Intranuclear and higher‐order chromatin organization of the major histone gene cluster in breast cancer

Abstract

Alterations in nuclear morphology are common in cancer progression. However, the degree to which gross morphological abnormalities translate into compromised higher-order chromatin organization is poorly understood. To explore the functional links between gene expression and chromatin structure in breast cancer, we performed RNA-seq gene expression analysis on the basal breast cancer progression model based on human MCF10A cells. Positional gene enrichment identified the major histone gene cluster at chromosome 6p22 as one of the most significantly upregulated (and not amplified) clusters of genes from the normal-like MCF10A to premalignant MCF10AT1 and metastatic MCF10CA1a cells. This cluster is subdivided into three sub-clusters of histone genes that are organized into hierarchical topologically associating domains (TADs). Interestingly, the sub-clusters of histone genes are located at TAD boundaries and interact more frequently with each other than the regions in-between them, suggesting that the histone sub-clusters form an active chromatin hub. The anchor sites of loops within this hub are occupied by CTCF, a known chromatin organizer. These histone genes are transcribed and processed at a specific sub-nuclear microenvironment termed the major histone locus body (HLB). While the overall chromatin structure of the major HLB is maintained across breast cancer progression, we detected alterations in its structure that may relate to gene expression. Importantly, breast tumor specimens also exhibit a coordinate pattern of upregulation across the major histone gene cluster. Our results provide a novel insight into the connection between the higher-order chromatin organization of the major HLB and its regulation during breast cancer progression.

Higher order genomic organization and regulatory compartmentalization for cell cycle control at the G1/S‐phase transition

“…While the overall chromatin structure of the major histone gene locus is maintained across breast cancer progression, the role of HLB genomic organization in regulating histone gene expression needs further validation. Importantly, breast tumor specimens also exhibit a coordinate pattern of upregulation across the Hist1 locus (Fritz et al, ). Our results provide a novel insight into the higher‐order chromatin organization of the major histone gene locus during breast cancer progression that may be clinically informative.…”

“…(Adapted from Figures and published in Fritz et al ()) The higher‐order chromatin organization of the major histone gene locus. (a) Pairwise DNA‐DNA interactions were analyzed via Hi‐C within the major histone gene cluster in the MCF10 cells.…”

Higher order genomic organization and epigenetic control maintain cellular identity and prevent breast cancer

“…CTCF is a major protein involved in insulator function and mediates intrachromosomal and interchromosomal looping interactions in vertebrates . Through interactions with chromatin remodeling proteins, histone modifying enzymes, and transcription factors, CTCF is implicated in a broad spectrum of critical regulatory functions including imprinting, X chromosome inactivation, and organizing the major histone locus . CTCF and its binding sites are mutated in many cancers, including breast cancer, suggesting its functions are perturbed upon malignant transformation …”

“…As expected with the increased proliferative state of breast cancer cells, this region is the most upregulated cluster of genes in breast cancer in vitro and in tumor samples relative to matched controls. In addition, CTCF is present within the HLB and occupies the TAD boundaries around the major histone gene locus, and therefore may play a critical role in the determination of the HCO of this nuclear body …”

“…Physiological control of gene expression is dependent on chromatin context and requires timely and dynamic interactions between transcription factors and coregulatory machinery that reside in specialized subnuclear microenvironments . Multiple levels of nuclear organization functionally contribute to biological control and are perturbed in cancer . Morphologically, cancer nuclei are generally larger, more irregularly shaped, and have altered subnuclear structures .…”