The Cistrome Data Browser(DB)at the website(cistrome.org/db)provides about 56,000 published human and mouse ChlP-seq,DNase-seq,and ATAC-seq chromatin profiles,which we have processed using uniform analysis and quality...The Cistrome Data Browser(DB)at the website(cistrome.org/db)provides about 56,000 published human and mouse ChlP-seq,DNase-seq,and ATAC-seq chromatin profiles,which we have processed using uniform analysis and quality control pipelines.The Cistrome DB Toolkit at the website(dbtoolkit.cistrome.org)was developed to allow users to investigate fundamental questions using this data collection.In this tutorial,we describe how to use the Cistrome DB to search for publicly available chromatin profiles,to assess sample quality,to access peak results,to visualize signal intensities,to explore DNA sequence motifs,and to identify putative target genes・We also describe the use of the Toolkit module to seek the factors most likely to regulate a gene of interest,the factors that bind to a given genomic interval(enhancer,SNP,etc.),and samples that have significant peak overlaps with user-defined peak sets.This tutorial guides biomedical researchers in the use of Cistrome DB resources to rapidly obtain valuable insights into gene regulatory questions.展开更多
Animal models provide myriad benefits to both experimental and clinical research. Unfortunately, in many situations, they fall short of expected results or provide contradictory results. In part, this can be the resul...Animal models provide myriad benefits to both experimental and clinical research. Unfortunately, in many situations, they fall short of expected results or provide contradictory results. In part, this can be the result of traditional molecular biological approaches that are relatively inefficient in elucidating underlying molecular mechanism. To improve the efficacy of animal models, a technological breakthrough is required. The growing availability and application of the high-throughput methods make systematic comparisons between human and animal models easier to perform. In the present study, we introduce the concept of the comparative systems biology, which we define as "comparisons of biological systems in different states or species used to achieve an integrated understanding of life forms with all their characteristic complexity of interactions at multiple levels". Furthermore, we discuss the applications of RNA-seq and ChIP-seq technologies to comparative systems biology between human and animal models and assess the potential applications for this approach in the future studies.展开更多
Deposition of the histone variant H2A.Z at gene bodies regulates transcription by modifying chromatin accessibility in plants. However, the role of H2A.Z enrichment at the promoter and enhancer regions is unclear, and...Deposition of the histone variant H2A.Z at gene bodies regulates transcription by modifying chromatin accessibility in plants. However, the role of H2A.Z enrichment at the promoter and enhancer regions is unclear, and how H2A.Z interacts with other mechanisms of chromatin modification to regulate gene expression remains obscure. Here, we mapped genome-wide H2A.Z, H3K4me3, H3K27me3, Pol II, and nucleosome occupancy in Arabidopsis inflorescence. We showed that H2A.Z preferentially associated with H3K4me3 at promoters, while it was found with H3K27me3 at enhancers, and that H2A.Z deposition negatively correlated with gene expression. In addition, we demonstrated that H2A.Z represses gene expression by establishing low gene accessibility at ＋1 nucleosome and maintaining high gene accessibility at -1 nucleosome. We further showed that the high measures of gene responsiveness correlate with the H2A.Z-associated closed ＋1 nucleosome structure. Moreover, we found that H2A.Z represses enhancer activity by promoting H3K27me3 and preventing H3K4me3 histone modifications. This study provides a framework for future studies of H2A.Z functions and opens up new aspects for decoding the interplay between chromatin modification and histone variants in transcrip- tional control.展开更多
