目的·研究Apc^(min/+)小鼠自发结肠肿瘤的空间表观遗传特征。方法·使用8月龄雄性Apc^(min/+)小鼠自发结肠肿瘤模型,搭建空间染色质可及性测序(assay for transposase-accessible chromatin with high-throughput sequencing,A...目的·研究Apc^(min/+)小鼠自发结肠肿瘤的空间表观遗传特征。方法·使用8月龄雄性Apc^(min/+)小鼠自发结肠肿瘤模型,搭建空间染色质可及性测序(assay for transposase-accessible chromatin with high-throughput sequencing,ATAC-seq)技术平台。摘取一颗小鼠结肠肿瘤,经冷冻包埋后,进行连续切片;一张组织切片使用苏木精-伊红染色观察其组织学特征,另一张相邻的组织切片进行空间ATAC-seq技术处理,得到带有空间位置信息的DNA文库后进行测序,得到该小鼠结肠肿瘤的空间染色质可及性数据。取同一只小鼠的另一颗肿瘤组织,经消化后得到细胞悬液,通过流式细胞术分选有活性的单细胞悬液,进行单细胞转录组测序,与空间染色质可及性数据联合分析此小鼠的结肠肿瘤微环境表观遗传学特征。结果·成功搭建稳定的空间ATAC-seq技术体系,并据此将小鼠的肿瘤分为恶性区域、非恶性区域以及恶性-非恶性边界区域;恶性区域富集到的转录因子包括NK2同源框转录因子5(NK2 homeobox 5,NKX2-5)、转录因子3(transcription factor 3,TCF3)等。在3个区域分别对转录因子进行富集,得到2种不同的表达趋势:一种为表达水平自恶性‒边界‒非恶性区域逐步降低;另一种为在恶性和边界区域表达水平高,在非恶性区域表达水平低。对不同区域的基因分析显示恶性区域的缺氧反应明显上调,转化生长因子(transforming growth factor,TGF)、Kirsten大鼠肉瘤病毒癌基因同源物(Kirsten rat sarcoma viral oncogene homolog,KRAS)信号通路显著上调,与细胞周期相关的功能明显增强。对肿瘤微环境中细胞间的相互作用分析发现不同区域的细胞互作强度具有显著差别,非恶性区域内部细胞的相互作用强,边界区与非恶性区以及恶性与非恶性区域的相互作用中等,恶性区与边界区的相互作用弱。结论·Apc^(min/+)小鼠结肠肿瘤呈高度空间异质性;肿瘤恶性区域富集了Tcf3等多种转录因子,恶性区域与边界、非恶性区域之间细胞相互作用相对较弱。展开更多
染色质转座酶可及性测序(assay for transposase-accessible chromatin with high-throughput sequencing,ATAC-seq)是通过转座酶Tn5切割开放的DNA区域并为之连接特异的测序接头(adaptor),以此来反映开放的染色质区域。其是基于高通量...染色质转座酶可及性测序(assay for transposase-accessible chromatin with high-throughput sequencing,ATAC-seq)是通过转座酶Tn5切割开放的DNA区域并为之连接特异的测序接头(adaptor),以此来反映开放的染色质区域。其是基于高通量测序对染色质开放区域进行研究的一项技术。ATAC-seq技术可以根据染色质开放特征在全基因组范围内构建染色质可及性图谱,从而识别各细胞亚群开放程度活跃的转录因子。在基础医学领域,ATAC-seq技术,迄今已被应用于多个物种的研究,其中就包括对人类胚胎、器官发育和细胞分化等的研究。文章对ATAC-seq的优势,以及该技术在人类发育相关研究中的应用和前景进行了综述,以期针对人类细胞分化发育、人类器官发育以及人类发育相关的疾病等相关研究的开展提供借鉴与参考。展开更多
染色质转座酶可及性测序(assay for transposase-accessible chromatin with high-throughput sequencing,ATAC-seq)是利用Tn5转座酶研究染色质可及性的高通量测序技术。ATAC-seq可以在全基因组范围内绘制染色质可及性图谱,揭示转录因...染色质转座酶可及性测序(assay for transposase-accessible chromatin with high-throughput sequencing,ATAC-seq)是利用Tn5转座酶研究染色质可及性的高通量测序技术。ATAC-seq可以在全基因组范围内绘制染色质可及性图谱,揭示转录因子结合位点以及核小体的位置。在医学领域,ATAC-seq技术是研究重大疾病发病机制、药物作用机制、新药研发和生物标志物功能等的新一代有力工具。本文对ATAC-seq技术的优势及其在复杂疾病研究中的应用和前景进行了综述,以期为人类复杂疾病基因表达调控机制等相关研究的开展提供借鉴与参考。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
Gene set scoring(GSS)has been routinely conducted for gene expression analysis of bulk or single-cell RNA sequencing(RNA-seq)data,which helps to decipher single-cell heterogeneity and cell type-specific variability by...Gene set scoring(GSS)has been routinely conducted for gene expression analysis of bulk or single-cell RNA sequencing(RNA-seq)data,which helps to decipher single-cell heterogeneity and cell type-specific variability by incorporating prior knowledge from functional gene sets.Single-cell assay for transposase accessible chromatin using sequencing(scATAC-seq)is a powerful technique for interrogating single-cell chromatin-based gene regulation,and genes or gene sets with dynamic regulatory potentials can be regarded as cell type-specific markers as if in single-cell RNA-seq(scRNA-seq).However,there are few GSS tools specifically designed for scATAC-seq,and the applicability and