Detecting Long-Range Enhancer-Promoter Interactions by Quantitative Chromosome Conformation Capture.
Chromosome conformation capture (3C) technology and its derivatives are currently the primary methodologies measuring contacts among genomic elements. In fact, the lion share of what is currently known about chromosome folding is based on 3C-related approaches. For example, distal enhancers are commonly in physically proximity with their target genes, forming chromatin loops. Additional layers of chromatin organization have been described using 3C-based techniques, including topological domains (TADs) and sub-TADs. Finally, inter-chromosomal interactions have been reported although they are much less frequent. 3C is becoming increasingly widespread in its use for understanding genome organization. Here we provide a protocol for quantitative 3C using real-time PCR analysis, along with essential quality controls and normalization methods.
Transcription Imaging Consortium, Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, VA, 20147, USA.
Wulan
W
Deng
Division of Hematology, The Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA. blobel@email.chop.edu.|The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA. blobel@email.chop.edu.
Gerd A
GA
Blobel
D000818:Animals; D002875:Chromosomes / Q000737:chemistry* / Q000235:genetics*; D004742:Enhancer Elements, Genetic; D006801:Humans; D009690:Nucleic Acid Conformation; D011401:Promoter Regions, Genetic; D060888:Real-Time Polymerase Chain Reaction; D015183:Restriction Mapping
3C; Chromatin looping; Chromosome conformation capture; Enhancer; Ligation; Promoter; Restriction enzyme; TaqMan; qPCR