Abstract
In this chapter, we have discussed how the dramatic evolution of DNA sequencing technology has made it possible to gather the whole genome sequence data rapidly and inexpensively. Efficient sequencing facilities could enhance our ability to understand genome biology to a great extent. In brief:•The automation of the di-deoxy sequencing method discovered by Frederick Sanger helped to decipher the major part of the human genome. A completely new technology, “sequencing by synthesis” (SBS), ushered in the “next-generation” sequencing (NGS) technology currently in large-scale use. The other popular NGS methods are “Oligo Ligation and Detection (SOLiD)” and “Nanopore sequencing” technology.•Based on NGS, several chromatin technologies have been developed to understand the functional genome organization. Chromatin technologies help to elucidate the signal-dependent folding and unfolding state of the genome in the context of gene expression.•Modern Genome-wide studies are made possible by advances in rapid and low-cost sequencing technologies. The mapping of single-strand breaks by genome-wide ligation of 3′-OH ends followed by sequencing (GLOE-Seq) portrays the genome's metabolic intermediates.•Enhancers are gene regulatory noncoding cis-elements, often situated far away from the gene (promoter). The functional organization of enhancers in different physiological and developmental contexts provides the most dynamic picture of the genome. Altered enhancer function may cause several diseases, including cancer.•Genome-wide distribution of RNA polymerase II (Pol II) in the context of histone modification marks defines the productive association of Pol II. RNA polymerase II binding to promoters, only in the presence of specific histone modification in the transcription start site and downstream catalyze the full-length transcript synthesis.•Methylation of DNA at cytosine is one of the most important epigenetic modifications involved in epigenetic memory. Genome-wide distribution of methylation (methylome) stably changes with metabolic and environmental cues. Methylome studies are performed by the bisulfite sequencing approach.•Genome organization dramatically alters during development. As the cells progress toward differentiation, the genome becomes more compact, with very few genes in an active state. Enhancer reorganization is essential for the lineage specificity and cellular identity. In the chromatin territories, the topologically associating domains (TADs) could be functionally heterogeneous. The evolutionarily conserved boundaries between the TADs restrict the spreading of heterochromatin.