Nonspecific bridging-induced attraction drives clustering of DNA-binding proteins and genome organization

Abstract

Molecular dynamics simulations are used to model proteins that diffuse to DNA, bind, and dissociate; in the absence of any explicit interaction between proteins, or between templates, binding spontaneously induces local DNA compaction and protein aggregation. Small bivalent proteins form into rows [as on binding of the bacterial histone-like nucleoid-structuring protein (H-NS)], large proteins into quasi-spherical aggregates (as on nanoparticle binding), and cylinders with eight binding sites (representing octameric nucleosomal cores) into irregularly folded clusters (like those seen in nucleosomal strings). Binding of RNA polymerase II and a transcription factor (NFκB) to the appropriate sites on four human chromosomes generates protein clusters analogous to transcription factories, multiscale loops, and intrachromosomal contacts that mimic those found in vivo. We suggest that this emergent behavior of clustering is driven by an entropic bridging-induced attraction that minimizes bending and looping penalties in the template.polymer physics | Brownian dynamics | chromatin looping | nucleosome D NA in living cells associates with proteins that continuously bind and dissociate. Some proteins affect local structure (such as histones and histone-like proteins), whereas others act globally to compact whole chromosomal segments [such as CCCTC-binding factor (CTCF)] (1-3). Bound proteins also cluster into supramolecular structures; for example, different transcription factors often bind to the same hot spots in the fly genome (4), and active molecules of RNA polymerase II coassociate in transcription factories (5, 6). In the latter case, clustering generates high local concentrations that facilitate production of the appropriate transcripts, as well as organizing the genome in 3D space.Against this background, biophysicists have begun to model DNA folding driven by DNA-binding proteins (3,(7)(8)(9)(10)(11)(12). Usually, the effects of DNA binding are incorporated into an effective potential that influences DNA dynamics; for instance, by stipulating that selected protein-binding regions in the polymer attract each other (11,12). Here, we use molecular dynamics (MD) to model proteins that diffuse to DNA, bind, and dissociate. In the absence of any explicit mutual attraction between proteins or between monomers in the polymer, we uncover an emergent property of the system: binding spontaneously induces protein clustering and genome compaction. For example, simulations yield structures seen experimentally when proteins representing bacterial histone-like nucleoid-structuring protein (H-NS) (1, 2, 13), gold nanoparticles (14, 15), and nucleosome cores bind to DNA. Using data derived from ChIP coupled to high-throughput sequencing (ChIP-seq) (16), we also model binding of RNA polymerase II and its transcription factor, NFκB, to the appropriate (cognate) sites on four human chromosomes; the two proteins spontaneously cluster into factories that are surrounded by loops that reflect those detected in cells using chromatin inte...

Cell cycle progression inCaulobacterrequires a nucleoid-associated protein with high AT sequence recognition

“…This clustering suggests that distant genomic loci are colocalized in 3D space, as has been observed for H-NS-bound loci in E. coli (37). In addition to H-NS, multiple NAPs are known to promote long-range intrachromosomal interactions through DNA bending, looping, compaction, and the stabilization of discrete subdomains (4,(55)(56)(57)(58)(59)(60)(61)(62)(63). It may be that the self-association of GapR molecules links together noncontiguous loci that contain AT-rich sequences.…”

Nonequilibrium Chromosome Looping via Molecular Slip Links

“…However, these data do not distinguish between CTCF-mediated loops and other contacts, which may either form stochastically or through other chromatin-binding proteins [31][32][33][34]. Chromatin…”

“…3d, inset, and This behaviour is reminiscent of the "bridging-induced attraction" [32,33] which drives the formation of protein clusters, although the underlying mechanism is here purely entropic.…”

Probing transient protein-mediated DNA linkages using nanoconfinement

“…The formation of very large loops (10s to 100s of kbp) in the emergence of chromatin organization and the necessity of this chromatin organization for normal cell function is an intensive focus of recent research. [7][8][9] In particular, the co-operative action of multiple protein copies in promoting DNA looping [10][11][12][13] and conformational change 14 has become a central question. Here we demonstrate a tool for detecting transient interactions that may be important in facilitating looping transitions (Fig.…”