DNA looping-dependent targeting of a chromatin remodeling factor

Eukaryotic genomes are highly complex structures that must be efficiently packaged into relatively small nuclei in order to accommodate multiple DNA-dependent processes, from transcription and DNA replication to DNA repair and recombination. The compaction of genomes is hierarchically achieved at two distinct levels: (1) the compaction of DNA into nucleosome arrays and (2) the three-dimensional (3D) folding of nucleosome arrays within the nucleus. The compaction of genomes is required for the proper regulation of DNA-dependent processes, and disruption of either is associated with complex human diseases. The 3D folding of nucleosome arrays within the nucleus is highly dynamic, with discrete chromosomes occupying distinct non-random “territories”. Within each chromosome territory, specific DNA “loops” are formed that uniquely juxtapose distally located DNA loci, bringing them into close proximity. DNA loops have been implicated in transcriptional regulation and transcriptional memory, although the molecular mechanisms for these phenomena remain to be determined. The compaction of DNA into nucleosome arrays is accomplished by wrapping DNA around an octamer of histone proteins. Eukaryotic organisms regulate DNA-dependent process through nucleosome arrays using highly conserved ATPdependent chromatin remodeling enzymes that utilizing the energy released from ATP hydrolysis to slide, evict or replace histones within nucleosomes. ATP-dependent chromatin remodeling enzymes are highly abundant, yet function only at very specific DNA looping-dependent targeting of a chromatin remodeling factor