performance of RNA-seq GSS tools on scATAC-seq data remain to be investigated.Here,we systematically benchmarked ten GSS tools,including four bulk RNA-seq tools,five scRNA-seq tools,and one scATAC-seq method.First,using matched scATAC-seq and scRNA-seq datasets,we found that the performance of GSS tools on scATAC-seq data was comparable to that on scRNA-seq,suggesting their applicability to scATAC-seq.Then,the performance of different GSS tools was extensively evaluated using up to ten scATAC-seq datasets.Moreover,we evaluated the impact of gene activity conversion,dropout imputation,and gene set collections on the results of GSS.Results show that dropout imputation can significantly promote the performance of almost all GSS tools,while the impact of gene activity conversion methods or gene set collections on GSS performance is more dependent on GSS tools or datasets.Finally,we provided practical guidelines for choosing appropriate preprocessing methods and GSS tools in different application scenarios.展开更多
Assay for transposase-accessible chromatin with high-throughput sequencing(ATAC-seq) is a technique widely used to investigate genome-wide chromatin accessibility. The recently published Omni-ATAC-seq protocol substan...Assay for transposase-accessible chromatin with high-throughput sequencing(ATAC-seq) is a technique widely used to investigate genome-wide chromatin accessibility. The recently published Omni-ATAC-seq protocol substantially improves the signal/noise ratio and reduces the input cell number. High-quality data are critical to ensure accurate analysis.Several tools have been developed for assessing sequencing quality and insertion size distribution for ATAC-seq data;however, key quality control(QC) metrics have not yet been established to accurately determine the quality of ATAC-seq data. Here, we optimized the analysis strategy for ATAC-seq and defined a series of QC metrics for ATAC-seq data,including reads under peak ratio(RUPr), background(BG), promoter enrichment(Pro En), subsampling enrichment(Sub En), and other measurements. We incorporated these QC tests into our recently developed ATAC-seq Integrative Analysis Package(AIAP) to provide a complete ATAC-seq analysis system, including quality assurance, improved peak calling, and downstream differential analysis. We demonstrated a significant improvement of sensitivity(20%–60%) in both peak calling and differential analysis by processing paired-end ATAC-seq datasets using AIAP. AIAP is compiled into Docker/Singularity, and it can be executed by one command line to generate a comprehensive QC report. We used ENCODE ATAC-seq data to benchmark and generate QC recommendations, and developed q ATACViewer for the userfriendly interaction with the QC report. The software, source code, and documentation of AIAP are freely available at https://github.com/Zhang-lab/ATAC-seq_QC_analysis.展开更多
