Generation of ChIP-Loop Libraries

5C Analysis of 3C, ChIP-Loop, and Control Libraries

This protocol describes the 5C method of detecting ligation products in 3C, ChIP-loop, or control libraries. The method starts with a purified 3C library, a purified ChIP-loop library, or a purified control library. Before starting the protocol, assess the quality of the library that will be used by performing semiquantitative polymerase chain reaction (PCR). Ligation products should be readily detectable and nearby restriction fragments should be ligated more frequently than distant fragments. The design of the 5C primers and methods to determine interaction frequencies are also described in this protocol.

3C-Based Chromatin Interaction Analyses

This introduction presents a molecular approach that uses formaldehyde cross-linking to investigate genome structure and function-chromosome conformation capture (3C). This approach allows us to determine the spatial proximity of distant functional genomic sites (by looping). 3C-based techniques to interrogate chromosome folding and long-range interactions between genomic sequences in vivo are detailed.

4C Analysis of 3C, ChIP-Loop, and Control Libraries

The 4C detection method starts with a 3C, ChIP-loop, or control library and then uses inverse polymerase chain reaction (PCR) to amplify all restriction fragments that are ligated to a single restriction fragment of interest. As a result, a genome-wide interaction profile of the restriction fragment of interest is obtained. Before starting a 4C experiment, first assess the quality of the 3C, ChIP-loop, or control library that will be studied by performing semiquantitative PCR with the library as template. This procedure ascertains that ligation products can be readily detected and that nearby restriction fragments become ligated more frequently than more distant fragments. Choice of a restriction enzyme for 4C analysis and determination of interaction frequencies using 4C are described in detail.

Polymerase Chain Reaction (PCR) Detection of 3C Ligation Products Present in 3C, ChIP-Loop, and Control Libraries: Library Titration and Interaction Frequency Analysis

In all 3C-based assays, the aim is to measure the frequency with which two loci interact within cells. This is achieved by determining the relative abundance of ligation products formed during the 3C protocol that carry sequences from both loci. Individual 3C ligation products that are present in a 3C library, the ChIP-loop library, or the control library can be detected by polymerase chain reaction (PCR) using locus-specific primers. The following protocol outlines the procedure to measure relative abundances of ligation products in these libraries using PCR. The first part of the protocol-library titration-is required only once to determine the linear range of PCR detection. Once the linear range of PCR detection is known for a given ligation product library, follow the second part-interaction analysis-to measure the abundance of ligation products of interest in that library. Specific issues regarding determining the relative abundance of ligation products, designing PCR primers, and quantifying interaction frequencies are also described.

Generation of Control Ligation Product Libraries for 3C Analyses

Control libraries are used to determine differences in the efficiency of polymerase chain reaction (PCR) primers in detecting 3C ligation products as well as any differences in the efficiency of amplification. Control libraries are generated by random ligation of restriction fragments so that each ligation product is present in equimolar amounts. This protocol begins with preparations of genomic DNA or BAC DNA preparations. The restriction enzyme used here should be the same as the one used for generation of the 3C or ChIP-loop library. For small genomes, such as those of bacteria and yeast, this protocol can be started with purified genomic DNA. For organisms with larger genomes, such as mouse and human, control libraries are generated from purified BAC clones that cover the genomic region under study. When the region of interest is large and multiple BAC clones are required, select BAC clones that overlap only minimally. Any gaps between the regions covered by the BACs should also be kept to a minimum. Several kits for purifying BAC clones are available (e.g., the Large-Construct Kit from QIAGEN). BAC clones should be mixed in equimolar amounts to ensure that each restriction fragment is present in equal concentration. This is achieved by quantifying the molar concentration of each BAC preparation using real-time PCR and primers that recognize the common BAC vector backbone. Alternatively, the concentration of BAC preparations can be quantified using gel quantification or a NanoDrop detection system.