Aluminum （AI） toxicity in plants is one of the primary constraints in crop production. Al3＋, the most toxic form of Al, is released into soil under acidic conditions and causes extensive damage to plants, especiall...Aluminum （AI） toxicity in plants is one of the primary constraints in crop production. Al3＋, the most toxic form of Al, is released into soil under acidic conditions and causes extensive damage to plants, especially in the roots. In rice, Al tolerance requires the ASR5 gene, but the molecular function of ASR5 has remained unknown. Here, we perform genome-wide analyses to identify ASR5-dependent Al-responsive genes in rice. Based on ASRS_RNAi silencing in plants, a global transcriptome analysis identified a total of 961 genes that were responsive to Al treatment in wildtype rice roots. Of these genes, 909 did not respond to Al in the ASR5_RNAi plants, indicating a central role for ASR5 in Al-responsive gene expression. Under normal conditions, without Al treatment, the ASR5 RNAi plants expressed 1.756 genes differentially compared to the wild-type plants, and 446 of these genes responded to AI treatment in the wild-type plants. Chromatin immunoprecipitation followed by deep sequencing identified 104 putative target genes that were directly regulated by ASR5 binding to their promoters, including the STAR1 gene, which encodes an ABC transporter required for AI tolerance. Motif analysis of the binding peak sequences revealed the binding motif for ASR5, which was confirmed via in vitro DNA-binding assays using the STAR1 promoter. These results demonstrate that ASR5 acts as a key transcription factor that is essential for AI-responsive gene expression and Al tolerance in rice.展开更多
A subfamily of four Phytochrome （phy）-Interacting bHLH transcription Factors （PIFs） collectively promote skotomorphogenic development in dark-grown seedlings. This activity is reversed upon exposure to light, by p...A subfamily of four Phytochrome （phy）-Interacting bHLH transcription Factors （PIFs） collectively promote skotomorphogenic development in dark-grown seedlings. This activity is reversed upon exposure to light, by photoacti- vated phy molecules that induce degradation of the PIFs, thereby triggering the transcriptional changes that drive a tran- sition to photomorphogenesis. The PIFs function both redundantly and partially differentially at the morphogenic level in this process, To identify the direct targets of PIF transcriptional regulation genome-wide, we analyzed the DNA-binding sites for all four PIFs by ChlP-seq analysis, and defined the genes transcriptionally regulated by each PIF, using RNA-seq analysis of pif mutants. Despite the absence of detectable differences in DNA-binding-motif recognition between the PIFs, the data show a spectrum of regulatory patterns, ranging from single PIF dominance to equal contributions by all four. Similarly, a broad array of promoter architectures was found, ranging from single PIF-binding sites, containing single sequence motifs, through multiple PIF-binding sites, each containing one or more motifs, with each site occupied prefer- entially by one to multiple PIFs. Quantitative analysis of the promoter occupancy and expression level induced by each PIF revealed an intriguing pattern. Although there is no robust correlation broadly across the target-gene population, examination of individual genes that are shared targets of multiple PIFs shows a gradation in correlation from strongly positive, through uncorrelated, to negative. This finding suggests a dual-layered mechanism of transcriptional regulation, comprising both a continuum of binding-site occupancy by each PIF and a superimposed layer of local regulation that acts differentially on each PIF, to modulate its intrinsic transcriptional activation capacity at each site, in a quantitative pattern that varies between the individual PIFs from gene to gene. These findings provide a framework for probing the mecha- nisms by which transcription factors with overlapping direct-target genes integrate and selectively transduce signals to their target networks.展开更多
The complexity of the epigenome landscape and transcriptional regulation is significantly increased during plant polyploidization,which drives genome evolution and contributes to the increased adaptability to diverse ...The complexity of the epigenome landscape and transcriptional regulation is significantly increased during plant polyploidization,which drives genome evolution and contributes to the increased adaptability to diverse environments.However,a comprehensive epigenome map of Brassica napus is still unavailable.In this study,we performed integrative analysis of five histone modifications,RNA polymerase Ⅱ CCU-pancy,DNA methylation,and transcriptomes in two B.napus lines(2063A and B409),and established global maps of regulatory elements,chromatin states,and their dynamics for the whole genome(including the An and Cn subgenomes)in four tissue types(young leaf,flower bud,silique,and root)of these two lines.Approximately 65.8% of the genome was annotated with different epigenomic signals.Compared with the Cn subgenome,the An subgenome possesses a higher level of active epigenetic marks and lower level of repressive epigenetic marks.Genes from subgenome-unique regions contribute to the major differences between the An and Cn subgenomes.Asymmetric histone modifications between homeologous gene pairs reflect their biased expression patterns.We identified a novel bivalent chromatin state(with H3K4me1 and H3K27me3)in B.napus that is associated with tissue-specific gene expression.Furthermore,we observed that different types of duplicated genes have discrepant patterns of histone modification and DNA methylation levels.Collectively,our findings provide a valuable epigenetic resource for allopolyploid plants.展开更多