Chromatin immunoprecipitation sequencing(Ch IP-seq)and the Assay for Transposase-Accessible Chromatin with high-throughput sequencing(ATAC-seq)have become essential technologies to effectively measure protein–DNA int...Chromatin immunoprecipitation sequencing(Ch IP-seq)and the Assay for Transposase-Accessible Chromatin with high-throughput sequencing(ATAC-seq)have become essential technologies to effectively measure protein–DNA interactions and chromatin accessibility.However,there is a need for a scalable and reproducible pipeline that incorporates proper normalization between samples,correction of copy number variations,and integration of new downstream analysis tools.Here we present Containerized Bioinformatics workflow for Reproducible Ch IP/ATAC-seq Analysis(Co BRA),a modularized computational workflow which quantifies Ch IP-seq and ATAC-seq peak regions and performs unsupervised and supervised analyses.Co BRA provides a comprehensive state-of-the-art Ch IP-seq and ATAC-seq analysis pipeline that can be used by scientists with limited computational experience.This enables researchers to gain rapid insight into protein–DNA interactions and chromatin accessibility through sample clustering,differential peak calling,motif enrichment,comparison of sites to a reference database,and pathway analysis.Co BRA is publicly available online at https://bitbucket.org/cfce/cobra.展开更多
Background Broilers stand out as one of the fastest-growing livestock globally,making a substantial contribution to animal meat production.However,the molecular and epigenetic mechanisms underlying the rapid growth an...Background Broilers stand out as one of the fastest-growing livestock globally,making a substantial contribution to animal meat production.However,the molecular and epigenetic mechanisms underlying the rapid growth and development of broiler chickens are still unclear.This study aims to explore muscle development patterns and regulatory networks during the postnatal rapid growth phase of fast-growing broilers.We measured the growth performance of Cornish(CC)and White Plymouth Rock(RR)over a 42-d period.Pectoral muscle samples from both CC and RR were randomly collected at day 21 after hatching(D21)and D42 for RNA-seq and ATAC-seq library construction.Results The consistent increase in body weight and pectoral muscle weight across both breeds was observed as they matured,with CC outpacing RR in terms of weight at each stage of development.Differential expression analysis identified 398 and 1,129 genes in the two dimensions of breeds and ages,respectively.A total of 75,149 ATAC-seq peaks were annotated in promoter,exon,intron and intergenic regions,with a higher number of peaks in the promoter and intronic regions.The age-biased genes and breed-biased genes of RNA-seq were combined with the ATAC-seq data for subsequent analysis.The results spotlighted the upregulation of ACTC1 and FDPS at D21,which were primarily associated with muscle structure development by gene cluster enrichment.Additionally,a noteworthy upregulation of MUSTN1,FOS and TGFB3 was spotted in broiler chickens at D42,which were involved in cell differentiation and muscle regeneration after injury,suggesting a regulatory role of muscle growth and repair.Conclusions This work provided a regulatory network of postnatal broiler chickens and revealed ACTC1 and MUSTN1 as the key responsible for muscle development and regeneration.Our findings highlight that rapid growth in broiler chickens triggers ongoing muscle damage and subsequent regeneration.These findings provide a foundation for future research to investigate the functional aspects of muscle development.展开更多
