Cell-type-specific organization of nuclear DNA into structural looped domains.
In the interphase nucleus of metazoan cells the DNA is organized in supercoiled loops anchored to a proteinaceous substructure known as the nuclear matrix (NM). The DNA is anchored to the NM by means of non-coding sequences of variable length known as matrix attachment regions or MARs operationally classified in structural-constitutive, resistant to high-salt extraction and transient-functional, non-resistant to high-salt extraction. The former are also known as true loop attachment regions or LARs that determine structural DNA loops. The DNA-NM interactions define a higher order structure within the cell nucleus (NHOS). We studied in a comparative fashion the NHOS in two primary cell types from the rat: hepatocytes and naive B lymphocytes, by analyzing the topological relationships between the NM and a set of eight short gene sequences located in six separate chromosomes and as such representing a coarse-grained, large-scale sample of the actual organization of nuclear DNA into structural loop domains. Our results indicate that such an organization is cell-type specific since most of the gene sequences studied showed significant differences in their relative position to the NM according to cell type. Such cell-type specific differences in the NHOS have no obvious correlation with the tissue-specific transcriptional activity of the corresponding genes, supporting the notion that permanent, structural DNA loops are different from transient, functional DNA loops that may be associated with transcription.
Facultad de Medicina, Universidad Autónoma del Estado de México, Toluca, México, Mexico.
Claudia
C
Trevilla-García
Armando
A
Aranda-Anzaldo
D000818:Animals; D001402:B-Lymphocytes / Q000378:metabolism*; D002478:Cells, Cultured; D004247:DNA / Q000737:chemistry* / Q000378:metabolism*; D022781:Hepatocytes / Q000378:metabolism*; D008297:Male; D015530:Nuclear Matrix / Q000378:metabolism*; D009690:Nucleic Acid Conformation; D051381:Rats; D017208:Rats, Wistar; D020133:Reverse Transcriptase Polymerase Chain Reaction
D004247:DNA