Gene expression is hence determined by interactions between DNA methylation, histone modification, and nucleosome positioning influencing chromatin structure.
(5) These mutations result in the impairment of DNA methylation, histone modification and nucleosome positioning, and are associated with aberrant gene expression.
These GO categories include: Transcription, DNA damage and repair, DNA replication, Cell cycle, RNA processing and splicing, Chromatin modification and nucleosome assembly, Translation, Transport, Apoptosis and Protein ubiquitination.
The open reading frame (ORF) is well annotated in the Saccharomyces Genome Database (SGD), and the initial ATG codon of yeast genes has also been used to evaluate signals such as histone modification and nucleosome positions [ 20, 21].
Several studies have shown that epigenetic processes, such as chromatin modification and nucleosome positioning alter, the affinity between DNA sequence and transcription factors (see Bock and Lengauer, 2008, for review).
Ovarian cancer (OC) is characterized by complex epigenetic alterations, including aberrant DNA methylation, histone modifications, and nucleosome positioning.
To gain molecular insight to this restricted expression, we compared histone modifications and nucleosome occupancy in this intron between expression permissive and restrictive cell lines.
A number of key metabolites, including SAM, acetyl-CoA, NAD, and ATP, serve as essential co-factors for many, perhaps most, epigenetic enzymes that regulate DNA methylation, post-translational histone modifications, and nucleosome position [38].
Although studies in this area remain at their infancy, it becomes clear that large-scale epigenetic reprograming, involving RNA-directed DNA methylation, chromatin modifications, and nucleosome remodeling, contributes to the establishment of transcriptionally repressive or permissive epigenetic landscapes.
At each stage, transcription factors interact not only with an existing landscape of histone modifications and nucleosome packing, but also with other bound factors, while they modify the landscape for later-arriving factors in ways that fundamentally affect the control of gene expression.
In general, gene expression is regulated epigenetically by DNA methylation, histone modifications, and nucleosome positioning.
