Epigenetics and genomic causality in development and chromatin research

In May 2016, an article published in the New Yorker about how environmental factors can change the activity of genes without altering the DNA sequence stirred a strong critical response of geneticists, epigeneticists, and other biologists. They criticized that the article ignored the primary role of transcription factors and RNA in the transcription process and disregarded the significance of specificity, by instead emphasizing histone modification and DNA methylation. They pointed to the fact that not only the specificity of cellular identity but also the response to stress was due to the actions of specific DNA-binding proteins (and, more rarely, RNA molecules) that regulate gene transcription. In an exceptional response, the author thanked their critics for their immensely detailed comments, admitting to having erred by omitting these scientific facts.
This anecdote illustrates the marginalization or exclusion of mechanisms based on DNA sequence, as the primary cause of gene expression changes that characterize many arguments of epigeneticists and the general public. This Research Topic aims at rectifying this omission.
1. The proposed Research Topic aims at highlighting the connection between events that are now called epigenetic and genes in different areas of research related to development. The focus is on gene regulation, genome architecture, genomic imprinting, developmental systems biology, evolutionary biology, and medicine.
2. The Research Topic aims at discussing various causes of developmental stability and canalization (Waddington), among them selection (preferred by Waddington), epigenetics, and complex hierarchical gene regulatory networks.
3. The research topic aims at exploring the many different meanings that the term epigenetics has recently adopted in developmental biology that include, among others:
- DNA and histone-modifying enzymes
- Cellular memory
- Self-organization processes of genome architecture based on gene activities in development
- The complex nature of the binding of transcription factors that require interaction with a more-or-less specific DNA sequence, in contrast to chromatin remodelers and modifiers that do not
- The role of transcription factors and other factors in opening chromatin, displacing nucleosomes, and initiating activating histone modifications
- The interaction of DNA sequence-specific transcription factors, repressors, and RNA polymerases with histone proteins, chromatin compaction, looping, etc., in gene regulation processes.
This Research Topic examines (i) the strong connection between genetic, genomic, and epigenetic processes and (ii) the broad spectrum of different meanings of epigenetics today.
Among the topics that we ask potential authors to address, either in research papers or in review papers, are the following:
• The origin of epigenetics from epigenesis
• The function of DNA methylation in development
• Transcription factors and other regulatory proteins as causal factors of histone and DNA modification and their role in chromatin remodeling
• The collaboration of transcription factors in the initiating, stabilizing, or silencing of gene expression programs
• The roles of gene expression and epigenetic factors in the emergence of the genome architecture
• The roles of DNA sequence events and epigenetics in cellular memory
• DNA sequence-based mechanisms and mechanisms of epigenetics in genomic imprinting
• The role of the genome and epigenetics in developmental systems biology
• The role of mutations and epigenetic factors in disease development.