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

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

“…Thus, it has been suggested that the NHOS is rather independent of functional constraints related to replication and/or transcription and that it is primarily established following structural and thermodynamic constraints that impinge on chromosomal DNA and the NM [Aranda-Anzaldo, 2012, 2016. This suggestion is consistent with recent evidence that the NHOS is not conserved between similar cell types from closely related species [Silva-Santiago et al, 2017]. Therefore, it becomes interesting to compare at the large scale the NHOS of postmitotic neurons, that normally do not replicate the genome, with that of hepatocytes and na€ ıve B lymphocytes, as well as to determine the local NHOS of the 162 kb genomic region of the albumin-family genes in postmitotic neurons which are unable to express such genes, because a similarity in the NHOS of neurons, either at the large scale or at the local level, when compared to that in hepatocytes or na€ ıve B lymphocytes may imply the signature of a functional constraint involved in determining the NHOS independently of the cell type.…”

“…Considering that in a given organism the nucleotide sequence of the genome is basically the same in all cells, it is likely that qualitative and quantitative differences in NM composition are mainly responsible for the cell‐type specificity of the NHOS. However, there is evidence that the NHOS is not conserved between similar cell types from two closely related species and considering that the set of proteins of a given cell type should be rather similar in the corresponding cells from the two closely related species, it has been suggested that known differences in the disposition of the syntenic blocks of nucleotides along the chromosomes of the species compared may result in different 3D configurations or topologies for the corresponding DNA fibers [Silva‐Santiago et al, ]. Indeed, DNA is a heteropolymer whose stiffness or flexibility varies along the chromosome depending on nucleotide composition [Travers, ].…”

“…the corresponding DNA fibers [Silva-Santiago et al, 2017]. Indeed, DNA is a heteropolymer whose stiffness or flexibility varies along the chromosome depending on nucleotide composition [Travers, 2004].…”

DNA Length Modulates the Affinity of Fragments of Genomic DNA for the Nuclear Matrix In Vitro

“…Such a differential could be explained in part by the known cell‐type specific differences in NM composition [Röber et al, ; Stuurman et al, ; Dent et al, ]. However, there is also evidence that similar cell types from closely related species show significant differences in their NHOS [Silva‐Santiago et al, ]. Thus considering that equivalent cell types performing the same functions in two closely related species possess quite similar sets of constituting proteins, then it is unlikely that the species‐specific differences in NHOS could be explained by significant differences in NM‐protein composition.…”

“…Such a differential could be explained in part by the known cell-type specific differences in NM composition [R€ ober et al, 1990;Stuurman et al, 1990;Dent et al, 2010]. However, there is also evidence that similar cell types from closely related species show significant differences in their NHOS [Silva-Santiago et al, 2017a]. Thus considering that equivalent cell types Fig.…”