CBP and RAD21 Proteins Bind at the Termini of Forum Domains in Human Chromosomes

Forum domains are 50-100-kb stretches of DNA delimited by the hotspots of double-strand breaks (DSBs). These domains possess coordinately expressed genes. However, molecular mechanisms of such regulation are not clear. It is assumed that the proteins specifically binding at the termini of domains can be involved in coordinated regulation of expression. In this study, we used the results of precise mapping of hotspots of DSBs and ChIP-Seq data for ten nuclear proteins in HEK293T cell line for a search of proteins specifically binding at forum-domain termini. We detected that two proteins, CBP and RAD24, which are known to be involved in epigenetic regulation of gene expression and formation of 3D chromosomal structures, bind at the termini. We assume that these proteins may be involved in coordinated expression of genes in forum domains.

Induction of the Erythroid Differentiation of K562 Cells Is Coupled with Changes in the Inter-Chromosomal Contacts of rDNA Clusters

The expression of clusters of rDNA genes influences pluripotency; however, the underlying mechanisms are not yet known. These clusters shape inter-chromosomal contacts with numerous genes controlling differentiation in human and Drosophila cells. This suggests a possible role of these contacts in the formation of 3D chromosomal structures and the regulation of gene expression in development. However, it has not yet been demonstrated whether inter-chromosomal rDNA contacts are changed during differentiation. In this study, we used human leukemia K562 cells and induced their erythroid differentiation in order to study both the changes in rDNA contacts and the expression of genes. We observed that approximately 200 sets of rDNA-contacting genes are co-expressed in different combinations in both untreated and differentiated K562 cells. rDNA contacts are changed during differentiation and coupled with the upregulation of genes whose products are mainly located in the nucleus and are highly associated with DNA- and RNA-binding, along with the downregulation of genes whose products mainly reside in the cytoplasm or intra- or extracellular vesicles. The most downregulated gene is ID3, which is known as an inhibitor of differentiation, and thus should be switched off to allow for differentiation. Our data suggest that the differentiation of K562 cells leads to alterations in the inter-chromosomal contacts of rDNA clusters and 3D structures in particular chromosomal regions as well as to changes in the expression of genes located in the corresponding chromosomal domains. We conclude that approximately half of the rDNA-contacting genes are co-expressed in human cells and that rDNA clusters are involved in the global regulation of gene expression.

Genes Possessing the Most Frequent DNA DSBs Are Highly Associated with Development and Cancers, and Essentially Overlap with the rDNA-Contacting Genes

Double-strand DNA breakes (DSBs) are the most deleterious and widespread examples of DNA damage. They inevitably originate from endogenous mechanisms in the course of transcription, replication, and recombination, as well as from different exogenous factors. If not properly repaired, DSBs result in cell death or diseases. Genome-wide analysis of DSBs has revealed the numerous endogenous DSBs in human chromosomes. However, until now, it has not been clear what kind of genes are preferentially subjected to breakage. We performed a genetic and epigenetic analysis of the most frequent DSBs in HEK293T cells. Here, we show that they predominantly occur in the active genes controlling differentiation, development, and morphogenesis. These genes are highly associated with cancers and other diseases. About one-third of the genes possessing frequent DSBs correspond to rDNA-contacting genes. Our data suggest that a specific set of active genes controlling morphogenesis are the main targets of DNA breakage in human cells, although there is a specific set of silent genes controlling metabolism that also are enriched in DSBs. We detected this enrichment by different activators and repressors of transcription at DSB target sites, as well breakage at promoters. We propose that both active transcription and silencing of genes give a propensity for DNA breakage. These results have implications for medicine and gene therapy.

Fragments of rDNA Genes Scattered over the Human Genome Are Targets of Small RNAs

Small noncoding RNAs of different origins and classes play several roles in the regulation of gene expression. Here, we show that diverged and rearranged fragments of rDNA units are scattered throughout the human genome and that endogenous small noncoding RNAs are processed by the Microprocessor complex from specific regions of ribosomal RNAs shaping hairpins. These small RNAs correspond to particular sites inside the fragments of rDNA that mostly reside in intergenic regions or the introns of about 1500 genes. The targets of these small ribosomal RNAs (srRNAs) are characterized by a set of epigenetic marks, binding sites of Pol II, RAD21, CBP, and P300, DNase I hypersensitive sites, and by enrichment or depletion of active histone marks. In HEK293T cells, genes that are targeted by srRNAs (srRNA target genes) are involved in differentiation and development. srRNA target genes are enriched with more actively transcribed genes. Our data suggest that remnants of rDNA sequences and srRNAs may be involved in the upregulation or downregulation of a specific set of genes in human cells. These results have implications for diverse fields, including epigenetics and gene therapy.

