Chromatin structure changes during various processes from a DNA sequence view

A perspective on the molecular simulation of DNA from structural and functional aspects

“…The physical properties of DNA at these different scales are all likely to contribute to its biological function and regulation. Information at the single base level, such as GC content, at the dinucleotide level, such as the CpG base step, at the oligomer level, such as TATA box and longer sequences ranging from poly A tract to CpG island (CGI), and even higher order sequence information such as the isochores or CGI forests and prairies 24,28,108 have all been shown to correlate with the realization of biological functions. The higher order structure formation of chromatin has been found to be dependent on the DNA sequence, and in many cases, simple sequence properties such as nucleotide and dinucleotide densities.…”

“…It was proposed that the local nucleotide content may potentially play a role in the structural organization of eukaryotic chromosomes. 24,27 The genomic sequence preference among different species and structural organization of chromatin were also found to correlate with body temperature control. 24,28 Therefore, future atomistic studies in this context considering different environmental factors and double-stranded DNA fragments having different dinucleotide sequences and counterions will help to understand the sequence preference in the phase separation mechanism, chromatin folding, dynamics and organization, which are associated with transcription, gene regulation and cell function.…”

“…Based on the densities of dinucleotide sequences, the genome can be divided into large (megabase scale) alternative domains of high and low CpG densities. 24,28 The CpG-rich/poor regions are associated with compartmentalization, which makes the 3D chromatin structure of higher and lower species distinctly different. 7,24,28,108 We found that higher species with an uneven dinucleotide distribution tend to have a more segregated chromatin structure than lower ones.…”

“…The sequential difference between different species also shows a correlation with their different responses to the environmental temperature considering that the latter was found to affect the domain segregation in the 3D chromatin structure. 24,28 …”

Progressive domain segregation in early embryonic development and underlying correlation to genetic and epigenetic changes

“…For mouse, researchers did find that an ultimately-successful pregnancy is characterized by significantly more min/day of relative low CBT (core body temperature) in the second day after mouse pairing which rightly corresponds to ZGA, than for pregnancies which subsequently terminated prematurely (Smarr et al, 2016). These observations give rise to the possibility that temperature shifts are closely coupled with large scale chromatin structural changes during embryonic development, in accordance with high temperatures to be favorable for segregation of the prairies, and low temperatures, for a more forest-prairie mixed chromatin structure (Liu et al, 2018;Quan et al, 2020).…”