Long-range DNA interactions are specifically altered by locked nucleic acid-targeting of a CTCF binding site.
Long-range DNA interactions play an important role in gene expression. CCCTC-binding factor (CTCF), a ubiquitously expressed and evolutionarily conserved 11-zinc-finger DNA binding protein, is intimately involved in gene regulation, helping to establish and maintain chromatin architecture and long-range DNA interactions. In order to study the effects of manipulating long range chromatin interactions in the regulation of the neurofibromatosis gene NF1, we targeted Zorro locked nucleic acids (Zorro LNA) to a single CTCF binding site at an NF1 locus in human fibroblast cells. Using chromatin immunoprecipitation, we determined that this Zorro LNA altered CTCF and RNA polymerase II binding at three separate and distinct regions in the NF1 gene. This change in protein binding was associated with changes in long-range DNA interactions at the NF1 locus and downregulation of NF1 gene expression. This study describes an efficient and convenient method to manipulate chromatin structure and alter gene expression that is regulated by long-range DNA interactions without changing the DNA sequence. The use of specific Zorro LNA probes may facilitate our efforts to understand the interactions between chromatin architecture and gene expression.
Medical Service, VA Palo Alto Health Care System and Department of Medicine, Stanford University School of Medicine, Palo Alto, CA 94304, USA.
Jian Qun
JQ
Ling
Aiju
A
Hou
Andrew R
AR
Hoffman
D001483:Base Sequence; D001665:Binding Sites / Q000235:genetics; D000076246:CCCTC-Binding Factor; D002460:Cell Line; D047369:Chromatin Immunoprecipitation; D004247:DNA / Q000235:genetics / Q000378:metabolism*; D005347:Fibroblasts / Q000166:cytology / Q000378:metabolism; D005786:Gene Expression Regulation; D006801:Humans; D008969:Molecular Sequence Data; D025542:Neurofibromin 1 / Q000235:genetics / Q000378:metabolism*; D009841:Oligonucleotides / Q000235:genetics / Q000378:metabolism*; D020641:Polymorphism, Single Nucleotide; D011485:Protein Binding; D012319:RNA Polymerase II / Q000235:genetics / Q000378:metabolism; D012097:Repressor Proteins / Q000235:genetics / Q000378:metabolism*; D020133:Reverse Transcriptase Polymerase Chain Reaction
D000076246:CCCTC-Binding Factor; C000619697:CTCF protein, human; D025542:Neurofibromin 1; D009841:Oligonucleotides; D012097:Repressor Proteins; C477371:locked nucleic acid; D004247:DNA; D012319:RNA Polymerase II