Imaging chromatin interactions at sub-kilobase resolution Via Tn5-FISH

Abstract

There is increasing interest in understanding how the three-dimensional organization of the genome is regulated. Different strategies have been employed to identify chromatin interactions genome wide. However, due to the current limitations in resolving genomic contacts, visualization and validation of these genomic loci with sub-kilobase resolution remain the bottleneck for many years. Here, we describe Tn5 transposase-based Fluorescence in situ Hybridization (Tn5-FISH), a Polymerase Chain Reaction (PCR)-based, cost-effective imaging method, which achieved the co-localization of genomic loci with sub-kilobase resolution, to fine dissect genome architecture at sub-kilobase resolution and to verify chromatin interactions detected by Chromatin Configuration Capture (3C)-derivative methods. Especially, Tn5-FISH is very useful to verify short-range chromatin interactions inside of contact domain and Topologically Associated Domain (TAD). It also offers one powerful molecular diagnosis tool for clinical detection of cytogenetic changes in cancers.the genomic resolution of traditional FISH based on BAC clones is too low to precisely label and to image the interactions within the genomic distance less than 500 Kb, such as inside of a TAD or contact domain, whereas most of the chromatin interactions identified by 3C-based techniques fall into this range [25][26][27] .There are advanced FISH techniques with higher genomic resolution, such as oligopaint 28 , HD-FISH 29 , CasFISH 30 and MB-FISH 31 , etc. But they are either very expensive 28,31 or require complex preparation 29,30 , which is difficult for laboratories that do not routinely use various FISH techniques to adopt and to study genomic loci. Molecular beacon-based FISH 31 can offer a resolution of 2.5 kb, but is also technically complex and lacks cost-effectiveness.Here we report a novel and cost-effective method named Tn5-FISH (Tn5 transposase based fluorescence in situ hybridization) that offers more than one order of magnitude higher resolution than traditional FISH. Tn5-FISH utilized the hyperactive Tn5 transposase for probe library construction, and PCR for probe library amplification and labeling. Foreign DNA sequences can be inserted into host genome with the help of Tn5 transposase through "cut and paste" mechanism 32 , which granted Tn5 transposase the ability to induce the DNA double breaks at insertion site. Efficient segmentation of targeted DNA sequence is favored in probe library construction 33,34 . With the aid of bioinformatic tools, we can obtain the repeat-free DNA sequence suitable for probing via genomic PCR.Then Tn5-FISH was employed to verify the chromatin interactions, for example, the ones inside of type II KRT locus in chromosome 12 of K562 cells measured by Hi-C contact map from published data. Triple-color Tn5-FISH can verify these interactions well, with triple-color traditional BAC FISH as positive control, indicating that Tn5-FISH is suitable to visualize specific genomic loci and chromatin interactions inside a typical TAD, in ei...