The Experts below are selected from a list of 264 Experts worldwide ranked by ideXlab platform

Tatiana G. Kutateladze - One of the best experts on this subject based on the ideXlab platform.

Yi Zhang - One of the best experts on this subject based on the ideXlab platform.

Silin Zhong - One of the best experts on this subject based on the ideXlab platform.

  • tissue specific hi c analyses of rice foxtail millet and maize suggest non canonical function of plant chromatin domains
    Journal of Integrative Plant Biology, 2020
    Co-Authors: Pengfei Dong, Xiaoyu Tu, Haoxuan Li, Donald Grierson, Pinghua Li, Jianhua Zhang, Silin Zhong
    Abstract:

    : Chromatins are not randomly packaged in the nucleus and their organization plays important roles in transcription regulation, which is best studied in the mammalian models. Using in situ Hi-C, we have compared the 3D chromatin architectures of rice mesophyll and endosperm, foxtail millet bundle sheath and mesophyll, and maize bundle sheath, mesophyll and endosperm tissues. We found that their global A/B compartment partitions are stable across tissues, while local A/B compartment has tissue-specific dynamic associated with differential gene expression. Plant domains are largely stable across tissues, while new domain border formations are often associated with transcriptional activation in the region. Genes inside plant domains are not conserved across species, and lack significant co-expression behavior unlike those in mammalian TADs. Although we only observed chromatin loops between gene islands in the large genomes, the maize loop gene pairs' syntenic orthologs have shorter physical distances in small genome monocots, suggesting that loops instead of domains might have conserved biological function. Our study showed that plants' chromatin features might not have conserved biological functions as the mammalian ones.

  • tissue specific hi c analyses of rice foxtail millet and maize suggest non canonical function of plant chromatin domains
    bioRxiv, 2019
    Co-Authors: Pengfei Dong, Xiaoyu Tu, Haoxuan Li, Donald Grierson, Pinghua Li, Jianhua Zhang, Silin Zhong
    Abstract:

    Abstract Chromatins are not randomly packaged in the nucleus and their organization plays important roles in transcription regulation. Using in situ Hi-C, we have compared the 3D chromatin architectures of rice mesophyll and endosperm, foxtail millet bundle sheath and mesophyll, and maize bundle sheath, mesophyll and endosperm tissues. We have also profiled their DNA methylation, open chromatin, histone modification and gene expression to investigate whether chromatin structural dynamics are associated with epigenome features changes. We found that plant global A/B compartment partitions are stable across tissues, while local A/B compartment has tissue-specific dynamic that is associated with differential gene expression. Plant domains are largely stable across tissues, while rare domain border changes are often associated with gene activation. Genes inside plant domains are not conserved across species, and lack significant co-expression behavior unlike those in mammalian cells. When comparing synteny gene pairs, we found those maize genes involved in gene island chromatin loops have shorter genomic distances in smaller genomes without gene island loops such as rice and foxtail millet, suggesting that they have conserved functions. Our study revealed that the 3D configuration of the plant chromatin is also complex and dynamic with unique features that need to be further examined.

Pengfei Dong - One of the best experts on this subject based on the ideXlab platform.

  • tissue specific hi c analyses of rice foxtail millet and maize suggest non canonical function of plant chromatin domains
    Journal of Integrative Plant Biology, 2020
    Co-Authors: Pengfei Dong, Xiaoyu Tu, Haoxuan Li, Donald Grierson, Pinghua Li, Jianhua Zhang, Silin Zhong
    Abstract:

    : Chromatins are not randomly packaged in the nucleus and their organization plays important roles in transcription regulation, which is best studied in the mammalian models. Using in situ Hi-C, we have compared the 3D chromatin architectures of rice mesophyll and endosperm, foxtail millet bundle sheath and mesophyll, and maize bundle sheath, mesophyll and endosperm tissues. We found that their global A/B compartment partitions are stable across tissues, while local A/B compartment has tissue-specific dynamic associated with differential gene expression. Plant domains are largely stable across tissues, while new domain border formations are often associated with transcriptional activation in the region. Genes inside plant domains are not conserved across species, and lack significant co-expression behavior unlike those in mammalian TADs. Although we only observed chromatin loops between gene islands in the large genomes, the maize loop gene pairs' syntenic orthologs have shorter physical distances in small genome monocots, suggesting that loops instead of domains might have conserved biological function. Our study showed that plants' chromatin features might not have conserved biological functions as the mammalian ones.

  • tissue specific hi c analyses of rice foxtail millet and maize suggest non canonical function of plant chromatin domains
    bioRxiv, 2019
    Co-Authors: Pengfei Dong, Xiaoyu Tu, Haoxuan Li, Donald Grierson, Pinghua Li, Jianhua Zhang, Silin Zhong
    Abstract:

    Abstract Chromatins are not randomly packaged in the nucleus and their organization plays important roles in transcription regulation. Using in situ Hi-C, we have compared the 3D chromatin architectures of rice mesophyll and endosperm, foxtail millet bundle sheath and mesophyll, and maize bundle sheath, mesophyll and endosperm tissues. We have also profiled their DNA methylation, open chromatin, histone modification and gene expression to investigate whether chromatin structural dynamics are associated with epigenome features changes. We found that plant global A/B compartment partitions are stable across tissues, while local A/B compartment has tissue-specific dynamic that is associated with differential gene expression. Plant domains are largely stable across tissues, while rare domain border changes are often associated with gene activation. Genes inside plant domains are not conserved across species, and lack significant co-expression behavior unlike those in mammalian cells. When comparing synteny gene pairs, we found those maize genes involved in gene island chromatin loops have shorter genomic distances in smaller genomes without gene island loops such as rice and foxtail millet, suggesting that they have conserved functions. Our study revealed that the 3D configuration of the plant chromatin is also complex and dynamic with unique features that need to be further examined.

Arthur D. Riggs - One of the best experts on this subject based on the ideXlab platform.

  • metaphase chromosome analysis by ligation mediated pcr heritable chromatin structure and a comparison of active and inactive x chromosomes
    Proceedings of the National Academy of Sciences of the United States of America, 1995
    Co-Authors: Maty Hershkovitz, Arthur D. Riggs
    Abstract:

    We report that ligation-mediated PCR (LMPCR) can be used for high-resolution study of metaphase chromosomes, and we discuss the role of metaphase chromatin structure in the preservation of differentiated cell states. The X chromosome-linked human PGK1 (phosphoglycerate kinase 1) promoter region was investigated, and euchromatic active X chromosome (Xa) metaphase chromatin was compared with interphase Xa chromatin and to heterochromatic inactive X chromosome (Xi) metaphase and interphase chromatin. We find that (i) good-quality data at single-nucleotide resolution can be obtained by LMPCR analysis of dimethyl sulfate-treated intact metaphase cells; (ii) transcription factors present on the Xa promoter of interphase chromatin are not present on metaphase chromatin, establishing that the transcription complex on the PGK1 promoter must form de novo each cell generation; and (iii) the dimethyl sulfate reactivity pattern of Xa and Xi chromatin at metaphase is very similar to that of naked DNA. These results are discussed in the context of models for heritable chromatin structure and epigenetic mechanisms for cell memory, and they are also relevant to more general aspects of chromatin structure and differences between euchromatin and heterochromatin.