br HMGB proteins and chromatin

HMGB proteins and chromatin structure The multifaceted roles played by HMGB (formerly called HMG-1 and -2) proteins in modulating chromatin structure, gene transcriptional activity and cellular phenotype have been covered in a number of recent reviews and readers are referred to these for in-depth coverage of these topics [6,14–17]. Here emphasis is placed on comparing the similarities and differences of these proteins with the other HMG families. The mammalian HMGB proteins are characterized by two tandem DNA-binding regions called HMG box domains followed by a 30 amino SMER 3 long acidic tail. Each of the approximately 80 amino acid long HMG box domains has a similar structure which is composed of three α-helices folded into an L-shaped configuration whose concave surface binds into the minor groove of DNA with limited or no sequence specificity [158]. The motion and the DNA-binding activity of the two HMG boxes are independent of each other and the acidic tail is unstructured [79], characteristics that, as is the case with HMGA proteins, impart considerable structural and substrate recognition flexibility to the proteins. The HMG box domain is an ancient structural motif that is present in one or more copies in non-HMG proteins in eukaryotic organisms ranging from yeast to sponges to plants [15]. HMG boxes bind to the minor groove of B-form DNA, significantly widen the groove and introducing a bend of 90° or more into the backbone. HMGB proteins also bind with high affinity to already distorted DNA structures such as four-way junctions, bulges, kinks and modified DNA containing cisplatin adducts [122]. The induction of DNA bends and the recognition of distorted DNA structures are the two main ways that HMGBs function as chromatin “architectural” proteins. For example, it has been suggested that HMGB-induced DNA bending produces an allosteric transition structure that promotes the recognition and binding by other proteins during the formation of functional multiprotein:DNA complexes. On the other hand, HMGB recognition and binding to already distorted DNA conformations is thought to be analogous to enzymes recognizing molecular structures that resemble transition states between reagents and products and, as a consequence, influences the rate of formation of multiprotein:DNA complexes [6]. HMGB proteins participate in, and facilitate, many different nuclear processes including transcription, replication, V(D)J recombination, DNA repair and other activities. HMGB proteins promote the transcription of genes through several mechanisms [6,15]. One mechanism is mediated by the ability of HMGB proteins to bind to nucleosomes [159]. HMGB can bind to DNA segments at the entry/exit of nucleosomes (whose 3D structure has been suggested to resemble a four-way junction [180]) in much the same way histone H1 [26]. However, in contrast to H1 binding, which is thought to lock nucleosomes in place and make them less mobile and less accessible to transcription factors [26], HMGB binding facilitates recruitment of chromatin remodeling proteins (e.g., ACF/CHRAC) that induce nucleosome sliding, thus exposing previously blocked regions of DNA [20]. A second mechanism, proposed on the basis of results from EMSA competition and other in vitro assays, involves HMGB in a context where it acts as a transcriptional repressor, binding to the TATA-binding protein (TBP) to form a stable HMG-1/TBP/TATA complex, which is proposed to inhibit the assembly of the preinitiation complex on gene promoters [37]. Additional experiments have demonstrated that the accessory transcription factor TFIIA can also bind to TBP and displace HMGB1 from the inhibitory HMGB1/TBP/TATA complex, thus allowing a stable preinitiation complex to form and promote the early stages of transcriptional initiation [38]. The generality of this proposed inhibitory role of HMGB in transcriptional initiation remains to be determined. A third, and much better characterized mechanism, is the so called “hit-and-run” mode of action in which HMGB proteins facilitate the stable binding of other transcription factors to their DNA recognition sites but then dissociates from any ternary complex that is formed leaving the partner protein stably bound to its DNA substrate (reviewed in [6]). In these cases, HMGB is thought to function as a transient protein chaperone that mediates a “match” and then leaves the couple alone after their union. HMGB proteins are know to make weak, but specific physical interactions with a number of different transcription factors including p53, all class I steroid receptors, TBP, RAG1, HOX and POU proteins, several NF-κB subunits and others. A number of different types of hit-and-run pathways involving HMGB and these transiently associating proteins have been reported but generally appear to fall into three distinct categories [15]. One pathway is exemplified by p53 which binds only very weakly to its recognition site in B-form linear DNA. In this case, HMGB first binds and bends the DNA, presents it to p53 which then binds tightly to its pre-bent recognition sequence and HMGB leaves the complex. A second pathway involves proteins such as RAG1 and the glucocorticoid receptor (GR). These proteins also bind only weakly to their recognition sequences in linear DNA but, as a result of binding, introduce a slight distortion in their target sites. HMGB recognizes and binds to these distorted structures with high affinity, thus stabilizing and strengthening the interaction of the partner protein (e.g., RAG1 or GR) to DNA and then HMGB leaves the complex. Interestingly, in the case of the glucocorticoid receptor, it has been demonstrated that these HMGB-GR interactions can only occur within the context of chromatin [7]. In a third pathway, HMGB interacts with its partner protein prior to their actual binding to DNA, a coordinated DNA binding/bending occurs following protein:DNA complex formation, straight away followed by exit of HMGB from the complex.