Impact of Chromatin 3D-Organization on Promoter–Superenhancer Interactions in Embryonic Stem vs Cancer Cells
- 作者: Eidelman Y.1,2, Andreev S.1,2
-
隶属关系:
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences
- National Research Nuclear University “MEPHI”
- 期: 卷 59, 编号 6 (2023)
- 页面: 676-686
- 栏目: МАТЕМАТИЧЕСКИЕ МОДЕЛИ И МЕТОДЫ
- URL: https://journals.rcsi.science/0016-6758/article/view/134608
- DOI: https://doi.org/10.31857/S0016675823060036
- EDN: https://elibrary.ru/SRUZYX
- ID: 134608
如何引用文章
详细
The interaction of enhancers and superenhancers (SE) with promoters is functionally significant for the regulation of gene expression. Pattern of these interactions plays a key role in various processes, such as differentiation, malignant transformation, etc. In order to quantify the relationship between 3D chromatin organization and promoter–SE contacts, a computational analysis of chromatin conformations near the murine Nanog pluripotency gene was performed for normal embryonic stem (mESC) and lymphoma (CH12LX) cells. Using biophysical modeling approach, the following parameters of the promoter–SE interactions were identified: the distribution of distances between the Nanog promoter and the SEs, the frequency of contacts with one and several SEs simultaneously. In normal mESC expressing Nanog, the frequency of contacts of promoters with SEs is higher than in cancer cells, and complex contacts with two or more SEs are more frequent. The modelling reveals a small subpopulation of cancer cells, where the promoter contacts simultaneously three SEs. The predicted subpopulation of cancer cells with multiple promoter–SE contacts may be predisposed to increased stemness and hypothetically be considered as a reservoir for generation of cancer stem cells.
作者简介
Yu. Eidelman
Emanuel Institute of Biochemical Physics, Russian Academy of Sciences; National Research Nuclear University “MEPHI”
编辑信件的主要联系方式.
Email: eidel@mail.ru
Russia, 119334, Moscow; Russia, 115409, Moscow
S. Andreev
Emanuel Institute of Biochemical Physics, Russian Academy of Sciences; National Research Nuclear University “MEPHI”
编辑信件的主要联系方式.
Email: andreev_sg@mail.ru
Russia, 119334, Moscow; Russia, 115409, Moscow
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