NA 26, while ChIP-seq technology profiles genome-wide protein-DNA interactions by utilizing next-generation

NA 26, while ChIP-seq technology profiles genome-wide protein-DNA interactions by utilizing next-generation parallel DNA sequencing 27. ENCODE (Encyclopedia of DNA Elements, www.encodeproject.org/) is an international collaborative project whose goal is to identify all functional elements in the human genome sequence. All the data generated by ENCODE, including ChIP-seq, RNA-seq, and Dnase-seq datasets in differential tissues, can be freely downloadable for research Lixisenatide chemical information purposes. Experimental strategies for discovering transcriptome-wide microRNA-mRNA regulatory interactions include Crosslinking and Immunoprecipitation followed by high-throughput sequencing (CLIP-seq), Photoactivatable-Ribonucleoside-Enhanced CLIP (PAR-CLIP), and individualCLIP (iCLIP) 28. Protein-protein interactions (PPIs) can be mapped by improving variations of yeast two-hybrid screening (Y2H) for direct binary interactions or by affinity- or immuno-purification to isolate protein complexes, followed by mass spectrometry (AP/MS) to identify indirect associations between proteins 5, 29. Rolland and colleague recently performed a systematic map of 13,944 high-quality human binary protein-protein interactions among 4,303 distinct proteins, providing unprecedented opportunities for understanding human diseases through the interactome 5, 30. In addition, mammalianmembrane two-hybrid assay (MaMTH) is a technique developed recently for detection of integral membrane PPIs 31. Some functional protein microarrays and mass spectroscopybased assays can also be used to identify the phosphorylation targets of individual protein kinases (i.e., kinase ubstrate interactions) 32. Recently, Saliba and colleagues developed a liposome microarray ased assay (LiMA) that measures protein recruitment to membranes in a quantitative and high-throughput manner, generating a large number of protein-lipid interactions 33. An automated high-throughput technology, LUMIER (luminescence-based mammalian interactome mapping), was also developed for mapping dynamic signaling networks in mammalian cells 34. The interactome data generated by these technologies have been stored in some databases, as well (Table 1). The ultimate goal of molecular biology is to interpret how genotypes account for different GW9662 cost phenotypes and diseases. High-throughput genotyping and phenotyping approaches have made great steps towards determining genotype determinants and their interactions in model organisms. For example, yeast genetic interaction studies are well established by Synthetic Genetic Array analysis (SGA) and Epistatic Miniarray Profiling (E-MAP) 35. Systematic analysis of genetic interactions in human cells is still in early stages of developmental application; however, Laufer and colleagues provided a detailed protocol for large-scale mapping of genetic interactions in human cells by combining RNA interference (RNAi) and automated imaging 36. In addition, advances in DNA sequencing technologies allow us to monitor the effects of common genetic variations in sequences at population levels. For example, single nucleotide polymorphism (SNP) genotyping arrays can measure genetic variations of SNPs among a population. Genome-wide association studies (GWAS) focus on examining statistical associations between common SNPs and complex phenotypic traits in a population, and have identified a large number of genetic loci that may be causally associated with major human diseases 37. SNP genotyping arrays also produce massiveAutho.NA 26, while ChIP-seq technology profiles genome-wide protein-DNA interactions by utilizing next-generation parallel DNA sequencing 27. ENCODE (Encyclopedia of DNA Elements, www.encodeproject.org/) is an international collaborative project whose goal is to identify all functional elements in the human genome sequence. All the data generated by ENCODE, including ChIP-seq, RNA-seq, and Dnase-seq datasets in differential tissues, can be freely downloadable for research purposes. Experimental strategies for discovering transcriptome-wide microRNA-mRNA regulatory interactions include Crosslinking and Immunoprecipitation followed by high-throughput sequencing (CLIP-seq), Photoactivatable-Ribonucleoside-Enhanced CLIP (PAR-CLIP), and individualCLIP (iCLIP) 28. Protein-protein interactions (PPIs) can be mapped by improving variations of yeast two-hybrid screening (Y2H) for direct binary interactions or by affinity- or immuno-purification to isolate protein complexes, followed by mass spectrometry (AP/MS) to identify indirect associations between proteins 5, 29. Rolland and colleague recently performed a systematic map of 13,944 high-quality human binary protein-protein interactions among 4,303 distinct proteins, providing unprecedented opportunities for understanding human diseases through the interactome 5, 30. In addition, mammalianmembrane two-hybrid assay (MaMTH) is a technique developed recently for detection of integral membrane PPIs 31. Some functional protein microarrays and mass spectroscopybased assays can also be used to identify the phosphorylation targets of individual protein kinases (i.e., kinase ubstrate interactions) 32. Recently, Saliba and colleagues developed a liposome microarray ased assay (LiMA) that measures protein recruitment to membranes in a quantitative and high-throughput manner, generating a large number of protein-lipid interactions 33. An automated high-throughput technology, LUMIER (luminescence-based mammalian interactome mapping), was also developed for mapping dynamic signaling networks in mammalian cells 34. The interactome data generated by these technologies have been stored in some databases, as well (Table 1). The ultimate goal of molecular biology is to interpret how genotypes account for different phenotypes and diseases. High-throughput genotyping and phenotyping approaches have made great steps towards determining genotype determinants and their interactions in model organisms. For example, yeast genetic interaction studies are well established by Synthetic Genetic Array analysis (SGA) and Epistatic Miniarray Profiling (E-MAP) 35. Systematic analysis of genetic interactions in human cells is still in early stages of developmental application; however, Laufer and colleagues provided a detailed protocol for large-scale mapping of genetic interactions in human cells by combining RNA interference (RNAi) and automated imaging 36. In addition, advances in DNA sequencing technologies allow us to monitor the effects of common genetic variations in sequences at population levels. For example, single nucleotide polymorphism (SNP) genotyping arrays can measure genetic variations of SNPs among a population. Genome-wide association studies (GWAS) focus on examining statistical associations between common SNPs and complex phenotypic traits in a population, and have identified a large number of genetic loci that may be causally associated with major human diseases 37. SNP genotyping arrays also produce massiveAutho.