Table 2 Current next-generation sequencing technologies that are suitable for pharmacogene regulatory element discovery
From: Pharmacogene regulatory elements: from discovery to applications
Technology | Description | References |
|---|---|---|
DNA methylation | ||
MethylC-Seq | Unmethylated cytosines are converted into uracil by bisulfite treatment, and the converted DNA is sequenced. Methylation is detected with single-base resolution by comparing the sequence of the converted DNA with that of the unconverted DNA, assuming efficient cytosine conversion | |
RRBS | Restriction digested DNA is size-selected, treated with bisulfite for cytosine conversion, and sequenced. Methylation is detected as described for MethylC-Seq. The reduced representational approach lessens the complexity of analysis and covers a reproducible fraction of the genomic space, but regions with a lack of restriction sites might be missed | |
MeDIP | Methylated DNA elements are enriched with an antibody that binds to 5-methylcytosine, and then sequenced | [82] |
MBD-Seq | Methylated DNA elements are enriched with recombinant methyl CpG binding domain of MBD2, and then sequenced | [83] |
CAP-Seq | The chromatography-based method uses the CXXC domain, which has a high affinity for unmethylated CpG sites, to enrich for DNA elements with methylated CpG sites | [84] |
MRE-Seq | A methylation-sensitive restriction enzyme is used, leaving unmethylated CpG sites available for sequencing | [85] |
Identification of regulatory elements | ||
ChIP-Seq | DNA is crosslinked and isolated via immunoprecipitation typically using an antibody for a transcription factor, regulatory co-factor, or chromatin mark. Subsequent sequencing allows identification of the binding sites of the DNA-associated protein or histone mark | |
DNase-Seq | DNase I hypersensitive sites are known to harbor regulatory elements. In this method, they are identified by sequencing DNase-digested DNA fragments | |
FAIRE-Seq | Nucleosome-depleted DNA elements associated with regulatory activities are isolated via phenol-chloroform phase separation and sequenced | |
ChIP-exo | Similar to ChIP-Seq, it is used for identification of DNA elements interacting with a protein of interest. It provides better resolution over ChIP-Seq by using an exonuclease to trim unbound DNA around the transcription factor binding site | [133] |
Expression profiling | ||
RNA-Seq | RNA fragments are converted to cDNA and sequenced for gene expression, isoform, and splicing analysis. Novel transcripts and isoforms can be recovered, but low-expression level transcripts may be missed unless sequencing coverage is sufficient | |
Chromosomal interactions | ||
Hi-C | DNA elements in close spatial proximity are crosslinked, ligated and sequenced. It allows for a genome-wide, high-resolution analysis of interacting DNA elements | [127] |
ChIA-PET | DNA elements interacting with a protein of interest are enriched via chromatin immunoprecipitation, crosslinked and ligated so that long-range interactions can be identified by sequencing | [128] |