title: Unraveling the 3D genome: genomics tools for multiscale exploration.
abstract: A decade of rapid method development has begun to yield exciting insights into the 3D architecture of the metazoan genome and the roles it may play in regulating transcription. Here we review core methods and new tools in the modern genomicist's toolbox at three length scales, ranging from single base pairs to megabase-scale chromosomal domains, and discuss the emerging picture of the 3D genome that these tools have revealed. Blind spots remain, especially at intermediate length scales spanning a few nucleosomes, but thanks in part to new technologies that permit targeted alteration of chromatin states and time-resolved studies, the next decade holds great promise for hypothesis-driven research into the mechanisms that drive genome architecture and transcriptional regulation.
authors.affiliation: Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.
authors.forename: Viviana I
authors.initials: VI
authors.lastname: Risca
authors.affiliation: Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA. Electronic address: wjg@stanford.edu.
authors.forename: William J
authors.initials: WJ
authors.lastname: Greenleaf
mesh_terms: D000818:Animals; D001483:Base Sequence; D002843:Chromatin / Q000235:genetics* / Q000648:ultrastructure; D044127:Epigenesis, Genetic; D015894:Genome, Human; D023281:Genomics; D006801:Humans; D009690:Nucleic Acid Conformation; D012984:Software
chemical_list: D002843:Chromatin
keywords: chromatin structure; genome architecture; genomics methods; transcriptional regulation