BackgroundHigher-order chromatin structure is often perturbed in cancer and other pathological states. Although several genetic and epigenetic differences have been charted between normal and breast cancer tissues, changes in higher-order chromatin organization during tumorigenesis have not been fully explored. To probe the differences in higher-order chromatin structure between mammary epithelial and breast cancer cells, we performed Hi-C analysis on MCF-10A mammary epithelial and MCF-7 breast cancer cell lines.ResultsOur studies reveal that the small, gene-rich chromosomes chr16 through chr22 in the MCF-7 breast cancer genome display decreased interaction frequency with each other compared to the inter-chromosomal interaction frequency in the MCF-10A epithelial cells. Interestingly, this finding is associated with a higher occurrence of open compartments on chr16–22 in MCF-7 cells. Pathway analysis of the MCF-7 up-regulated genes located in altered compartment regions on chr16–22 reveals pathways related to repression of WNT signaling. There are also differences in intra-chromosomal interactions between the cell lines; telomeric and sub-telomeric regions in the MCF-10A cells display more frequent interactions than are observed in the MCF-7 cells.ConclusionsWe show evidence of an intricate relationship between chromosomal organization and gene expression between epithelial and breast cancer cells. Importantly, this work provides a genome-wide view of higher-order chromatin dynamics and a resource for studying higher-order chromatin interactions in two cell lines commonly used to study the progression of breast cancer.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-015-0768-0) contains supplementary material, which is available to authorized users.

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Bone sialoprotein (BSP) is a highly modified, anionic phosphoprotein that is expressed almost exclusively in mineralizing connective tissues and has been shown to be a potent nucleator of hydroxyapatite (HA). Two polyglutamic acid (poly[E]) regions, predicted to be in an ␣-helical conformation and located in the amino-terminal half of the molecule, are believed to be responsible for this activity. Using a prokaryotic expression system, full-length rat BSP was expressed and tested for HA nucleating activity in a steady-state agarose gel system. The unmodified protein is less potent than native bone BSP, indicating a role for the post-translational modifications in HA nucleation. domains, were expressed and tested for nucleating activity. Whereas the peptide encompassing the second poly[E] domain was capable of nucleating HA, the first domain peptide showed no activity. The conformation of the wild-type and mutated proteins and peptides were studied by circular dichroism and small angle x-ray scattering, and no secondary structure was evident. These results demonstrate that a sequence of at least eight contiguous glutamic acid residues is required for the nucleation of HA by BSP and that this nucleating "site" is not ␣-helical in conformation.Mineralization of the extracellular matrix in bone, dentin, and cementum is a complex, poorly understood process that is believed to involve both hydroxyapatite-nucleating and -modulating noncollagenous proteins. In bone, it has been postulated that type I collagen acts as a structural matrix, whereas HA nucleation is mediated by an anionic phosphoprotein (1-3). Of the noncollagenous proteins, bone sialoprotein (BSP) 1 is the most likely candidate. The highly anionic nature of BSP and its spatio-temporal pattern of expression have led investigators to propose a role of this protein in the mineralization of bone (1-4).Mammalian BSPs contain an average of 327 amino acids, which includes a 16-residue signal sequence. The protein has a molecular mass of ϳ33-34 kDa. However, post-translational modifications, including both N-and O-linked glycosylation, tyrosine sulfation, and serine and threonine phosphorylation, constitute 50% of the total mature protein weight of ϳ75 kDa. Analysis of the mammalian BSP cDNAs reveals a 45% level of sequence identity, plus an additional 10 -23% in conservative replacements. However, identity of up to 90% is observed in and around two polyglutamic acid sequences (poly[E]); an ArgGly-Asp (RGD) cell-binding motif; sites of phosphorylation, sulfation, and glycosylation; and sequences near the amino and carboxyl termini, which are rich in tyrosine residues (5).Normally BSP expression is limited almost exclusively to mineralized connective tissues, and its expression is localized to areas of bone formation. By in situ hybridization, it has been shown that BSP expression occurs in osteoblasts actively engaged in bone formation and is found at low or undetectable levels in other regions of mineralized tissue (6 -11). Transfection of BSP into nonmineralizin...

Bone sialoprotein (BSP) is an anionic phosphorylated glycoprotein that is expressed almost exclusively in mineralized tissues and has been shown to be a potent nucleator of hydroxyapatite formation. The binding of BSP to collagen is thought to be important for the initiation of bone mineralization and in the adhesion of bone cells to the mineralized matrix. Using a solid phase assay, we have investigated the interaction between BSP and collagen. Initial studies showed that raising the ionic strength, decreasing the pH below 7, or introducing divalent cations diminishes but does not abolish the binding of BSP to collagen, indicating that the interaction is only partly electrostatic in nature. Both boneextracted and recombinant (r)BSP exhibited similar binding affinities, indicating that post-translational modifications are not critical for binding. To identify the collagen-binding domain, recombinant peptides of BSP were studied. Peptide rBSP-(1-100) binds to type I collagen with an affinity similar to that of full-length rBSP, whereas peptides containing the sequences 99 -201 or 200 -301 do not bind. Further studies showed that rBSP-(1-75) competitively inhibits the binding of rBSP-(1-100), whereas rBSP-(21-100) inhibits binding to a lesser extent, and rBSP-(43-100) does not inhibit binding. These results suggest that the collagen-binding site of rat BSP is within the sequence 21-42, with residues N-terminal of this region likely also involved. This site was confirmed by the demonstration of collagen-binding activity of a synthetic peptide corresponding to residues 19 -46. The collagen-binding domain, which is highly conserved among species, is enriched in hydrophobic residues and lacks acidic residues. We conclude that residues 19 -46 of BSP represent a novel collagenbinding site. Bone sialoprotein (BSP)1 is a highly anionic phosphoprotein normally expressed only in mineralized tissues and at sites of new mineral formation (1, 2). Studies by nuclear magnetic resonance, circular dichroism (CD), and small angle x-ray scattering have concluded that BSP has a flexible conformation with very little, if any, secondary structure (3-6).BSP has been shown to be involved in cell attachment, cell signaling, hydroxyapatite binding, hydroxyapatite nucleation, and collagen binding (7). It has been proposed that the unstructured, flexible nature of BSP is required for its function as a bridging molecule with multiple binding partners (3). An understanding of the interaction between BSP and collagen is important, as the matrix-mineral relationship in bone is characterized by the presence of hydroxyapatite crystals in the hole zones of the collagen fibrils and by their preferential orientation parallel to the fibril axes (8 -10). To account for this pattern of initial mineral deposition, it is believed that BSP, which has been shown to be a potent nucleator of hydroxyapatite in vitro (5,11,12), is closely associated with type I collagen fibrils.An interaction between BSP and collagen type I has been described previously. BSP, b...