High-throughput data used in bioinformatics physical distance between enhancers and their target gene promoters (which could be upto 1 Mb apart) genome compartmentization location specific effect on expression DNA methylation histone modification mutations gene duplication genome rearrangement essential biological processes gene regulation networks phylogenomic relationships High-throughput data used in bioinformatics Epigenetic Genomic Whole exome sequencing Transcripto-mic Ribosome profiling Proteomic Protein and RNA Structure Cistromic Genome architecture somatic mutations in coding regions alternatively spliced isoforms Fig. ? Major types of high-throughput data and their key information relevant to drug discovery. genome-wise binding sites of proteins (e.g., transcription factors) differential gene regulation somatic mutation alternative splicing different transcription start and termination sites binding and docking properties location of charged residues for electrostatic interactions enzyme-substrate and ligand-protein interactions translation regulation translation mechanisms (e.g., cap-dependent or internal ribosomal entry) differential translation initiation, elongation and termination translation rate of individual proteins differential protein abundance posttranslational modification signal peptide and cellular localization

Applications of data Molecular biology Molecular evolution Molecular phylogenetics Molecular ecology Developmental biology Biomedical sciences Biopharmaceutical sciences Genetics/epigenetics ……

Recruiting methyl-CpG binding proteins Negatively charged DNA backbone wrapping tightly around histone CpG DNA methylation LM: bisulfite sequencing BQ: what is the methylation signal? Why some CpG methylated and some not? Flanking signal or trans-acting factors or both? Gene on/off Recruiting deacetylase to restore positive charge to histone (hypothetical) negatively charged epigenetic writer, reader or eraser DNA/protein binding mediated by DNA methylation, methy-CpG binding proteins, acetylation/deacetylation, and electrostatic interaction LM: ChIP-on-chip, ChIP-Seq BQ: What are the signals on protein binding sites at sequence and structural level? What is the spatial (tissue- or cell-specific) and temporal (developmental) pattern of protein/DNA binding? What is the effect of changed electric charge of histone through acetylation/deacetylation affect electrostatic interaction with other DNA-binding proteins Fig. ? A general framework of epigenetic effects on gene expression, through 1) DNA methylation and histone acetylation/deacetylation, 2) alteration of DNA-binding proteins and consequent protein-DNA and protein-protein interactions, and 3) alteration of long-distance interactions such as enhancer-promotor interactions. LM – laboratory method, BQ: sample bioinformatic questions. - + Histone deacetylated DNA Alteration of long-distance interaction patterns changes genome architecture (e.g., enhancers and promoters far apart along the genome are brought together) LM: Hi-C BQ: How much variation in gene expression can be explained by its physical location? What genes tend to be spatially associated? What genes tend to change its physical location in response to intra- and extracellular environment? DNA enhancer Protein complex bringing the two together promoter