期刊
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
卷 22, 期 17, 页码 -出版社
MDPI
DOI: 10.3390/ijms22179150
关键词
transcription factor binding sites; E-box; bHLH; co-factors; ChIP-seq; pioneer factors; dimerization
资金
- la Caixa Foundation [100010434]
- Ministerio de Ciencia e Innovacion, Spain [PID2019-104700GA-I00]
- NIH [R01HG010898-01]
- [LCF/BQ/PI19/11690010]
The transcriptome of every cell is controlled by a complex network of interactions between transcription factors and their binding sites on DNA. Disruption of this network can lead to organism malfunction or serve as a substrate for positive natural selection. Understanding the specific determinants of TF-DNA interactions is challenging, as it involves integrating multiple mechanisms such as DNA motif preferences, post-translational modifications, and epigenetic modifications.
The transcriptome of every cell is orchestrated by the complex network of interaction between transcription factors (TFs) and their binding sites on DNA. Disruption of this network can result in many forms of organism malfunction but also can be the substrate of positive natural selection. However, understanding the specific determinants of each of these individual TF-DNA interactions is a challenging task as it requires integrating the multiple possible mechanisms by which a given TF ends up interacting with a specific genomic region. These mechanisms include DNA motif preferences, which can be determined by nucleotide sequence but also by DNA's shape; post-translational modifications of the TF, such as phosphorylation; and dimerization partners and co-factors, which can mediate multiple forms of direct or indirect cooperative binding. Binding can also be affected by epigenetic modifications of putative target regions, including DNA methylation and nucleosome occupancy. In this review, we describe how all these mechanisms have a role and crosstalk in one specific family of TFs, the basic helix-loop-helix (bHLH), with a very conserved DNA binding domain and a similar DNA preferred motif, the E-box. Here, we compile and discuss a rich catalog of strategies used by bHLH to acquire TF-specific genome-wide landscapes of binding sites.
作者
我是这篇论文的作者
点击您的名字以认领此论文并将其添加到您的个人资料中。
推荐
暂无数据