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Hot spots of DNA double-strand breaks and genomic contacts of human rDNA units are involved in epigenetic regulation.

Tchurikov NA, Fedoseeva DM, Sosin DV, Snezhkina AV, Melnikova NV, Kudryavtseva AV, Kravatsky YV, Kretova OV - J Mol Cell Biol (2014)

Bottom Line: We observed that rDNA units corresponded to the most fragile sites in human chromosomes and that these units possessed at least nine specific regions containing clusters of extremely frequently occurring DSBs, which were located exclusively in non-coding intergenic spacer (IGS) regions.Our rDNA-4C data indicate that the regions of IGS containing the hot spots of DSBs often form contacts with specific regions in different chromosomes, including the pericentromeric regions, as well as regions that are characterized by H3K27ac and H3K4me3 marks, CTCF binding sites, ChIA-PET and RIP signals, and high levels of DSBs.The data suggest a strong link between chromosome breakage and several different mechanisms of epigenetic regulation of gene expression.

View Article: PubMed Central - PubMed

Affiliation: Department of Epigenetic Mechanisms of Gene Expression Regulation, Engelhardt Institute of Molecular Biology, Moscow 119334, Russia tchurikov@eimb.ru.

No MeSH data available.


Related in: MedlinePlus

The major contacts of rDNA units in the sequenced portion of the human genome. (A) Design of the 4C-rDNA experiment for analysis of genome-wide contacts of rDNA units at R4 and R5. A physical map of the 12-kb region containing R4 and R5 and the positions of EcoRI sites (E) and only the nearest FaeI site (F) to the EcoRI site at the coordinate 30487 are shown. The primers selected inside the 415-bp EcoRI-FaeI fragment are shown. The major steps of the 4C procedure are illustrated by a scheme. rDNA fragments are not shown to scale. Details of the procedure are described in Supplementary Methods. (B) Circos presentation of rDNA contacts representing at least 1000 mapped 4C reads. Only one rDNA unit was included at the tip of chr14. rDNA contacts with particular regions inside 16 chromosomes are presented. (C) The major sites of contacts of rDNA units are shown along cytobands in chr1, chr2, chr3, chr4, chr9, and chr21 as visualized in the Integrated Genome Browser (Affymetrix) (http://bioviz.org/igb/). The mapping was performed in the human genome assembly of February 2009 (GRC37/hg19).
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MJU038F5: The major contacts of rDNA units in the sequenced portion of the human genome. (A) Design of the 4C-rDNA experiment for analysis of genome-wide contacts of rDNA units at R4 and R5. A physical map of the 12-kb region containing R4 and R5 and the positions of EcoRI sites (E) and only the nearest FaeI site (F) to the EcoRI site at the coordinate 30487 are shown. The primers selected inside the 415-bp EcoRI-FaeI fragment are shown. The major steps of the 4C procedure are illustrated by a scheme. rDNA fragments are not shown to scale. Details of the procedure are described in Supplementary Methods. (B) Circos presentation of rDNA contacts representing at least 1000 mapped 4C reads. Only one rDNA unit was included at the tip of chr14. rDNA contacts with particular regions inside 16 chromosomes are presented. (C) The major sites of contacts of rDNA units are shown along cytobands in chr1, chr2, chr3, chr4, chr9, and chr21 as visualized in the Integrated Genome Browser (Affymetrix) (http://bioviz.org/igb/). The mapping was performed in the human genome assembly of February 2009 (GRC37/hg19).

Mentions: We observed that R1–R9 islands of low nucleosome occupancy merge into heterochromatic regions of the IGS. Heterochromatin regions are prone to forming both intra- and inter-chromosomal contacts, and human NORs interact with one another, as well as with the non-NORs (Manuelidis and Borden, 1988). Therefore, we decided to detect all the contacts in the entire genome of a 2.2-kb IGS fragment containing R4 and R5 hot spots using a 4C approach. Figure 5A shows schematically the procedure used for amplification of different genomic EcoRI-FaeI fragments ligated in cross-linked chromatin preparations with an EcoRI site at coordinate 30487 of the rDNA unit. R5 and R4 are located at distances of 2218 and 1136 bp from this coordinate, respectively.Figure 5


Hot spots of DNA double-strand breaks and genomic contacts of human rDNA units are involved in epigenetic regulation.

