#Looped domains with protein scaffold plus#

Subsequent work demonstrated both the constitutive (SAR-like) and the facultative (MAR-like) function of the elements depending on the context. the characterization of matrix-associated regions (MARs) the first examples of which supported the immunoglobulin kapp-chain enhancer according to its occupancy with transcription factors.the description of scaffold-attachment elements (SARs) by Laemmli and coworkers, which were thought to demarcate the borders of a given chromatin domain.In retrospect it is of note that the discovery of S/MARs has two major routes: Context-dependent properties Ĭurrent views of the nuclear matrix envision it as a dynamic entity, which changes its properties along the requirements of the cell nucleus-much the same as the cytoskeleton adapts its structure and function to external signals.

#Looped domains with protein scaffold plus#

While the number of S/MARs in the human genome has been estimated to approach 64,000 (chromatin domains) plus an additional 10,000 (replication foci), in 2007 still only a minor fraction (559 for all eukaryotes) had met the standard criteria for an annotation in the S/MARt database. S/MARs have been classified as either being constitutive (acting as permanent domain boundaries in all cell types) or facultative (cell type- and activity-related) depending on their dynamic properties. An increased propensity to separate the DNA strands (the so-called 'stress induced duplex destabilization' potential, SIDD) can serve the formation of secondary structures such as cruciforms or slippage structures, which are recognizable features for a number of enzymes ( DNAses, topoisomerases, poly(ADP-ribosyl) polymerases and enzymes of the histone-acetylation and DNA-methylation apparatus). Instead, their function requires a pattern of 'AT-patches' that confer the propensity for local strand unpairing under torsional strain.īioinformatics approaches support the idea that, by these properties, S/MARs not only separate a given transcriptional unit (chromatin domain) from its neighbors, but also provide platforms for the assembly of factors enabling transcriptional events within a given domain. Although prototype elements consist of AT-rich regions several hundred base pairs in length, the overall base composition is definitely not the primary determinant of their activity. S/MARs do not have an obvious consensus sequence. Being association points for common nuclear structural proteins S/MARs are required for authentic and efficient chromosomal replication and transcription, for recombination and chromosome condensation. They occur at the flanks of transcribed regions, in 5´- introns, and also at gene breakpoint cluster regions (BCRs). S/MARs map to non-random locations in the genome. This nuclear skeleton acts as a dynamic support for many specialized events concerning the readout a spread of genetic information (see below). It has been known for many years that a polymer meshwork, a so-called ' nuclear matrix' or 'nuclear-scaffold' is an essential component of eukaryotic nuclei. Studies on individual genes led to the conclusion that the dynamic and complex organization of the chromatin mediated by S/MAR elements plays an important role in the regulation of gene expression. These elements constitute anchor points of the DNA for the chromatin scaffold and serve to organize the chromatin into structural domains. As architectural DNA components that organize the genome of eukaryotes into functional units within the cell nucleus, S/MARs mediate structural organization of the chromatin within the nucleus. The term S/MAR ( scaffold/matrix attachment region), otherwise called SAR ( scaffold-attachment region), or MAR ( matrix-associated region), are sequences in the DNA of eukaryotic chromosomes where the nuclear matrix attaches. Transcription is terminated (III) followed by dissociation of the transcription complex (IV) Topological changes are propagated once the gene is pulled through the transcriptional machinery (II). When functional demands require the specific translocation of the constituent gene to the matrix, facultative S/MARs responds to topological changes which are initiated by the association of transcription factors (TF) and supported by histone acetylation. A chromatin domain with constitutive S/MARs at its termini (I). S/MAR-functions: constitutive and facultative.