Determining the binding sites of the transcription factor is important for understanding of transcriptional regulation. Transcription factor c-Jun plays an important role in cell growth, differentiation and developmen...Determining the binding sites of the transcription factor is important for understanding of transcriptional regulation. Transcription factor c-Jun plays an important role in cell growth, differentiation and development, but the binding sites and the target genes are not clearly defined in the whole human genome. In this study, we performed a ChIP-Seq experiment to identify c-Jun binding site in the human genome. Forty-eight binding sites were selected to process further evaluation by dsDNA microarray assay. We identified 283 c-Jun binding sites in K562 cells. Data analysis showed that 48.8% binding sites located within 100 kb of the upstream of the annotated genes, 28.6% binding sites comprised consensus TRE/CRE motif （5′-TGAC/GTCA-3′, 5′-TGACGTCA-3′） and variant sequences. Forty-two out of the selected 48 binding sites were found to bind the c-Jun homodimer in dsDNA microarray analysis. Data analysis also showed that 1569 genes are located in the neighborhood of the 283 binding sites and 191 genes in the neighborhood of the 42 binding sites validated by dsDNA microarray. We consulted 38 c-Jun target genes in previous studies and 16 among these 38 genes were also detected in this study. The identification of c-Jun binding sites and potential target genes in the genome scale may improve our fundamental understanding in the molecular mechanisms underlying the transcription regulation related to c-Jun.展开更多
Functional genomics employs dozens of OMICs technologies to explore the functions of DNA, RNA and protein regulators in gene regulation processes. Despite each of these technologies being powerful tools on their own, ...Functional genomics employs dozens of OMICs technologies to explore the functions of DNA, RNA and protein regulators in gene regulation processes. Despite each of these technologies being powerful tools on their own, fike the parable of blind men and an elephant, any one single technology has a limited ability to depict the complex regulatory system. Integrative OMICS approaches have emerged and become an important area in biology and medicine. It provides a precise and effective way to study gene regulations. Results： This article reviews current popular OMICs technologies, OMICs data integration strategies, and bioinformatics tools used for multi-dimensional data integration. We highlight the advantages of these methods, particularly in elucidating molecular basis of biological regulatory mechanisms. Conclusions： To better understand the complexity of biological processes, we need powerful bioinformatics tools to integrate these OMICs data. Integrating multi-dimensional OMICs data will generate novel insights into system-level gene regulations and serves as a foundation for further hypothesis-driven research.展开更多
OCT4, a member of the POU family of gene products, is an octamer motif-binding transcription factor. As it is known to play a crucial role in cancer processes including proliferation, invasion, and chemoradioresistanc...OCT4, a member of the POU family of gene products, is an octamer motif-binding transcription factor. As it is known to play a crucial role in cancer processes including proliferation, invasion, and chemoradioresistance, it is important to identify the direct targets of OCT4 in living cancer cells. Here, chromatin immunoprecipitation-sequencing （ChlP-seq） was used to identify OCT4 binding sites in glioblastoma cancer cells. The results showed that 5438 OCT4 binding sites were localized in the glioblastoma cancer genome and that these sites contained a consensus sequence TTTkswTw （k=T or G, s=C or G, w=A or T）, which occurred 3931 times in 2312 OCT4 binding regions. Furthermore, binding motifs of some other transcription factors were identified in OCT4 binding regions. Our results provide a valuable dataset for understanding gene regulation mechanisms underlying the function of OCT4 in glioblastoma cancer.展开更多
基金The authors would like to acknowledge Dr.Zhiping Weng for providing the backup of the Cistrome DB and Dr.Ting Wang for the Wash U Epigenome Gateway BrowserThis work is supported by National Institutes of Health of US(U24 CA237617).
