While previous studies have shown that histone modifications could influence plant growth and devel- opment by regulating gene transcription, knowledge about the relationships between these modifications and gene expr...While previous studies have shown that histone modifications could influence plant growth and devel- opment by regulating gene transcription, knowledge about the relationships between these modifications and gene expression is still limited. This study used chromatin immunoprecipitation followed by high-throughput sequencing （ChlP-Seq）, to investigate the genome-wide distribution of four histone modifications： di and trimethylation of H3K4 （H3K4me2 and H3K4me3） and acylation of H3K9 and H3K27 （H3K9ac and H3K27ac） in Oryza sativa L. japonica. By analyz- ing published DNase-Seq data, this study explored DNase-Hypersensitive （DH） sites along the rice genome. The histone marks appeared mainly in generic regions and were enriched around the transcription start sites （TSSs） of genes. This analysis demonstrated that the four histone modifications and the DH sites were all associated with active transcription. Furthermore, the four histone modifications were highly concurrent with transcript regions-a promising feature that was used to predict missing genes in the rice gene annotation. The predictions were further validated by experimentally confirming the transcription of two predicted missing genes. Moreover, a sequence motif analysis was constructed in order to identify the DH sites and many putative transcription factor binding sites.展开更多
Chromatin immunoprecipitation coupled with massive parallel sequencing （ChlP-seq） is a powerful technology to identify the genome-wide locations of DNA binding proteins such as transcription factors or modified hist...Chromatin immunoprecipitation coupled with massive parallel sequencing （ChlP-seq） is a powerful technology to identify the genome-wide locations of DNA binding proteins such as transcription factors or modified histones. As more and more experimental laboratories are adopting ChlP-seq to unravel the transcriptional and epigenetic regulatory mechanisms, computational analyses of ChlP-seq also become increasingly comprehensive and sophisticated. In this article, we review current computational methodology for ChlP-seq analysis, recommend useful algorithms and workflows, and introduce quality control measures at different analytical steps. We also discuss how ChlP-seq could be integrated with other types of genomic assays, such as gene expression profiling and genome-wide association studies, to provide a more comprehensive view of gene regulatory mechanisms in important physiological and pathological processes.展开更多
基金This work was supported by grants from the Natural Science Foundation of China （31071125, 31025018, and 31028011） and the Ministry of Education of China （NCET-09-0735）, as well as the National Institutes of Health of US （grant no. GM99409）.We thank Qunlian Zhang for technical support and Yiwen Chen for critical suggestion. No conflict of interest declared.
文摘While previous studies have shown that histone modifications could influence plant growth and devel- opment by regulating gene transcription, knowledge about the relationships between these modifications and gene expression is still limited. This study used chromatin immunoprecipitation followed by high-throughput sequencing （ChlP-Seq）, to investigate the genome-wide distribution of four histone modifications： di and trimethylation of H3K4 （H3K4me2 and H3K4me3） and acylation of H3K9 and H3K27 （H3K9ac and H3K27ac） in Oryza sativa L. japonica. By analyz- ing published DNase-Seq data, this study explored DNase-Hypersensitive （DH） sites along the rice genome. The histone marks appeared mainly in generic regions and were enriched around the transcription start sites （TSSs） of genes. This analysis demonstrated that the four histone modifications and the DH sites were all associated with active transcription. Furthermore, the four histone modifications were highly concurrent with transcript regions-a promising feature that was used to predict missing genes in the rice gene annotation. The predictions were further validated by experimentally confirming the transcription of two predicted missing genes. Moreover, a sequence motif analysis was constructed in order to identify the DH sites and many putative transcription factor binding sites.
基金This work was supported by the National Basic Research （973） Program of China （No. 2010CB944904）, National Natural Science Foundation of China （No. 31028011）, and National Institutes of Health （No. HG4069）.
文摘Chromatin immunoprecipitation coupled with massive parallel sequencing （ChlP-seq） is a powerful technology to identify the genome-wide locations of DNA binding proteins such as transcription factors or modified histones. As more and more experimental laboratories are adopting ChlP-seq to unravel the transcriptional and epigenetic regulatory mechanisms, computational analyses of ChlP-seq also become increasingly comprehensive and sophisticated. In this article, we review current computational methodology for ChlP-seq analysis, recommend useful algorithms and workflows, and introduce quality control measures at different analytical steps. We also discuss how ChlP-seq could be integrated with other types of genomic assays, such as gene expression profiling and genome-wide association studies, to provide a more comprehensive view of gene regulatory mechanisms in important physiological and pathological processes.
