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Paper text:
a major goal of genomic studies is to understand the regulatory architecture of the genome ; how , for example , powerful regulatory elements , such as enhancers and silencers , which have the ability to act over large genomic distances , are constrained to act only on appropriate transcription units .
there is considerable evidence for a domain model of genomic regulatory architecture where the actions of long - range regulatory elements are confined within chromosomal domains [ 1 - 3 ] .
the promiscuity of enhancers is restricted to regulation of transcription units within the same domain . in this model of genome organisation ,
insulator elements are proposed to play a key role as domain gate - keepers , shielding genes within the domain from the influence of outside regulatory elements .
how insulators function is still unclear but they have been proposed to associate together to form chromosomal loops providing a physical basis for chromosomal domains .
insulator elements have been shown to have appropriate activities for such a role ; they are defined by their ability to block enhancer - promoter interaction and/or to provide boundaries between different chromatin states and have been demonstrated to be involved in chromosome looping .
but does the segregation of the genome into domains through the formation of chromosomal loops really represent the endogenous function of insulator elements ?
although this question has been asked in the past , recent results in drosophila emphasising links between insulators and the regulation of transcription have once again brought it into focus .
a number of proteins have been associated with insulator function in drosophila , including the suppressor of hairy - wing [ su(hw ) ] protein , ccctc - binding factor ( ctcf ) , centrosomal protein 190 ( cp190 ) , boundary element - associated factor ( beaf ) , gaga factor ( gaf )   and zeste - white-5 ( zw5 ) , and over the past few years , genomic binding sites for several insulator components have been mapped [ 12 - 18 ] . in support of the domain model ,
these studies reveal associations between particular insulator components and boundaries of chromatin state domains ; for example , bartkuhn et al .  
document that cp190 and ctcf binding correlates strikingly with the boundaries of repressive chromatin domains marked by the h3k27me3 modification .
this accords with genomic studies in vertebrates demonstrating that ctcf binding sites mark chromatin state boundaries .
however , the drosophila genomic mapping experiments also reveal a strong association between particular insulator components and transcription start sites .
this is especially true for some components , cp190 , gaf and beaf , but not for su(hw ) , suggesting that there may be distinct types of insulator complexes .
beaf 32a and b were initially identified as factors binding to an insulator element ( scs ' ) associated with the 87a hsp70 heat shock locus .
insulator activity is dependent on beaf binding sites and beaf is involved in the formation of a chromosomal loop through interaction with zw5 bound to a second element ( scs ) .
domain boundary credentials , more than 85% of the 1820 beaf binding sites in the genome are less than 300 bp from transcription start sites .
many ( 50% ) of these beaf peaks are associated with head - to - head gene pairs , although these beaf sites do not appear to function to insulate these adjacent promoter regions from each other .
sharing of components between insulators and promoters may fit with shared structural features of these elements ( for example , both ctcf - binding sites and active transcription start sites are marked by the presence of specific histone variants and are associated with nucleosomes containing both the h3.3 and h2a.z variants ) . while this may be interpreted as indicating a link between insulators and transcriptional regulation
insulator components may serve a variety of functions and not all their binding sites are necessarily associated with insulator function .
however , other experimental approaches provide support for a fundamental role for insulator - promoter interaction . it has been known for some time that some promoters can behave as insulators in enhancer - blocking assays .
however , it was never clear whether the mechanism of enhancer - block was the same in both cases .
recently , chopra et al .   have uncovered a connection between promoters with enhancer - blocking activity and the presence of stalled rna polymerase ii ( pol ii ) .
testing the ability of several hox gene promoters to exhibit enhancer - blocking , promoters associated with stalled pol ii showed blocking function whereas several unstalled promoters did not .
the enhancer - blocking activity was dependent on the function of the elongation factors negative elongation factor ( nelf ) and drb sensitivity - inducing factor ( dsif ) , which are thought to stabilise pol ii at the pause site .
however , the key observation that draws together insulators and promoters is that the enhancer - blocking activity of two bithorax - complex insulators , fab7 and fab8 , is also dependent on the elongation factors nelf and dsif . as fab7 and fab8
do not seem to contain stalled polymerase , the implication is that the insulators interact with promoters to inhibit elongation .
this fits with observations , using damid ( dna adenine methyltransferase identification ) or chromosomal conformation capture , that the fab7 and fab8 insulators can form loops that bring them into contact with promoter regions of the abd - b hox gene and that this configuration is associated with repression of abd - b transcription . in support of the generality of interaction between insulators and
the regulation of transcription elongation , jiang et al .   found considerable overlap between beaf and nelf binding sites .
in addition , vertebrate studies using chromatin topology assays have identified insulator - promoter associations at several loci , including igf2-h19   and cftr .
overall , the above combination of genomic binding site location and functional analysis currently indicates a more intimate relationship between insulators and the regulation of gene transcription than is suggested by the domain boundary / chromosome loop model .
insulators may serve a diverse range of functions ; as classical boundaries , as boundaries of regulatory regions , and as regulators of transcription .
even the regulatory effects of insulators can apparently be diverse ; beaf appears to be predominantly required to facilitate transcription whereas the above interactions between the fab insulators and abd - b promoters occur in a repressive context .
it is feasible that insulator elements in general are involved in the specification of chromosomal topology ; this could provide a common function but , depending on the context , could have diverse consequences for chromatin state and transcriptional regulation .
insulator elements have long been associated with a proposed domain boundary function , ensuring appropriate associations between regulatory elements and transcription units through the physical organisation of the genome into looped domains . 
 recent experiments in drosophila have , however , highlighted a more direct involvement of insulators in transcriptional regulation .