The organization of a large transcriptional unit (Fyn) into structural DNA loops is cell-type specific and independent of transcription

In the interphase nucleus of metazoan cells the DNA is organized in supercoiled loops anchored to a nuclear matrix (NM). The DNA is anchored by non-coding sequences known as MARs, in situ operationally classified in structural-constitutive and transient-functional. We have previously shown that the organization of the multi-gene rat-albumin family locus into structural DNA loops is remarkably different between primary hepatocytes, where such genes are expressed, and naïve B lymphocytes, where such genes are not expressed. These results together with previous observations from other authors suggested that the local organization into structural DNA loops might determine the potential for a gene to be expressed or not. Thus in the present work we determined the organization of the Fyn locus, a single large transcriptional unit, into structural DNA loops in both primary rat hepatocytes and B lymphocytes. Our results indicate that the organization of the Fyn locus in structural DNA loops is cell type-specific and yet the gene is expressed in both cell types, supporting the notion that in vivo the organization of DNA into structural loops is primarily determined by factors independent of transcription but also that transcription adapts to work upon radically different structural DNA loop organizations.

► Genomic DNA is organized in structural loops attached to a nuclear matrix.
► The organization of Fyn in DNA loops is different in two primary cell types.
► Fyn is expressed in both primary cell types.
► Transcription do not determined organization of the genome in structural DNA loops.
► No functional correlation between structural DNA loops and transcriptional units.