Epigenetics, Chromatin Structure and Transcription Regulation

Dear Colleagues,

The spatiotemporal coordination of gene expression is achieved through the concerted activity of a wide-range of factors and mechanisms that act on different genomic scales. On a larger scale, chromosomes are organized into domains of similar chromatin states, which are positioned at non-random positions within the nuclear space. At intermediate levels, DNA loops are formed that are constrained within topologically associating domains (TADs). At the local level, DNA methylation, histone tail modifications, and chromatin remodeling complexes synergistically modulate interactions between promoters and transcription factors, and thereby regulate gene activity. The collective action of all of these components ultimately determines cellular identity and function, and when misregulated can result in malignant phenotypes.

The ever-evolving developments in microscopy and genomics technologies have enabled the measurement of a multitude of modalities in the same cell or tissue, over time and on the same molecule, thereby starting to provide possibilities to determine the interdependencies of multifaceted gene activity control. These studies are further aided by the development of versatile systems to selectively, conditionally, and acutely deplete proteins, or otherwise manipulate their functions. In parallel, the application of increasingly advanced computational simulations, machine learning algorithms, and biophysical modeling approaches provides means with which to make predictions about the underlying mechanisms, thereby opening up hypotheses for experimental validation.

This Special Issue will be devoted to research into chromatin structure, epigenetics, the organization of the genome within the nucleus, and the coordination of nuclear processes, with an emphasis on the spatiotemporal control of gene transcription.

Prof. Dr. Jop Kind
Dr. Daan Noordermeer
Guest Editors

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• three-dimensional genome organization
• nucleosomes and chromatin structure
• epigenetics/histone modications
• transcription factor networks
• imprinting/X inactivation
• zygotic genome activation
• pioneer transcription factors and mitotic bookmarking
• evolution of nuclear processes and transcriptional regulation
• heterogeneity of nuclear processes and transcriptional regulation:
  • single-cell and spatial-omics
  • super-resolution and live-cell imaging
  • structural biology and single-molecule sequencing.
• computational biology, machine learning and simulations, and biophysical modeling for nuclear processes as well as transcriptional regulation