Electric oscillation and coupling of chromatin regulate chromosome packaging and transcription in eukaryotic cells
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Zhao and Zhan Theoretical Biology and Medical Modelling 2012, 9:27 http://www.tbiomed.com/content/9/1/27
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Electric oscillation and coupling of chromatin regulate chromosome packaging and transcription in eukaryotic cells Yue Zhao* and Qimin Zhan * Correspondence: alexanderyz@ gmail.com State key laboratory of molecular oncology, Cancer Institute & Hospital of Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100021, China
Abstract Transcription in eukaryotic cells is efficiently spatially and temporally regulated, but how this genome-wide regulation is achieved at the physical level remains unclear, given the limited transcriptional resources within the nucleus and the sporadic linear arrangements of genes within chromosomes. In this article, we provide a physical model for chromatin cluster formation, based on oscillation synchronization and clustering of different chromatin regions, enabling efficient systemic genome-wide regulation of transcription. We also propose that the electromagnetic field generated by oscillation of chromatin is the driving force for chromosome packing during M phase. We further explore the physical mechanisms for chromatin oscillation cluster (COC) formation, and long-distance chromatin kissing. The COC model, which connects the dots between chromatin epigenetic modification and higher-order nuclear organization, answers many important questions, such as how the CCCTC-binding factor CTCF contributes to higher-order chromatin organization, and the mechanism of sequential transcriptional activation of HOX clusters. In the COC model, long non-coding RNAs function as oscillation clustering adaptors to recruit chromatin modification factors to specific sub-nuclear regions, fine-tuning transcriptional events in the chromatin oscillation clusters. Introns of eukaryotic genes have evolved to promote the clustering of transcriptionally co-regulated genes in these sub-nuclear regions. Keywords: Oscillation cluster, Long non-coding RNA, Electromagnetic field, CTCF, HOX, Chromosome packaging, Intron
Background The regulation of eukaryotic gene transcription can be viewed as forming order out of chaos. To understand it, it is necessary to explore the physical nature of oscillating heterogeneous chromatin regions with nonlinear contacts and interactions. Recent advances in the fields of applied mathematics and physics together with technologies evolved from the application of high-throughput DNA sequencing allow us to envision nuclear chromatin organization as clustered. This knowledge provides us with new insights into the regulation of gene transcription, the functions of long non-coding RNAs and the evolution of introns in eukaryotic cells. Lieberman-Aiden et al. reported that genome-wide Hi-C maps indicate a fractal globule model for chromatin conformation that enables maximally dense packing while © 2012 Zhao and Zhan; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License
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