In this project, we compare the binding sites of TFs from the ENCODE Consortium against random points and we perform hypothesis testing and statistical tests for the location of TFs and Histone Modifiers relative to the boundaries of LADs and TADs. Furthermore, we examine the distribution of Transcription Start Sites (TSS) from the GENCODE project within or outside TADs’ and LADs’ boundaries, and we measure the distance of the former from the latter, as well as from the center of each 3D DNA conformation. Simultaneously, we address the type of transcript that arises from each TSS, with our focus being placed on protein coding genes. In addition, we identify the recent evolutionary forces that shape the patterns of polymorphisms in relation to LAD and TAD boundaries within Human and Mice populations. Thus, we provide insights into whether recent, within populations evolution acts on the 3D structures of DNA within the nucleus. Finally, using Dn/Ds measurements we examine whether older selective forces have been applied on genes located within or outside TADs and LADs.