Meiosis is a highly complex process significantly influenced by transcriptional regulation.However,studies on the mechanisms that govern transcriptomic changes during meiosis,especially in prophase I,are limited.Here,...Meiosis is a highly complex process significantly influenced by transcriptional regulation.However,studies on the mechanisms that govern transcriptomic changes during meiosis,especially in prophase I,are limited.Here,we performed single-cell ATAC-seq of human testis tissues and observed reprogramming during the transition from zygotene to pachytene spermatocytes.This event,conserved in mice,involved the deactivation of genes associated with meiosis after reprogramming and the activation of those related to spermatogenesis before their functional onset.Furthermore,we identified 282 transcriptional regulators(TRs)that underwent activation or deactivation subsequent to this process.Evidence suggested that physical contact signals from Sertoli cells may regulate these TRs in spermatocytes,while secreted ENHO signals may alter metabolic patterns in these cells.Our results further indicated that defective transcriptional reprogramming may be associated with non-obstructive azoospermia(NOA).This study revealed the importance of both physical contact and secreted signals between Sertoli cells and germ cells in meiotic progression.展开更多
在真核生物中,染色质作为遗传物质DNA的载体,直接参与基因的表达调控。染色质的可及性是指染色质中的DNA能与转录因子等蛋白复合物结合的区域,对染色质可及性的测定可为获取开放区域的信息、核小体定位信息以及转录因子结合信息提供基...在真核生物中,染色质作为遗传物质DNA的载体,直接参与基因的表达调控。染色质的可及性是指染色质中的DNA能与转录因子等蛋白复合物结合的区域,对染色质可及性的测定可为获取开放区域的信息、核小体定位信息以及转录因子结合信息提供基础依据。随着高通量测序技术的进步以及测序成本的降低,研究者已开发多种研究染色质可及性的测序方法,该文介绍4种常见的染色质可及性测序方法,对其中的染色质转座酶可及性测序(assay for transposase-accessible chromatin with high-throughput sequencing,ATAC-seq)的原理和数据分析方法进行重点描述,讨论ATAC-seq的应用与发展趋势,为染色质可及性以及基因表达调控的研究提供参考。展开更多
文摘染色质转座酶可及性测序(assay for transposase-accessible chromatin with high-throughput sequencing,ATAC-seq)是通过转座酶Tn5切割开放的DNA区域并为之连接特异的测序接头(adaptor),以此来反映开放的染色质区域。其是基于高通量测序对染色质开放区域进行研究的一项技术。ATAC-seq技术可以根据染色质开放特征在全基因组范围内构建染色质可及性图谱,从而识别各细胞亚群开放程度活跃的转录因子。在基础医学领域,ATAC-seq技术,迄今已被应用于多个物种的研究,其中就包括对人类胚胎、器官发育和细胞分化等的研究。文章对ATAC-seq的优势,以及该技术在人类发育相关研究中的应用和前景进行了综述,以期针对人类细胞分化发育、人类器官发育以及人类发育相关的疾病等相关研究的开展提供借鉴与参考。
文摘染色质转座酶可及性测序(assay for transposase-accessible chromatin with high-throughput sequencing,ATAC-seq)是利用Tn5转座酶研究染色质可及性的高通量测序技术。ATAC-seq可以在全基因组范围内绘制染色质可及性图谱,揭示转录因子结合位点以及核小体的位置。在医学领域,ATAC-seq技术是研究重大疾病发病机制、药物作用机制、新药研发和生物标志物功能等的新一代有力工具。本文对ATAC-seq技术的优势及其在复杂疾病研究中的应用和前景进行了综述,以期为人类复杂疾病基因表达调控机制等相关研究的开展提供借鉴与参考。
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(Grant No.T2222007 to Xiaohui Wu).
