A chromosome-level genome assembly of the bread wheat variety Chinese Spring(CS)has recently been published.Genome-wide identification of regulatory elements(REs)responsible for regulating gene activity is key to furt...A chromosome-level genome assembly of the bread wheat variety Chinese Spring(CS)has recently been published.Genome-wide identification of regulatory elements(REs)responsible for regulating gene activity is key to further mechanistic studies.Because epigenetic activity can reflect RE activity,defining chromatin states based on epigenomic features is an effective way to detect REs.Here,we present the web-based platform Chinese Spring chromatin state(CSCS),which provides CS chromatin signature information.CSCS indudes 15 recently published epigenomic data sets including open chromatin and major chromatin marks,which are further partitioned into 15 distinct chromatin states.CSCS curates detailed information about these chromatin states,with trained self-organization mapping(SOM)for segments in all chromatin states and JBrowse visualization for genomic regions or genes.Motif analysis for genomic regions or genes,GO analysis for genes and SOM analysis for new epige-nomic data sets are also integrated into CSCS.In summary,the CSCS database contains the combina-torial patterns of chromatin signatures in wheat and facilitates the detection of functi onal elements and further clarification of regulatory activities.We illustrate how CSCS enables biological insights using one example,demonstrating that CSCS is a highly useful resource for intensive data mining.CSCS is available at http://bioinfo.cemps.ac.cn/CSCS/.展开更多
Long non-coding RNAs(lncRNAs) belong to a large and complex family of RNAs, which play many important roles in regulating gene expression. However, the mechanism underlying the dynamic expression of lncRNAs is still n...Long non-coding RNAs(lncRNAs) belong to a large and complex family of RNAs, which play many important roles in regulating gene expression. However, the mechanism underlying the dynamic expression of lncRNAs is still not very clear. In order to identify lncRNAs and clarify the mechanisms involved, we collected basic information and highlighted the mechanisms underlying lncRNA expression and regulation. Overall, lncRNAs are regulated by several similar transcription factors and protein-coding genes. Epigenetic modification(DNA methylation and histone modification) can also downregulate lncRNA levels in tissues and cells. Moreover, lncRNAs may be degraded or cleaved via interaction with miRNAs and miRNAassociated protein complexes. Furthermore, alternative RNA splicing(AS) may play a significant role in the post-transcriptional regulation of lncRNAs.展开更多
为探究急性感染期猪伪狂犬病病毒(PRV)在宿主细胞内基因组染色质的状态,首先建立PRV实时荧光定量PCR(qPCR)方法并测定0.1 MOI PRV感染Neuro-2a细胞后病毒基因组的复制动态,然后收集PRV感染Neuro-2a细胞的样品进行染色质免疫共沉淀试验(C...为探究急性感染期猪伪狂犬病病毒(PRV)在宿主细胞内基因组染色质的状态,首先建立PRV实时荧光定量PCR(qPCR)方法并测定0.1 MOI PRV感染Neuro-2a细胞后病毒基因组的复制动态,然后收集PRV感染Neuro-2a细胞的样品进行染色质免疫共沉淀试验(CHIP),并通过qPCR测定病毒部分DNA与组蛋白H3结合形成的染色质状态。结果显示,PRV急性感染Neuro-2a细胞后,部分基因组以染色质结构存在,并与病毒复制有一定相关性。本研究成功建立用于研究PRV基因组染色质状态的CHIP试验方法,为PRV急性感染期表观遗传学研究提供依据。展开更多
基金This study was supported by the Strategic Priority Resea rch Program of the Chinese Academy of Sciences(XDB27010302).
文摘A chromosome-level genome assembly of the bread wheat variety Chinese Spring(CS)has recently been published.Genome-wide identification of regulatory elements(REs)responsible for regulating gene activity is key to further mechanistic studies.Because epigenetic activity can reflect RE activity,defining chromatin states based on epigenomic features is an effective way to detect REs.Here,we present the web-based platform Chinese Spring chromatin state(CSCS),which provides CS chromatin signature information.CSCS indudes 15 recently published epigenomic data sets including open chromatin and major chromatin marks,which are further partitioned into 15 distinct chromatin states.CSCS curates detailed information about these chromatin states,with trained self-organization mapping(SOM)for segments in all chromatin states and JBrowse visualization for genomic regions or genes.Motif analysis for genomic regions or genes,GO analysis for genes and SOM analysis for new epige-nomic data sets are also integrated into CSCS.In summary,the CSCS database contains the combina-torial patterns of chromatin signatures in wheat and facilitates the detection of functi onal elements and further clarification of regulatory activities.We illustrate how CSCS enables biological insights using one example,demonstrating that CSCS is a highly useful resource for intensive data mining.CSCS is available at http://bioinfo.cemps.ac.cn/CSCS/.
文摘Long non-coding RNAs(lncRNAs) belong to a large and complex family of RNAs, which play many important roles in regulating gene expression. However, the mechanism underlying the dynamic expression of lncRNAs is still not very clear. In order to identify lncRNAs and clarify the mechanisms involved, we collected basic information and highlighted the mechanisms underlying lncRNA expression and regulation. Overall, lncRNAs are regulated by several similar transcription factors and protein-coding genes. Epigenetic modification(DNA methylation and histone modification) can also downregulate lncRNA levels in tissues and cells. Moreover, lncRNAs may be degraded or cleaved via interaction with miRNAs and miRNAassociated protein complexes. Furthermore, alternative RNA splicing(AS) may play a significant role in the post-transcriptional regulation of lncRNAs.
文摘为探究急性感染期猪伪狂犬病病毒(PRV)在宿主细胞内基因组染色质的状态,首先建立PRV实时荧光定量PCR(qPCR)方法并测定0.1 MOI PRV感染Neuro-2a细胞后病毒基因组的复制动态,然后收集PRV感染Neuro-2a细胞的样品进行染色质免疫共沉淀试验(CHIP),并通过qPCR测定病毒部分DNA与组蛋白H3结合形成的染色质状态。结果显示,PRV急性感染Neuro-2a细胞后,部分基因组以染色质结构存在,并与病毒复制有一定相关性。本研究成功建立用于研究PRV基因组染色质状态的CHIP试验方法,为PRV急性感染期表观遗传学研究提供依据。
