Deciphering the RNA:DNA triplex binding code of ncRNAs and studying its interaction with chromatin

破译 ncRNA 的 RNA:DNA 三链体结合密码并研究其与染色质的相互作用

• 批准号: 88471535
• 负责人: Professor Dr. Gernot M. Längst
• 金额: --
• 依托单位: Lehrstuhl für Biochemie III
• 依托单位国家: 德国
• 项目类别: Research Grants
• 资助国家: 德国
• 项目状态: 未结题
• 来源: https://gepris.dfg.de/gepris/projekt/88471535?language=en
• 关键词: Deciphering; RNA; DNA; triplex; binding

The formation of specific triple helices, whereby an RNA strand binds to the major groove of DNA, is one means of sequence specific targeting of long and short non-coding RNA to genomic DNA. Triple helix formation is suggested to play an essential role in many nuclear processes, like antisense-mediated gene regulation, changing epigenetic states of genomic domains, regulating chromatin density, genome accessibility and recently it was suggested that the organization of the topologically associated domains and nuclear architecture is determined by a triplex-RNA mechanism. Despite the many implicated functions only little is known about the biophysical parameters of triple helix formation and its functional interaction with chromatin. Three different triple helix binding motifs exist and still no comprehensive data on sequence motifs/lengths, binding affinities, mutational impacts etc. exist, to predict binding affinities of potential motifs. We showed that motifs have very different and unexpected binding properties that currently do not allow to predict, if a poly-purine motif serves as a potential binding site in vivo. We show that many published triplex binding site predictions are wrong. Furthermore, nucleosome positioning relative to the triplex targeting site strongly affects triplex stability and we suggest that the histone post-translational modifications will further affect binding. We propose elucidating the biophysical properties of the triplex binding code and determine its interaction with chromatin to build a bioinformatic tool predicting the binding affinity of potential triplex forming elements in RNA. We think that our work presents an essential repository for addressing the mechanistical and functional impact of RNA binding to chromatin in vivo.

特异性三螺旋的形成，由此RNA链结合到DNA的大沟，是长和短非编码RNA序列特异性靶向基因组DNA的一种手段。三螺旋的形成被认为在许多核过程中发挥重要作用，如反义介导的基因调控，改变基因组结构域的表观遗传状态，调节染色质密度，基因组可及性，最近有人提出，拓扑相关结构域和核结构的组织是由三链RNA机制决定的。尽管有许多涉及的功能，只有很少的是已知的三螺旋形成的生物物理参数和它的功能与染色质的相互作用。存在三种不同的三螺旋结合基序，并且仍然没有关于序列基序/长度、结合亲和力、突变影响等的综合数据，以预测潜在基序的结合亲和力。我们发现，基序有非常不同的和意想不到的结合特性，目前不允许预测，如果一个聚嘌呤基序作为一个潜在的结合位点在体内。我们发现，许多已发表的三链体结合位点的预测是错误的。此外，相对于三链体靶向位点的核小体定位强烈影响三链体的稳定性，我们认为组蛋白的翻译后修饰将进一步影响结合。我们建议阐明三链体结合代码的生物物理特性，并确定其与染色质的相互作用，以建立一个生物信息学工具，预测潜在的三链体形成元件在RNA中的结合亲和力。我们认为，我们的工作提出了一个重要的知识库，解决机制和功能的影响，RNA结合染色质在体内。