文摘The Cistrome Data Browser(DB)at the website(cistrome.org/db)provides about 56,000 published human and mouse ChlP-seq,DNase-seq,and ATAC-seq chromatin profiles,which we have processed using uniform analysis and quality control pipelines.The Cistrome DB Toolkit at the website(dbtoolkit.cistrome.org)was developed to allow users to investigate fundamental questions using this data collection.In this tutorial,we describe how to use the Cistrome DB to search for publicly available chromatin profiles,to assess sample quality,to access peak results,to visualize signal intensities,to explore DNA sequence motifs,and to identify putative target genes・We also describe the use of the Toolkit module to seek the factors most likely to regulate a gene of interest,the factors that bind to a given genomic interval(enhancer,SNP,etc.),and samples that have significant peak overlaps with user-defined peak sets.This tutorial guides biomedical researchers in the use of Cistrome DB resources to rapidly obtain valuable insights into gene regulatory questions.
基金supported by the National Natural Science Foundation of China (31123005)the Chinese Academy of Sciences (Y002731071)the National Basic Research Program of China (2009CB941300)
文摘Animal models provide myriad benefits to both experimental and clinical research. Unfortunately, in many situations, they fall short of expected results or provide contradictory results. In part, this can be the result of traditional molecular biological approaches that are relatively inefficient in elucidating underlying molecular mechanism. To improve the efficacy of animal models, a technological breakthrough is required. The growing availability and application of the high-throughput methods make systematic comparisons between human and animal models easier to perform. In the present study, we introduce the concept of the comparative systems biology, which we define as "comparisons of biological systems in different states or species used to achieve an integrated understanding of life forms with all their characteristic complexity of interactions at multiple levels". Furthermore, we discuss the applications of RNA-seq and ChIP-seq technologies to comparative systems biology between human and animal models and assess the potential applications for this approach in the future studies.
文摘Deposition of the histone variant H2A.Z at gene bodies regulates transcription by modifying chromatin accessibility in plants. However, the role of H2A.Z enrichment at the promoter and enhancer regions is unclear, and how H2A.Z interacts with other mechanisms of chromatin modification to regulate gene expression remains obscure. Here, we mapped genome-wide H2A.Z, H3K4me3, H3K27me3, Pol II, and nucleosome occupancy in Arabidopsis inflorescence. We showed that H2A.Z preferentially associated with H3K4me3 at promoters, while it was found with H3K27me3 at enhancers, and that H2A.Z deposition negatively correlated with gene expression. In addition, we demonstrated that H2A.Z represses gene expression by establishing low gene accessibility at ＋1 nucleosome and maintaining high gene accessibility at -1 nucleosome. We further showed that the high measures of gene responsiveness correlate with the H2A.Z-associated closed ＋1 nucleosome structure. Moreover, we found that H2A.Z represses enhancer activity by promoting H3K27me3 and preventing H3K4me3 histone modifications. This study provides a framework for future studies of H2A.Z functions and opens up new aspects for decoding the interplay between chromatin modification and histone variants in transcrip- tional control.
文摘Aluminum （AI） toxicity in plants is one of the primary constraints in crop production. Al3＋, the most toxic form of Al, is released into soil under acidic conditions and causes extensive damage to plants, especially in the roots. In rice, Al tolerance requires the ASR5 gene, but the molecular function of ASR5 has remained unknown. Here, we perform genome-wide analyses to identify ASR5-dependent Al-responsive genes in rice. Based on ASRS_RNAi silencing in plants, a global transcriptome analysis identified a total of 961 genes that were responsive to Al treatment in wildtype rice roots. Of these genes, 909 did not respond to Al in the ASR5_RNAi plants, indicating a central role for ASR5 in Al-responsive gene expression. Under normal conditions, without Al treatment, the ASR5 RNAi plants expressed 1.756 genes differentially compared to the wild-type plants, and 446 of these genes responded to AI treatment in the wild-type plants. Chromatin immunoprecipitation followed by deep sequencing identified 104 putative target genes that were directly regulated by ASR5 binding to their promoters, including the STAR1 gene, which encodes an ABC transporter required for AI tolerance. Motif analysis of the binding peak sequences revealed the binding motif for ASR5, which was confirmed via in vitro DNA-binding assays using the STAR1 promoter. These results demonstrate that ASR5 acts as a key transcription factor that is essential for AI-responsive gene expression and Al tolerance in rice.
