Chapter 2 - Applications of Deep Sequencing to Developmental Systems

Abstract

High throughput sequencing is a powerful new tool for obtaining information about nucleic acids. RNA-seq permits both new gene discovery and “digital” quantitation of all RNA levels. ChIP-seq assesses the genomic locations of bound proteins, protein modifications and DNA modifications. DNAse-seq identifies genomic regions that are in open chromatin states. Techniques like ChIA-PET can discover sites of short- and long-range DNA looping. These technologies provide critical insights into the mechanisms of gene regulation at the genome-wide level, revealing how cells make decisions both during normal development and in disease states.