title: Chromatin organization measured by AluI restriction enzyme changes with malignancy and is regulated by the extracellular matrix and the cytoskeleton.
abstract: Given that expression of many genes changes when cells become malignant or are placed in different microenvironments, we asked whether these changes were accompanied by global reorganization of chromatin. We reasoned that sequestration or exposure of chromatin-sensitive sites to restriction enzymes could be used to detect this reorganization. We found that AluI-sensitive sites of nonmalignant cells were relatively more exposed compared to their malignant counterparts in cultured cells and human tumor samples. Changes in exposure and sequestration of AluI-sensitive sites in normal fibroblasts versus fibrosarcoma or those transfected with oncogenes, nonmalignant breast cells versus carcinomas and poorly metastatic versus highly invasive melanoma were shown to be independent of the cell cycle and may be influenced by proteins rich in disulfide bonds. Remarkably, regardless of degree of malignancy, AluI-sensitive sites became profoundly sequestered when cells were incubated with laminin, Matrigel, or a circular RGD peptide (RGD-C), but became exposed when cells were placed on collagen I or in serum-containing medium. Disruption of the actin cytoskeleton led to exposure, whereas disruption of microtubules or intermediate filaments exerted a sequestering effect. Thus, AluI-sensitive sites are more sequestered with increasing malignant behavior, but the sequestration and exposure of these sites is exquisitely sensitive to information conferred to the cell by molecules and biomechanical forces that regulate cellular and tissue architecture.
authors.affiliation: Department of Pathology, University of Illinois at Chicago, 1819 W. Polk Street, 446 CMW (MC 847), Chicago, IL 60612, USA. amanioti@uic.edu
authors.forename: Andrew J
authors.initials: AJ
authors.lastname: Maniotis
authors.forename: Klara
authors.initials: K
authors.lastname: Valyi-Nagy
authors.forename: John
authors.initials: J
authors.lastname: Karavitis
authors.forename: Jonas
authors.initials: J
authors.lastname: Moses
authors.forename: Viveka
authors.initials: V
authors.lastname: Boddipali
authors.forename: Ying
authors.initials: Y
authors.lastname: Wang
authors.forename: Rafael
authors.initials: R
authors.lastname: Nuñez
authors.forename: Suman
authors.initials: S
authors.lastname: Setty
authors.forename: Zarema
authors.initials: Z
authors.lastname: Arbieva
authors.forename: Mina J
authors.initials: MJ
authors.lastname: Bissell
authors.forename: Robert
authors.initials: R
authors.lastname: Folberg
mesh_terms: D018929:Cell Culture Techniques; D045744:Cell Line, Tumor; D002471:Cell Transformation, Neoplastic / Q000235:genetics*; D002843:Chromatin / Q000235:genetics*; D003094:Collagen; D003599:Cytoskeleton / Q000378:metabolism*; D004262:DNA Restriction Enzymes; D004273:DNA, Neoplasm / Q000032:analysis; D004338:Drug Combinations; D005109:Extracellular Matrix / Q000378:metabolism*; D005434:Flow Cytometry; D015972:Gene Expression Regulation, Neoplastic; D006801:Humans; D007797:Laminin; D046529:Microscopy, Electron, Transmission; D009369:Neoplasms / Q000235:genetics*; D011509:Proteoglycans
chemical_list: D002843:Chromatin; D004273:DNA, Neoplasm; D004338:Drug Combinations; D007797:Laminin; D011509:Proteoglycans; C059485:matrigel; D003094:Collagen; D004262:DNA Restriction Enzymes