文摘A subfamily of four Phytochrome （phy）-Interacting bHLH transcription Factors （PIFs） collectively promote skotomorphogenic development in dark-grown seedlings. This activity is reversed upon exposure to light, by photoacti- vated phy molecules that induce degradation of the PIFs, thereby triggering the transcriptional changes that drive a tran- sition to photomorphogenesis. The PIFs function both redundantly and partially differentially at the morphogenic level in this process, To identify the direct targets of PIF transcriptional regulation genome-wide, we analyzed the DNA-binding sites for all four PIFs by ChlP-seq analysis, and defined the genes transcriptionally regulated by each PIF, using RNA-seq analysis of pif mutants. Despite the absence of detectable differences in DNA-binding-motif recognition between the PIFs, the data show a spectrum of regulatory patterns, ranging from single PIF dominance to equal contributions by all four. Similarly, a broad array of promoter architectures was found, ranging from single PIF-binding sites, containing single sequence motifs, through multiple PIF-binding sites, each containing one or more motifs, with each site occupied prefer- entially by one to multiple PIFs. Quantitative analysis of the promoter occupancy and expression level induced by each PIF revealed an intriguing pattern. Although there is no robust correlation broadly across the target-gene population, examination of individual genes that are shared targets of multiple PIFs shows a gradation in correlation from strongly positive, through uncorrelated, to negative. This finding suggests a dual-layered mechanism of transcriptional regulation, comprising both a continuum of binding-site occupancy by each PIF and a superimposed layer of local regulation that acts differentially on each PIF, to modulate its intrinsic transcriptional activation capacity at each site, in a quantitative pattern that varies between the individual PIFs from gene to gene. These findings provide a framework for probing the mecha- nisms by which transcription factors with overlapping direct-target genes integrate and selectively transduce signals to their target networks.
基金This work was financially supported by the National Natural Science Foundation of China(31930032,31701163,31771422,and 31771402)the National Key Research and Development Program of China(2016YFD0101300 and 2018YFC1604000)+3 种基金the China Postdoctoral Science Foundation(2017M612479)the Fundamental Research Funds for the Central Universities(2662018py033)the open funds of the National Key Laboratory of Crop Genetic Improvement(ZK201906)the Program for Modern Agricultural Industrial Technology System of China(grant no.CARS-12).
文摘The complexity of the epigenome landscape and transcriptional regulation is significantly increased during plant polyploidization,which drives genome evolution and contributes to the increased adaptability to diverse environments.However,a comprehensive epigenome map of Brassica napus is still unavailable.In this study,we performed integrative analysis of five histone modifications,RNA polymerase Ⅱ CCU-pancy,DNA methylation,and transcriptomes in two B.napus lines(2063A and B409),and established global maps of regulatory elements,chromatin states,and their dynamics for the whole genome(including the An and Cn subgenomes)in four tissue types(young leaf,flower bud,silique,and root)of these two lines.Approximately 65.8% of the genome was annotated with different epigenomic signals.Compared with the Cn subgenome,the An subgenome possesses a higher level of active epigenetic marks and lower level of repressive epigenetic marks.Genes from subgenome-unique regions contribute to the major differences between the An and Cn subgenomes.Asymmetric histone modifications between homeologous gene pairs reflect their biased expression patterns.We identified a novel bivalent chromatin state(with H3K4me1 and H3K27me3)in B.napus that is associated with tissue-specific gene expression.Furthermore,we observed that different types of duplicated genes have discrepant patterns of histone modification and DNA methylation levels.Collectively,our findings provide a valuable epigenetic resource for allopolyploid plants.
