput in vivo chromatin profiling method is still lacking in plants.Here,we developed a transient and simplified cleavage under targets and tagmentation(tsCUT&Tag)that combines transient expression of transcription factor proteins in protoplasts with a simplified CUT&Tag without nucleus extraction.Our tsCUT&Tag method provided higher data quality and signal resolution with lower sequencing depth compared with traditional ChIP-seq.Furthermore,we developed a strategy combining tsCUT&Tag with machine learning,which has great potential for profiling the TFBL across plant development.
基金supported by the National Natural Science Foundation of China(32200667)Shandong Provincial Special Funds for Taishan Scholars(tsqn202306104)+1 种基金Hainan Province“South China Sea New Star”Science and Technology Innovation Talent Platform Project(NHXXRCXM202365)Hainan Provincial Joint Project of Sanya Yazhou Bay Science and Technology City Grant(2021JJLH0090)。
文摘Bivalve mollusks represent a taxonomically and economically significant clade within Mollusca.However,the regulatory mechanisms governing their embryonic development remain poorly characterized.The dwarf surf clam(Mulinia lateralis),characterized by a short generation time and high fecundity,has recently gained recognition as an ideal model system for bivalve embryological research.This study explored the epigenetic mechanisms driving embryogenesis in M.lateralis,with a particular focus on the maternal-to-zygotic transition(MZT),by integrating chromatin-state profiling and transcriptomic analysis.For the first time in this species,CUT&Tag was employed to generate high-resolution landscapes of histone modifications H3K4me1,H3K4me3,H3K27me3,and H3K27ac across key developmental stages.The resulting data revealed extensive reprogramming of histone marks,indicating dynamic shifts in chromatin architecture during early embryonic development.Integration with transcriptomic data identified the timing of MZT in M.lateralis between the morula and gastrula stages and highlighted a suite of candidate genes essential for embryogenesis.These findings provide mechanistic insight into chromatin-mediated control of bivalve embryogenesis and establish M.lateralis as a robust platform for epigenomic research in marine invertebrates,with implications for functional gene studies and aquaculture advancement.
基金supported by the National Key Research And Development Program of China(2022YFD1300204)。
文摘Hair follicle stem cell(HFSC),capable of self-renewal and differentiation in hair follicle,represents an emerging stem cell model for regenerative medicine.The interaction between HFSC and dermal papilla cell(DPC)governs hair follicle development.FGF7 functions as a paracrine protein regulating epithelial proliferation,differentiation and migration.The single-cell transcriptome profling and immunofuorescence analysis demonstrated that FGF7 localizes at DPC,while FGF7 receptor(FGFR2)expresses in both DPC and HFSC.Through co-culture experiments of HFSC and DPC,the results indicated that FGF7 secreted from DPC promotes the proliferation of DPC and HFSC via Wnt signaling pathway and induces HFSC differentiation.Furthermore,CUT&Tag assay revealed genomic colocalization between FGF7 and pluripotency-related genes and GSK3β.Electrophoretic mobility shift assay(EMSA)demonstrated that FGF7 interacts with the promoter region of CISH and PRKX.This research provides valuable insights into the molecular mechanisms underlying the hair cycle.Understanding the interaction between HFSC and DPC,as well as the role of FGF7,may advance regenerative medicine and hair loss treatment.
文摘染色体免疫共沉淀测序(Chromatin immunoprecipitation followed by sequencing,ChIP-seq)是研究DNA-蛋白质互作的有力工具,被广泛用于RNA聚合酶、转录因子和组蛋白修饰等在基因组上的精确定位。近年来,在ChIP-seq技术的基础上,科学家提出了一系列研究DNA-蛋白质互作的技术方法,提高了测序分辨率,降低了实验成本,极大推动了表观基因组学的发展。本文综述了多种DNA-蛋白质互作研究技术的原理及其应用场景,介绍了在单细胞水平上研究DNA-蛋白质互作的实现方法,并展望其未来发展的方向。
基金supported by National Key Research and Development Program of China(2022YFC2304800)National Natural Science Foundation of China(U22A20274 and 82203305)+1 种基金Guangdong Basic and Applied Basic Research Foundation of Guangzhou Joint Fund(2022B1515120039,China)Science and Technology Projects in Guangzhou(2024B03J0326,China).
文摘Despite therapy with potent antiviral agents,chronic hepatitis B(CHB)patients remain at high risk of hepatocellular carcinoma(HCC).While metabolites have been rediscovered as active drivers of biological processes including carcinogenesis,the specific metabolites modulating HCC risk in CHB patients are largely unknown.Here,we demonstrate that baseline plasma from CHB patients who later developed HCC during follow-up exhibits growth-promoting properties in a case-control design nested within a large-scale,prospective cohort.Metabolomics analysis reveals a reduction in long-chain acylcarnitines(LCACs)in the baseline plasma of patients with HCC development.LCACs preferentially inhibit the proliferation of HCC cells in vitro at a physiological concentration and prevent the occurrence of HCC in vivo without hepatorenal toxicity.Uptake and metabolism of circulating LCACs increase the intracellular level of acetyl coenzyme A,which upregulates histone H3 Lys14 acetylation at the promoter region of KLF6 gene and thereby activates KLF6/p21 pathway.Indeed,blocking LCAC metabolism attenuates the difference in KLF6/p21 expression induced by baseline plasma of HCC/non-HCC patients.The deficiency of circulating LCACs represents a driver of HCC in CHB patients with viral control.These insights provide a promising direction for developing therapeutic strategies to reduce HCC risk further in the antiviral era.
