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The chicken domain of alpha-globin genes represents a useful model to study regulation of globin genes expression. Current evidence suggests that spatial organization of genomic domains plays and important role in regulation of gene expression. We have previously found that activation of globin gene transcription correlates with a spatial reconfiguration of the alpha-globin gene domain resulting in an assembly of the active chromatin hub. Here, in order to get more information on a possible relation between transcription and large-scale chromatin folding, we have studied the spatial configuration of an extended (2.5 Mb) segment of chicken chromosome 14 harboring the domain of alpha-globin genes in cultured lymphoid cells, cultured erythroid cells, and cultured erythroid cells stimulated to a terminal differentiation resulting in activation of globin gene transcription. The results obtained demonstrate that active transcription of globin genes correlates with a limited decompaction of a relatively large area harboring the alpha-globin gene domain, although the domain itself became more compact apparently due to the formation of an active chromatin hub, ACH. Importantly, organization of the area under study into topologically-associated domains and spatial separation of active and repressed chromatin compartments remain virtually the same in all three cell lines studied. [ABSTRACT FROM AUTHOR]

How enhancers regulate their target genes in the context of 3D chromatin organization is extensively studied and models which do not require direct enhancer-promoter contact have recently emerged. Here, we use the activation of estrogen receptor-dependent enhancers in a breast cancer cell line to study enhancer-promoter communication at two loci. This allows high temporal resolution tracking of molecular events from hormone stimulation to efficient gene activation. We examine how both enhancer-promoter spatial proximity assayed by DNA fluorescence in situ hybridization, and contact frequencies resulting from chromatin in situ fragmentation and proximity ligation, change dynamically during enhancer-driven gene activation. These orthogonal methods produce seemingly paradoxical results: upon enhancer activation enhancer-promoter contact frequencies increase while spatial proximity decreases. We explore this apparent discrepancy using different estrogen receptor ligands and transcription inhibitors. Our data demonstrate that enhancer-promoter contact frequencies are transcription independent whereas altered enhancer-promoter proximity depends on transcription. Our results emphasize that the relationship between contact frequencies and physical distance in the nucleus, especially over short genomic distances, is not always a simple one., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Gómez Acuña et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

In this study, we delve into the impact of genotoxic anticancer drug treatment on the chromatin structure of human cells, with a particular focus on the effects of doxorubicin. Using Hi-C, ChIP-seq, and RNA-seq, we explore the changes in chromatin architecture brought about by doxorubicin and ICRF193. Our results indicate that physiologically relevant doses of doxorubicin lead to a local reduction in Hi-C interactions in certain genomic regions that contain active promoters, with changes in chromatin architecture occurring independently of Top2 inhibition, cell cycle arrest, and differential gene expression. Inside the regions with decreased interactions, we detected redistribution of RAD21 around the peaks of H3K27 acetylation. Our study also revealed a common structural pattern in the regions with altered architecture, characterized by two large domains separated from each other. Additionally, doxorubicin was found to increase CTCF binding in H3K27 acetylated regions. Furthermore, we discovered that Top2-dependent chemotherapy causes changes in the distance decay of Hi-C contacts, which are driven by direct and indirect inhibitors. Our proposed model suggests that doxorubicin-induced DSBs cause cohesin redistribution, which leads to increased insulation on actively transcribed TAD boundaries. Our findings underscore the significant impact of genotoxic anticancer treatment on the chromatin structure of the human genome.