Our genome contains an estimated number of 400,000 to 1.4 million enhancers. These are regulatory sequences mostly located outside exons of protein-coding genes either close to or far away from the transcription start site(s) of genes on the chromosome. Together with gene promoters, they are principal cell-intrinsic genomic elements assuring the activity and accurate regulation of transcription of genes, in terms of the steady-state mRNA levels and spatio-temporal precision. During early embryogenesis and subsequent organogenesis, enhancers co-regulate decisions in cell fate and differentiation, and thus creation of cell diversity. Such regulatory sequences operate often in a context of extrinsic cell stimulation by polypeptide growth factors, the signaling cascade of which is interpreted and further executed in the nucleus by transcription factors, assuring RNAPol2-mediated activation of sets of genes by their binding to promoter and enhancer sequences. These precise molecular actions must take place in a cell nucleus of 6-μm diameter average, and wherein 2m of DNA is highly compacted and present as architecturally ordered chromatin (DNA and bound proteins), as individual chromosomes. This chromatin in general, as well as its typical nucleosomes, but also enhancer and promoter sequences, are epigenetically marked (biochemically modified, in various ways). This collectively assures that the chromatin opens locally when gene transcription activation is needed, and gene-specific enhancers must thereby achieve physical proximity, which can be documented by chromatin conformation capture (3C) analyses, with the promoter of their cognate gene. At the same time, a set of biochemical marks, including those modifying histone-3 (H3) in the nucleosome, facilitates the identification of candidate enhancers. Importantly, like key protein-coding genes, sequence variation or mutation of enhancers can lead or contribute to congenital syndromes and chronic disease. Hence, both experimental studies of enhancers (including their identification in small population of embryonic cells) and key developmental transcription factors (including how their own level and activity are regulated, but also which genes and regulatory sequences they bind to), are fundamental to understanding cell-based health and disease of the entire organism. The research in this PhD thesis addresses these fundamental aspects of genetic and molecular control of embryogenesis, and at the same time investigates the mechanisms of gene regulation. It presents two lines of experimental as well as bio-informatics work, one in vivo and one in cell culture, specifically in the formation of flexible joints in developing limbs and chondrogenesis in the latter, and neural differentiation of pluripotent embryonic cells, respectively. The mechanisms of gene regulation most relevant to this PhD research are described in Chapter 1, which also includes an overview of these molecular regulations as well as mutations in regulatory elements that link to selected human limb malformations. The experimental part of research line-1 reports on the production, for the first time, of a genome-wide candidate-enhancer atlas of the joint interzone and adjacent phalanges, respectively. This work includes integrative analysis of transcriptomic data from RNA-sequencing together with H3K27ac and H3K4me1 signatures obtained by ChIP-sequencing (Chapter 3). It then reports on contribution to the establishment of a low-T2C (a targeted 3C-assay) protocol applicable to cell populations or in vivo samples available as low cell numbers, like for synovial joints (Chapter 4). Then, this low-T2C protocol is used to investigate the genomic region encompassing the Dact2 and Smoc2 genes, and identify and characterize their enhancers in the interzone during synovial joint development, which were also validated using a zebrafish larvae enhancer assay (Chapter 5). In research line-2, using neural differentiation of embryonic stem cells (ESCs), the thesis reports on the demonstration of dynamic DNA-loops in and around the human ZEB2 locus (including its 3.5 Mb-long gene desert), and co-operation between the newly identified enhancers, including in human neuroprogenitor cells (NPCs) (Chapter 6). The DNA-binding transcription factor ZEB2 is studied by many teams in different fields, but maps of its genome-wide binding sites are urgently needed. This PhD thesis therefore also includes ChIP-sequencing of Zeb2 (endogenously tagged in mouse ESCs, guaranteeing normal levels of Zeb2 production) in ESC-derived cultures of NPCs (Chapter 7). This work aims at identifying Zeb2-dependent, directly controlled target genes, as well as candidate TFs that regulate Zeb2 gene expression via its identified enhancers, and illustrates for the first time how critical the identified autoregulation of Zeb2. This PhD research as a whole combines two experimental models, multi-omics methods, and functional assays to investigate multiple regulatory mechanisms, in genome-wide as well as locus-specific studies. It documents dynamic changes in 3D chromatin architecture, enhancer signatures and activity, to reveal the underlying principles of precise control of gene expression during development and differentiation.