rDNA Clusters Make Contact with Genes that Are Involved in Differentiation and Cancer and Change Contacts after Heat Shock Treatment
Human rDNA clusters form numerous contacts with different chromosomal regions as evidenced by chromosome conformation capture data. Heterochromatization of rDNA genes leads to heterochromatization in different chromosomal regions coupled with the activation of the transcription of genes related to d...
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MDPI AG
2019-11-01
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| Series: | Cells |
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| Online Access: | https://www.mdpi.com/2073-4409/8/11/1393 |
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| author | Nickolai A. Tchurikov Daria M. Fedoseeva Elena S. Klushevskaya Ivan Y. Slovohotov Vladimir R. Chechetkin Yuri V. Kravatsky Olga V. Kretova |
| author_facet | Nickolai A. Tchurikov Daria M. Fedoseeva Elena S. Klushevskaya Ivan Y. Slovohotov Vladimir R. Chechetkin Yuri V. Kravatsky Olga V. Kretova |
| author_sort | Nickolai A. Tchurikov |
| collection | DOAJ |
| description | Human rDNA clusters form numerous contacts with different chromosomal regions as evidenced by chromosome conformation capture data. Heterochromatization of rDNA genes leads to heterochromatization in different chromosomal regions coupled with the activation of the transcription of genes related to differentiation. These data suggest a role for rDNA clusters in the regulation of many human genes. However, the genes that reside within the rDNA-contacting regions have not been identified. The purpose of this study was to detect and characterize the regions where rDNA clusters make frequent contacts and to identify and categorize genes located in these regions. We analyzed the regions that contact rDNA using 4C data and show that these regions are enriched with genes specifying transcription factors and non-coding RNAs involved in differentiation and development. The rDNA-contacting genes are involved in neuronal development and are associated with different cancers. Heat shock treatment led to dramatic changes in the pattern of rDNA-contacting sites, especially in the regions possessing long stretches of H3K27ac marks. Whole-genome analysis of rDNA-contacting sites revealed specific epigenetic marks and the transcription sites of 20−100 nt non-coding RNAs in these regions. The rDNA-contacting genes jointly regulate many genes that are involved in the control of transcription by RNA polymerase II and the development of neurons. Our data suggest a role for rDNA clusters in the differentiation of human cells and carcinogenesis. |
| first_indexed | 2024-03-12T07:11:59Z |
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| institution | Directory Open Access Journal |
| issn | 2073-4409 |
| language | English |
| last_indexed | 2024-03-12T07:11:59Z |
| publishDate | 2019-11-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Cells |
| spelling | doaj.art-2f9ac5da5ff24e1bacf891ed8f9378442023-09-02T23:02:23ZengMDPI AGCells2073-44092019-11-01811139310.3390/cells8111393cells8111393rDNA Clusters Make Contact with Genes that Are Involved in Differentiation and Cancer and Change Contacts after Heat Shock TreatmentNickolai A. Tchurikov0Daria M. Fedoseeva1Elena S. Klushevskaya2Ivan Y. Slovohotov3Vladimir R. Chechetkin4Yuri V. Kravatsky5Olga V. Kretova6Department of Epigenetic Mechanisms of Gene Expression Regulation, Engelhardt Institute of Molecular Biology Russian Academy of Sciences, 119334 Moscow, RussiaDepartment of Epigenetic Mechanisms of Gene Expression Regulation, Engelhardt Institute of Molecular Biology Russian Academy of Sciences, 119334 Moscow, RussiaDepartment of Epigenetic Mechanisms of Gene Expression Regulation, Engelhardt Institute of Molecular Biology Russian Academy of Sciences, 119334 Moscow, RussiaDepartment of Epigenetic Mechanisms of Gene Expression Regulation, Engelhardt Institute of Molecular Biology Russian Academy of Sciences, 119334 Moscow, RussiaDepartment of Epigenetic Mechanisms of Gene Expression Regulation, Engelhardt Institute of Molecular Biology Russian Academy of Sciences, 119334 Moscow, RussiaDepartment of Epigenetic Mechanisms of Gene Expression Regulation, Engelhardt Institute of Molecular Biology Russian Academy of Sciences, 119334 Moscow, RussiaDepartment of Epigenetic Mechanisms of Gene Expression Regulation, Engelhardt Institute of Molecular Biology Russian Academy of Sciences, 119334 Moscow, RussiaHuman rDNA clusters form numerous contacts with different chromosomal regions as evidenced by chromosome conformation capture data. Heterochromatization of rDNA genes leads to heterochromatization in different chromosomal regions coupled with the activation of the transcription of genes related to differentiation. These data suggest a role for rDNA clusters in the regulation of many human genes. However, the genes that reside within the rDNA-contacting regions have not been identified. The purpose of this study was to detect and characterize the regions where rDNA clusters make frequent contacts and to identify and categorize genes located in these regions. We analyzed the regions that contact rDNA using 4C data and show that these regions are enriched with genes specifying transcription factors and non-coding RNAs involved in differentiation and development. The rDNA-contacting genes are involved in neuronal development and are associated with different cancers. Heat shock treatment led to dramatic changes in the pattern of rDNA-contacting sites, especially in the regions possessing long stretches of H3K27ac marks. Whole-genome analysis of rDNA-contacting sites revealed specific epigenetic marks and the transcription sites of 20−100 nt non-coding RNAs in these regions. The rDNA-contacting genes jointly regulate many genes that are involved in the control of transcription by RNA polymerase II and the development of neurons. Our data suggest a role for rDNA clusters in the differentiation of human cells and carcinogenesis.https://www.mdpi.com/2073-4409/8/11/1393rdna clusters4cgene ontologychromatin marksepigeneticsdevelopmentdifferentiationheat shock |
| spellingShingle | Nickolai A. Tchurikov Daria M. Fedoseeva Elena S. Klushevskaya Ivan Y. Slovohotov Vladimir R. Chechetkin Yuri V. Kravatsky Olga V. Kretova rDNA Clusters Make Contact with Genes that Are Involved in Differentiation and Cancer and Change Contacts after Heat Shock Treatment Cells rdna clusters 4c gene ontology chromatin marks epigenetics development differentiation heat shock |
| title | rDNA Clusters Make Contact with Genes that Are Involved in Differentiation and Cancer and Change Contacts after Heat Shock Treatment |
| title_full | rDNA Clusters Make Contact with Genes that Are Involved in Differentiation and Cancer and Change Contacts after Heat Shock Treatment |
| title_fullStr | rDNA Clusters Make Contact with Genes that Are Involved in Differentiation and Cancer and Change Contacts after Heat Shock Treatment |
| title_full_unstemmed | rDNA Clusters Make Contact with Genes that Are Involved in Differentiation and Cancer and Change Contacts after Heat Shock Treatment |
| title_short | rDNA Clusters Make Contact with Genes that Are Involved in Differentiation and Cancer and Change Contacts after Heat Shock Treatment |
| title_sort | rdna clusters make contact with genes that are involved in differentiation and cancer and change contacts after heat shock treatment |
| topic | rdna clusters 4c gene ontology chromatin marks epigenetics development differentiation heat shock |
| url | https://www.mdpi.com/2073-4409/8/11/1393 |
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