Interchromosomal Contacts of rDNA Clusters in Three Human Cell Lines Are Associated with Silencing of Genes Controlling Morphogenesis

To study the rDNA contacts with genes in three human cell lines of different origin, we used 4C approach. Our data indicate that the same set of about five hundred genes frequently shape contacts with rDNA clusters in HEK293T, K652, and hESM01 cells. Gene ontology search suggests that the genes are involved in development and morphogenesis. Approximately one hundred of these genes are highly associated with silencing by H3K27me3 mark in different normal cells, including bronchial epithelial cells, keratinocytes, myoblasts, monocytes, endothelial cells, kidney epithelial cells, and some others. We conclude that the concerted silencing of specific group of rDNA-contacting genes controlling development occurs during differentiation. We assume that the phase separation mechanisms may be involved in the rDNA-mediated silencing of a set of genes via the contacts with inactive rDNA clusters.

Dynamics of Whole-Genome Contacts of Nucleoli in Drosophila Cells Suggests a Role for rDNA Genes in Global Epigenetic Regulation

Chromosomes are organized into 3D structures that are important for the regulation of gene expression and differentiation. Important role in formation of inter-chromosome contacts play rDNA clusters that make up nucleoli. In the course of differentiation, heterochromatization of rDNA units in mouse cells is coupled with the repression or activation of different genes. Furthermore, the nucleoli of human cells shape the direct contacts with genes that are involved in differentiation and cancer. Here, we identified and categorized the genes located in the regions where rDNA clusters make frequent contacts. Using a 4C approach, we demonstrate that in Drosophila S2 cells, rDNA clusters form contacts with genes that are involved in chromosome organization and differentiation. Heat shock treatment induces changes in the contacts between nucleoli and hundreds of genes controlling morphogenesis. We show that nucleoli form contacts with regions that are enriched with active or repressive histone marks and where small non-coding RNAs are mapped. These data indicate that rDNA contacts are involved in the repression and activation of gene expression and that rDNA clusters orchestrate large groups of Drosophila genes involved in differentiation.

[Drosophila rDNA Genes Shape the Stable Contacts with the Tlk Gene at the Expression Area of Small RNAs and Affect on Looped Domains inside the Gene]

In experiments on mouse and human cells it was demonstrated that rDNA plays an important role in epigenetic regulation of many genes. To identify and study rDNA-contacting genes in Drosophila we used the 4С (circular chromosome conformation capture) approach. We detected very stable contacts of rDNA genes within a 5-kb region inside the Tlk gene residing in X chromosome. This 5-kb region corresponds to small RNAs. After heat shock treatment both the amount of contacts, and the expression level of the gene were increased. Tlk and Rala are genes that share the same short bidirectional promoter but exhibit different expression levels. Around the region of rDNA contacts inside the Tlk gene, looped domains were formed. We conclude that rDNA contact-dependent epigenetic regulation is guided by small RNAs and that the contacts are involved in rearrangements of the looped domains.

[Contact Sites of rDNA Clusters with FANK1 Gene Correspond to Repressed Chromatin]

rDNA genes play an important role in epigenetic regulation and in differentiation of eukaryotic cells. Using the 4C (circular chromosome conformation capture) approach and model HEK293T cells, we analyzed the rDNA-contacting gene FANK1, using anchor located inside rDNA genes. At the 5' end of the FANK1 gene we detected frequent contacts with rDNA clusters. The contact sites coincide with the border where chromatin state changes and nucleosome positioning. The adjacent genes DHX32, BCCIP and UROS are located in the active chromatin and are transcribed, but do not contact with rDNA genes, while FANK1 gene is silenced, and is located in repressed chromatin. Heat shock treatment dramatically changes the pattern of rDNA contacts in the region and induces about 4-fold increase in activation of the FANK1 gene. We conclude that rDNA contacts may be involved in repression of the FANK1 gene.

Interchromosomal Contacts of rDNA Clusters with DUX Genes in Human Chromosome 4 Are Very Sensitive to Heat Shock Treatment

In order to study the effects of heat shock treatment on the distribution of rDNA contacts at the region possessing DUX genes inside chromosome 4 we used 4C approach. Our data indicate that the treatment removes the frequent rDNA contacts in this region. The recent data on involvement of superenhancers that are decorated by broad H3K27ac marks in the phase separation mechanisms and the previous data demonstrating that these broad marks are the favorite sites of rDNA contacts taken together with our data on sensitivity of the contacts to the heat shock treatment suggest that the phase separation mechanisms are involved in the reversible rDNA-mediated regulation of gene expression via the contacts.