基金supported by the National Natural Science Foundation of China(Nos.30973375 and 30600152)
文摘Determining the binding sites of the transcription factor is important for understanding of transcriptional regulation. Transcription factor c-Jun plays an important role in cell growth, differentiation and development, but the binding sites and the target genes are not clearly defined in the whole human genome. In this study, we performed a ChIP-Seq experiment to identify c-Jun binding site in the human genome. Forty-eight binding sites were selected to process further evaluation by dsDNA microarray assay. We identified 283 c-Jun binding sites in K562 cells. Data analysis showed that 48.8% binding sites located within 100 kb of the upstream of the annotated genes, 28.6% binding sites comprised consensus TRE/CRE motif （5′-TGAC/GTCA-3′, 5′-TGACGTCA-3′） and variant sequences. Forty-two out of the selected 48 binding sites were found to bind the c-Jun homodimer in dsDNA microarray analysis. Data analysis also showed that 1569 genes are located in the neighborhood of the 283 binding sites and 191 genes in the neighborhood of the 42 binding sites validated by dsDNA microarray. We consulted 38 c-Jun target genes in previous studies and 16 among these 38 genes were also detected in this study. The identification of c-Jun binding sites and potential target genes in the genome scale may improve our fundamental understanding in the molecular mechanisms underlying the transcription regulation related to c-Jun.
基金Our work was supported by a Direct Grant for Research from The Chinese University of Hong Kong, Hong Kong SAR, China （No. 4053150） to JQ, research grants from Research Grants Council, Hong Kong SAR, China （No. 17121414M）, the National Natural Science Foundation of China （Nos. 81572786 and 91529303）, startup funds from Mayo Clinic （Mayo Clinic Arizona and Center for Individualized Medicine） to JW, and the National Natural Science Foundation of China （No. 11526144） and the Natural Science Foundation of Guangdong （No. 2016A030310038） to YH.
文摘Functional genomics employs dozens of OMICs technologies to explore the functions of DNA, RNA and protein regulators in gene regulation processes. Despite each of these technologies being powerful tools on their own, fike the parable of blind men and an elephant, any one single technology has a limited ability to depict the complex regulatory system. Integrative OMICS approaches have emerged and become an important area in biology and medicine. It provides a precise and effective way to study gene regulations. Results： This article reviews current popular OMICs technologies, OMICs data integration strategies, and bioinformatics tools used for multi-dimensional data integration. We highlight the advantages of these methods, particularly in elucidating molecular basis of biological regulatory mechanisms. Conclusions： To better understand the complexity of biological processes, we need powerful bioinformatics tools to integrate these OMICs data. Integrating multi-dimensional OMICs data will generate novel insights into system-level gene regulations and serves as a foundation for further hypothesis-driven research.
基金supported by the Ministry of Science and Technology, China(Nos. 2004CB518707, 2006DFA32950, 2006AA02Z4A2, 2006AA02A303, 2007DFC30360, and 2008DFA11320)the National Natural Science Foundation of China (No. 81101580)
文摘OCT4, a member of the POU family of gene products, is an octamer motif-binding transcription factor. As it is known to play a crucial role in cancer processes including proliferation, invasion, and chemoradioresistance, it is important to identify the direct targets of OCT4 in living cancer cells. Here, chromatin immunoprecipitation-sequencing （ChlP-seq） was used to identify OCT4 binding sites in glioblastoma cancer cells. The results showed that 5438 OCT4 binding sites were localized in the glioblastoma cancer genome and that these sites contained a consensus sequence TTTkswTw （k=T or G, s=C or G, w=A or T）, which occurred 3931 times in 2312 OCT4 binding regions. Furthermore, binding motifs of some other transcription factors were identified in OCT4 binding regions. Our results provide a valuable dataset for understanding gene regulation mechanisms underlying the function of OCT4 in glioblastoma cancer.
