Techniques Analyzing Chromatin Modifications at Specific Single Loci

In a multicellular organism such as Homo sapiens, gene expression is precisely regulated at multiple levels. Besides the information stored in DNA, that information in DNA/histone modifications, which function through epigenetic inheritance, has been heavily discussed in the last few decades. To read the information stored in DNA/histone modifications during transcription, complex machineries are required for correct interpretation. Up to now, scientists have discovered "modifiers" that modify a specific locus on chromatin, for example, methyltransferase G9a methylates histone H3 at lysine 9. We also know DNA/histone modifications have their specific reader proteins - for example, chromodomain-containing protein recognizes methylated lysine. Furthermore, during the process of transcription initiation, the chromatin-remodeling complex unwraps the chromatin for binding of regulatory factors. All these findings are based on breakthroughs on techniques to dissect and image the chromatin structure at multiple dimensions, ranging from detection of a population of cells, a single cell, to a single locus observation. With the recently emerged CRISPR technique, it is possible to engineer the mammalian cell genome as we have done in yeast cells. That will broaden our vision by deciphering the deep secrets of the "Life Code" in multicellular organisms. In this chapter, we will look into how new techniques lead us on to the discoveries concerning chromatin organization and gene expression.