Tchurikov NA, Fedoseeva DM, Sosin DV, Snezhkina AV, Melnikova NV, Kudryavtseva AV, Kravatsky YV, Kretova OV - J Mol Cell Biol (2014)

The major contacts of rDNA units in the sequenced portion of the human genome. (A) Design of the 4C-rDNA experiment for analysis of genome-wide contacts of rDNA units at R4 and R5. A physical map of the 12-kb region containing R4 and R5 and the positions of EcoRI sites (E) and only the nearest FaeI site (F) to the EcoRI site at the coordinate 30487 are shown. The primers selected inside the 415-bp EcoRI-FaeI fragment are shown. The major steps of the 4C procedure are illustrated by a scheme. rDNA fragments are not shown to scale. Details of the procedure are described in Supplementary Methods. (B) Circos presentation of rDNA contacts representing at least 1000 mapped 4C reads. Only one rDNA unit was included at the tip of chr14. rDNA contacts with particular regions inside 16 chromosomes are presented. (C) The major sites of contacts of rDNA units are shown along cytobands in chr1, chr2, chr3, chr4, chr9, and chr21 as visualized in the Integrated Genome Browser (Affymetrix) (http://bioviz.org/igb/). The mapping was performed in the human genome assembly of February 2009 (GRC37/hg19).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4524424&req=5

MJU038F5: The major contacts of rDNA units in the sequenced portion of the human genome. (A) Design of the 4C-rDNA experiment for analysis of genome-wide contacts of rDNA units at R4 and R5. A physical map of the 12-kb region containing R4 and R5 and the positions of EcoRI sites (E) and only the nearest FaeI site (F) to the EcoRI site at the coordinate 30487 are shown. The primers selected inside the 415-bp EcoRI-FaeI fragment are shown. The major steps of the 4C procedure are illustrated by a scheme. rDNA fragments are not shown to scale. Details of the procedure are described in Supplementary Methods. (B) Circos presentation of rDNA contacts representing at least 1000 mapped 4C reads. Only one rDNA unit was included at the tip of chr14. rDNA contacts with particular regions inside 16 chromosomes are presented. (C) The major sites of contacts of rDNA units are shown along cytobands in chr1, chr2, chr3, chr4, chr9, and chr21 as visualized in the Integrated Genome Browser (Affymetrix) (http://bioviz.org/igb/). The mapping was performed in the human genome assembly of February 2009 (GRC37/hg19).
Mentions: We observed that R1–R9 islands of low nucleosome occupancy merge into heterochromatic regions of the IGS. Heterochromatin regions are prone to forming both intra- and inter-chromosomal contacts, and human NORs interact with one another, as well as with the non-NORs (Manuelidis and Borden, 1988). Therefore, we decided to detect all the contacts in the entire genome of a 2.2-kb IGS fragment containing R4 and R5 hot spots using a 4C approach. Figure 5A shows schematically the procedure used for amplification of different genomic EcoRI-FaeI fragments ligated in cross-linked chromatin preparations with an EcoRI site at coordinate 30487 of the rDNA unit. R5 and R4 are located at distances of 2218 and 1136 bp from this coordinate, respectively.Figure 5

Bottom Line: We observed that rDNA units corresponded to the most fragile sites in human chromosomes and that these units possessed at least nine specific regions containing clusters of extremely frequently occurring DSBs, which were located exclusively in non-coding intergenic spacer (IGS) regions.Our rDNA-4C data indicate that the regions of IGS containing the hot spots of DSBs often form contacts with specific regions in different chromosomes, including the pericentromeric regions, as well as regions that are characterized by H3K27ac and H3K4me3 marks, CTCF binding sites, ChIA-PET and RIP signals, and high levels of DSBs.The data suggest a strong link between chromosome breakage and several different mechanisms of epigenetic regulation of gene expression.

View Article: PubMed Central - PubMed

Affiliation: Department of Epigenetic Mechanisms of Gene Expression Regulation, Engelhardt Institute of Molecular Biology, Moscow 119334, Russia tchurikov@eimb.ru.

No MeSH data available.


Related in: MedlinePlus