核小体
染色质
生物
组蛋白
抄写(语言学)
转录因子
计算生物学
DNA
RNA聚合酶Ⅱ
发起人
遗传学
细胞生物学
表观遗传学
DNA结合位点
基因组
连接器DNA
基因
作者
Fangjie Zhu,Lucas Farnung,Eevi Kaasinen,Biswajyoti Sahu,Yimeng Yin,Bei Wei,Svetlana O. Dodonova,Patrick Cramer,Jussi Taipale
出处
期刊:bioRxiv
日期:2017-12-28
卷期号:: 240598-
摘要
Nucleosomes cover most of the genome and are thought to be displaced by transcription factors (TFs) in regions that direct gene expression. However, the modes of interaction between TFs and nucleosomal DNA remain largely unknown. Here, we use nucleosome consecutive affinity-purification systematic evolution of ligands by exponential enrichment (NCAP-SELEX) to systematically explore interactions between the nucleosome and 220 TFs representing diverse structural families. Consistently with earlier observations, we find that the vast majority of TFs have less access to nucleosomal DNA than to free DNA. The motifs recovered from TFs bound to nucleosomal and free DNA are generally similar; however, steric hindrance and scaffolding by the nucleosome result in specific positioning and orientation of the motifs. Many TFs preferentially bind close to the end of nucleosomal DNA, or to periodic positions at its solvent-exposed side. TFs often also bind nucleosomal DNA in a particular orientation, because the nucleosome breaks the local rotational symmetry of DNA. Some TFs also specifically interact with DNA located at the dyad position where only one DNA gyre is wound, whereas other TFs prefer sites spanning two DNA gyres and bind specifically to each of them. Our work reveals striking differences in TF binding to free and nucleosomal DNA, and uncovers a rich interaction landscape between the TFs and the nucleosome.
科研通智能强力驱动
Strongly Powered by AbleSci AI