文摘Gene set scoring(GSS)has been routinely conducted for gene expression analysis of bulk or single-cell RNA sequencing(RNA-seq)data,which helps to decipher single-cell heterogeneity and cell type-specific variability by incorporating prior knowledge from functional gene sets.Single-cell assay for transposase accessible chromatin using sequencing(scATAC-seq)is a powerful technique for interrogating single-cell chromatin-based gene regulation,and genes or gene sets with dynamic regulatory potentials can be regarded as cell type-specific markers as if in single-cell RNA-seq(scRNA-seq).However,there are few GSS tools specifically designed for scATAC-seq,and the applicability and performance of RNA-seq GSS tools on scATAC-seq data remain to be investigated.Here,we systematically benchmarked ten GSS tools,including four bulk RNA-seq tools,five scRNA-seq tools,and one scATAC-seq method.First,using matched scATAC-seq and scRNA-seq datasets,we found that the performance of GSS tools on scATAC-seq data was comparable to that on scRNA-seq,suggesting their applicability to scATAC-seq.Then,the performance of different GSS tools was extensively evaluated using up to ten scATAC-seq datasets.Moreover,we evaluated the impact of gene activity conversion,dropout imputation,and gene set collections on the results of GSS.Results show that dropout imputation can significantly promote the performance of almost all GSS tools,while the impact of gene activity conversion methods or gene set collections on GSS performance is more dependent on GSS tools or datasets.Finally,we provided practical guidelines for choosing appropriate preprocessing methods and GSS tools in different application scenarios.
基金supported by the National Institutes of Health(Grant Nos.U24ES026699,U01HG009391,and R25DA027995)the Goldman Sachs Philanthropy Fund(Emerson Collective)Chan Zuckerberg Initiative,United States。
文摘Assay for transposase-accessible chromatin with high-throughput sequencing(ATAC-seq) is a technique widely used to investigate genome-wide chromatin accessibility. The recently published Omni-ATAC-seq protocol substantially improves the signal/noise ratio and reduces the input cell number. High-quality data are critical to ensure accurate analysis.Several tools have been developed for assessing sequencing quality and insertion size distribution for ATAC-seq data;however, key quality control(QC) metrics have not yet been established to accurately determine the quality of ATAC-seq data. Here, we optimized the analysis strategy for ATAC-seq and defined a series of QC metrics for ATAC-seq data,including reads under peak ratio(RUPr), background(BG), promoter enrichment(Pro En), subsampling enrichment(Sub En), and other measurements. We incorporated these QC tests into our recently developed ATAC-seq Integrative Analysis Package(AIAP) to provide a complete ATAC-seq analysis system, including quality assurance, improved peak calling, and downstream differential analysis. We demonstrated a significant improvement of sensitivity(20%–60%) in both peak calling and differential analysis by processing paired-end ATAC-seq datasets using AIAP. AIAP is compiled into Docker/Singularity, and it can be executed by one command line to generate a comprehensive QC report. We used ENCODE ATAC-seq data to benchmark and generate QC recommendations, and developed q ATACViewer for the userfriendly interaction with the QC report. The software, source code, and documentation of AIAP are freely available at https://github.com/Zhang-lab/ATAC-seq_QC_analysis.
基金funding from the National Institutes of Health,United States(Grant Nos.2PO1CA163227 and P01CA250959)。
文摘Chromatin immunoprecipitation sequencing(Ch IP-seq)and the Assay for Transposase-Accessible Chromatin with high-throughput sequencing(ATAC-seq)have become essential technologies to effectively measure protein–DNA interactions and chromatin accessibility.However,there is a need for a scalable and reproducible pipeline that incorporates proper normalization between samples,correction of copy number variations,and integration of new downstream analysis tools.Here we present Containerized Bioinformatics workflow for Reproducible Ch IP/ATAC-seq Analysis(Co BRA),a modularized computational workflow which quantifies Ch IP-seq and ATAC-seq peak regions and performs unsupervised and supervised analyses.Co BRA provides a comprehensive state-of-the-art Ch IP-seq and ATAC-seq analysis pipeline that can be used by scientists with limited computational experience.This enables researchers to gain rapid insight into protein–DNA interactions and chromatin accessibility through sample clustering,differential peak calling,motif enrichment,comparison of sites to a reference database,and pathway analysis.Co BRA is publicly available online at https://bitbucket.org/cfce/cobra.
