Myriad interactions between DNA and proteins that take place throughout the length of an organism's genome ultimately allow cells to read, repair, package, and copy DNA sequence. How cells properly orchestrate and control these critical DNA:protein interactions is a fundamental question in biology. A unifying theme across such diverse DNA:protein interactions is that they always require some form of local mechanical distortion of DNA like bending, twisting, or kinking. Therefore, DNA:protein interactions can potentially be modulated and controlled by the local mechanical properties of DNA such as its bendability. Structural studies, dynamic experiments, and computational works have suggested that the mechanical properties of the DNA polymer are not constant, but vary along its length depending on local sequence, via a "mechanical code". Over decades, this has given rise to the hypothesis that sequence may be able to significantly control the local mechanical properties of DNA, and via it, control the critical DNA:protein interactions that in turn allow sequence itself to be read, repaired, copied, and packaged. In other words, via the mechanical code, DNA sequence might be able to control its own regulation. If this hypothesis is true, because of its potential generality and likelihood of relevance in all examples of DNA:protein interactions in all organisms, it would represent a transformative step in our understanding of life and in our ability to control it. Towards this end, we recently developed high-throughput experimental methods to measure, for the first time, how the mechanical properties of DNA vary with sequence along large regions of the genomes of various organisms. Via other experiments, we showed that these sequence-encoded variations in DNA bendability regulate critical processes related to the reading, copying, and packaging of DNA. Genetic information in DNA sequence is further modified by chemical alterations to DNA such as methylation (addition of a methyl group mainly to the cytosine base of DNA). DNA methylation is of fundamental importance in altering which genes along DNA are expressed. While certain cellular factors have been found to recognise methylated DNA, how DNA methylation achieves so many broad downstream effects is not fully understood. Recently, it has been suggested that one of the ways in which DNA methylation could exercise control over DNA transactions is by modifying the local physical and mechanical properties of DNA. If true, DNA methylation might allow cells to dynamically alter the "mechanical code" itself, as a means of gaining a broad regulatory handle on many different DNA:protein interactions. A significant roadblock to exploring this hypothesis has been the lack of high-throughput methods to provide the basic characterization of how DNA methylation, at various points along an organism's vast genome, alter the local mechanical properties of DNA depending on local sequence context. Here we propose to extend the capabilities of our high-throughput experimental techniques to make it possible to characterize the mechanical consequences of DNA methylation in high-throughput throughout the genome. We will compare our findings with other genome wide data, and perform other high-throughput biochemical experiments on how DNA sequence and methylation affect protein:DNA interactions. We expect to develop a comprehensive understanding of how DNA methylation, via its impact on the local physical properties of DNA, impacts the local structure of chromatin and the expression of individual genes. As DNA methylation accompanies processes like embryonic development, cellular adaptation to environmental changes, and genetic diseases like cancers, this project lays the foundations for future efforts at understanding how such critically important processes in biology might, in part, achieve their effects by gaining a handle on the physical properties of DNA.