SATB1-mediated functional packaging of chromatin into loops.
Mammalian genomes are organized into multiple layers of higher-order chromatin structure, and in this organization chromatin looping is a striking and crucial feature that brings together distal genomic loci into close spatial proximity. Such three-dimensional organization of chromatin has been suggested to be functionally important in gene regulation. Many important questions need to be addressed, such as what types of nuclear proteins are responsible for folding chromatin into loops, whether there are any genomic marks that serve as the core sites of chromatin folding events, how distal genomic sites are brought together, and what are the biological consequences for interactions between distal genomic loci. In order to address these fundamental questions, it is essential to devise and employ methods that can capture higher-order structures formed by specific nuclear proteins at high resolution. In this article, in order to describe methods of analyzing protein-mediated chromatin interactions, we will use as an example a global genome-organizer protein, SATB1, which mediates chromatin looping.
Life Sciences Division, Lawrence Berkeley National Laboratory, University of California, Berkeley, CA 94720, USA. TKohwi-Shigematsu@lbl.gov
Terumi
T
Kohwi-Shigematsu
Yoshinori
Y
Kohwi
Keiko
K
Takahashi
Hunter W
HW
Richards
Stephen D
SD
Ayers
Hye-Jung
HJ
Han
Shutao
S
Cai
D000818:Animals; D001483:Base Sequence; D001665:Binding Sites; D002843:Chromatin / Q000235:genetics*; D047369:Chromatin Immunoprecipitation / Q000379:methods; D002874:Chromosome Mapping / Q000379:methods; D003432:Cross-Linking Reagents / Q000737:chemistry; D005557:Formaldehyde / Q000737:chemistry; D006801:Humans; D036961:Matrix Attachment Region Binding Proteins / Q000502:physiology*; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation
D002843:Chromatin; D003432:Cross-Linking Reagents; D036961:Matrix Attachment Region Binding Proteins; C076189:SATB1 protein, human; D005557:Formaldehyde