基金supported by the National Key Research and Development Program of China(2022YFF1000204)the National Natural Science Foundation of China(32102535)the Key Research and Development Program of Hainan province(ZDYF2023XDNY036)。
文摘Background Broilers stand out as one of the fastest-growing livestock globally,making a substantial contribution to animal meat production.However,the molecular and epigenetic mechanisms underlying the rapid growth and development of broiler chickens are still unclear.This study aims to explore muscle development patterns and regulatory networks during the postnatal rapid growth phase of fast-growing broilers.We measured the growth performance of Cornish(CC)and White Plymouth Rock(RR)over a 42-d period.Pectoral muscle samples from both CC and RR were randomly collected at day 21 after hatching(D21)and D42 for RNA-seq and ATAC-seq library construction.Results The consistent increase in body weight and pectoral muscle weight across both breeds was observed as they matured,with CC outpacing RR in terms of weight at each stage of development.Differential expression analysis identified 398 and 1,129 genes in the two dimensions of breeds and ages,respectively.A total of 75,149 ATAC-seq peaks were annotated in promoter,exon,intron and intergenic regions,with a higher number of peaks in the promoter and intronic regions.The age-biased genes and breed-biased genes of RNA-seq were combined with the ATAC-seq data for subsequent analysis.The results spotlighted the upregulation of ACTC1 and FDPS at D21,which were primarily associated with muscle structure development by gene cluster enrichment.Additionally,a noteworthy upregulation of MUSTN1,FOS and TGFB3 was spotted in broiler chickens at D42,which were involved in cell differentiation and muscle regeneration after injury,suggesting a regulatory role of muscle growth and repair.Conclusions This work provided a regulatory network of postnatal broiler chickens and revealed ACTC1 and MUSTN1 as the key responsible for muscle development and regeneration.Our findings highlight that rapid growth in broiler chickens triggers ongoing muscle damage and subsequent regeneration.These findings provide a foundation for future research to investigate the functional aspects of muscle development.
基金supported by the National Natural Science Foundation of China(82271645)National Key Research and Development Program of China(2021YFC2700200 to F.S.)。
文摘Meiosis is a highly complex process significantly influenced by transcriptional regulation.However,studies on the mechanisms that govern transcriptomic changes during meiosis,especially in prophase I,are limited.Here,we performed single-cell ATAC-seq of human testis tissues and observed reprogramming during the transition from zygotene to pachytene spermatocytes.This event,conserved in mice,involved the deactivation of genes associated with meiosis after reprogramming and the activation of those related to spermatogenesis before their functional onset.Furthermore,we identified 282 transcriptional regulators(TRs)that underwent activation or deactivation subsequent to this process.Evidence suggested that physical contact signals from Sertoli cells may regulate these TRs in spermatocytes,while secreted ENHO signals may alter metabolic patterns in these cells.Our results further indicated that defective transcriptional reprogramming may be associated with non-obstructive azoospermia(NOA).This study revealed the importance of both physical contact and secreted signals between Sertoli cells and germ cells in meiotic progression.
文摘在真核生物中,染色质作为遗传物质DNA的载体,直接参与基因的表达调控。染色质的可及性是指染色质中的DNA能与转录因子等蛋白复合物结合的区域,对染色质可及性的测定可为获取开放区域的信息、核小体定位信息以及转录因子结合信息提供基础依据。随着高通量测序技术的进步以及测序成本的降低,研究者已开发多种研究染色质可及性的测序方法,该文介绍4种常见的染色质可及性测序方法,对其中的染色质转座酶可及性测序(assay for transposase-accessible chromatin with high-throughput sequencing,ATAC-seq)的原理和数据分析方法进行重点描述,讨论ATAC-seq的应用与发展趋势,为染色质可及性以及基因表达调控的研究提供参考。
