The nuclear higher-order structure defined by the set of topological relationships between DNA and the nuclear matrix is species-specific in hepatocytes.

During the interphase the nuclear DNA of metazoan cells is organized in supercoiled loops anchored to constituents of a nuclear substructure or compartment known as the nuclear matrix. The stable interactions between DNA and the nuclear matrix (NM) correspond to a set of topological relationships that define a nuclear higher-order structure (NHOS). Current evidence suggests that the NHOS is cell-type-specific. Biophysical evidence and theoretical models suggest that thermodynamic and structural constraints drive the actualization of DNA-NM interactions. However, if the topological relationships between DNA and the NM were the subject of any biological constraint with functional significance then they must be adaptive and thus be positively selected by natural selection and they should be reasonably conserved, at least within closely related species. We carried out a coarse-grained, comparative evaluation of the DNA-NM topological relationships in primary hepatocytes from two closely related mammals: rat and mouse, by determining the relative position to the NM of a limited set of target sequences corresponding to highly-conserved genomic regions that also represent a sample of distinct chromosome territories within the interphase nucleus. Our results indicate that the pattern of topological relationships between DNA and the NM is not conserved between the hepatocytes of the two closely related species, suggesting that the NHOS, like the karyotype, is species-specific.

The Set of Structural DNA-Nuclear Matrix Interactions in Neurons Is Cell-Type Specific and Rather Independent of Functional Constraints.

In metazoans, nuclear DNA is organized during the interphase in negatively supercoiled loops anchored to a compartment or substructure known as the nuclear matrix. The interactions between DNA and the nuclear matrix (NM) are of higher affinity than those between DNA and chromatin proteins since the last ones do not resist the procedures for extracting the NM. The structural interactions DNA-NM constitute a set of topological relationships that define a nuclear higher order structure (NHOS) although there are further higher order levels of organization within the nucleus. So far, the evidence derived from studies with primary hepatocytes and naïve B lymphocytes indicates that the NHOS is cell-type specific at the local and at the large-scale level, and so it has been suggested that such NHOS is primary determined by structural and thermodynamic constraints. We carried out a comparative characterization of the NHOS of postmitotic cortical neurons with that of hepatocytes and naïve B lymphocytes. Our results indicate that the NHOS of neurons is completely different at the large scale and at the local level from that one observed in hepatocytes or in naïve B lymphocytes, confirming on the one hand that the set of structural DNA-NM interactions is cell-type specific and supporting, on the other hand the notion that structural constraints that impinge on chromosomal DNA and the NM are more important for determining this NHOS than functional constraints related to replication and/or transcription. J. Cell. Biochem. 118: 2151-2160, 2017. © 2016 Wiley Periodicals, Inc.