In eukaryotes, DNA is tightly wound into a complex called chromatin. Thanks to the process of chromatin remodeling, this complex can be "opened" so that specific genes are expressed.
Read "Examining Histone Modifications with Chromatin Immunoprecipitation and Quantitative PCR." Look for the overview: The specific modified histones occur in specific locations along a big domain. Then look at the details: How do scientists identify a modified histone molecule? How do they know where it was in the DNA strand?
Read "Chromatin and DNase I Sensitivity." Histones of the nucleosomes act as gatekeepers of gene expression. When histones open up, investigators can detect a new sensitivity to added DNase I near active genes.
When genes are coiled and compacted into chromatin, they're no longer accessible to transcription factors. So how does the cell know where to uncoil in a process called chromatin remodeling?
DNA methylation occurs generally in areas where genes are silent for long periods. Read "The Role of Methylation in Gene Expression" under the Gene Expression and Regulation topic room.
