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CASCADE: A high-throughput assay to characterize gene-regulatory complexes affected by single-nucleotide polymorphisms

CASCADE：一种高通量测定，用于表征受单核苷酸多态性影响的基因调控复合物

基本信息

批准号：
10042422
负责人：
TREVOR W SIGGERS
金额：
$ 45.38万
依托单位：
BOSTON UNIVERSITY (CHARLES RIVER CAMPUS)
依托单位国家：
美国
项目类别：
财政年份：
2020
资助国家：
美国
起止时间：
2020-08-15 至 2024-01-31
项目状态：
已结题

项目摘要

Project Summary Studies have identified thousands of single-nucleotide polymorphisms (SNPs) associated with a range of diseases, but the causal nucleotide changes and mechanisms remain largely unknown. A current bottleneck in the field is that characterization of SNP mechanism greatly lags SNP identification. Analyses suggest that causal variants underlying disease risk are often non-coding SNP (ncSNPs) that function through their effects on gene expression. The primary means by which ncSNPs affect gene expression is by altering binding sites for transcription factor-cofactor (TF-CoF) complexes. Therefore, a major challenge in understanding disease susceptibility and etiology is to characterize the mechanisms by which the thousands of ncSNPs disrupt the binding of TF-CoF complexes to alter gene expression. To address this challenge, we have recently developed CASCADE – a high-throughput microarray- based method to screen the impact of ncSNPs on the DNA-binding of TF-CoF complexes. In this proposal, we will use our CASCADE approach to study TF-CoF complexes in diverse immune cell states, and study their disruption by disease-associated ncSNPs. To determine the cell state-dependence of our ncSNP annotations and TF-CoF complexes, we will examine results using cell lines as well as primary human cells. To assess CoF specificity for TF classes, and which CoFs are affected by the largest number of ncSNPs (i.e., assay coverage), we will study TF-CoF complexes comprising diverse CoFs and CoF subcomponents. Our goal is to develop CASCADE as a general high-throughput platform to biophysically characterize the regulatory complexes affected by ncSNPs.

项目摘要研究已经确定了数千种与一系列疾病相关的单核苷酸多态性（SNP）。疾病，但因果核苷酸的变化和机制仍然在很大程度上未知。电流该领域的瓶颈是SNP机制的表征大大滞后于SNP鉴定。分析提示潜在疾病风险因果变异通常是非编码SNP（ncSNP），通过它们对基因表达的影响。ncSNP影响基因表达的主要方式是通过改变转录因子-辅因子（TF-CoF）复合物的结合位点。因此，一个主要理解疾病易感性和病因学的挑战是表征数以千计的ncSNP破坏TF-CoF复合物的结合以改变基因表达。为了应对这一挑战，我们最近开发了CASCADE -一种高通量微阵列- 的方法来筛选ncSNPs对TF-CoF复合物的DNA结合的影响。在这建议，我们将使用我们的CASCADE方法来研究不同免疫细胞状态下的TF-CoF复合物，并研究它们被疾病相关的ncSNPs破坏。为了确定我们的细胞状态依赖性， ncSNP注释和TF-CoF复合物，我们将使用细胞系以及原代人体细胞评估TF类别的CoF特异性，以及哪些CoF受最大的 ncSNP的数量（即，检测覆盖率），我们将研究包含不同CoF的TF-CoF复合物， CoF子组件。我们的目标是将CASCADE开发为通用高通量平台，生物药理学表征受ncSNP影响的调节复合物。

项目成果

期刊论文数量（3）

专著数量（0）

科研奖励数量（0）

会议论文数量（0）

专利数量（0）

Parallelized multidimensional analytic framework applied to mammary epithelial cells uncovers regulatory principles in EMT.

DOI：
10.1038/s41467-023-36122-x
发表时间：
2023-02-08
期刊：
NATURE COMMUNICATIONS
影响因子：
16.6
作者：
Paul, Indranil;Bolzan, Dante;Youssef, Ahmed;Gagnon, Keith A.;Hook, Heather;Karemore, Gopal;Oliphant, Michael U. J.;Lin, Weiwei;Liu, Qian;Phanse, Sadhna;White, Carl;Padhorny, Dzmitry;Kotelnikov, Sergei;Chen, Christopher S.;Hu, Pingzhao;Denis, Gerald V.;Kozakov, Dima;Raught, Brian;Siggers, Trevor;Wuchty, Stefan;Muthuswamy, Senthil K.;Emili, Andrew
通讯作者：
Emili, Andrew

Widespread perturbation of ETS factor binding sites in cancer.

DOI：
10.1038/s41467-023-36535-8
发表时间：
2023-02-17
期刊：
NATURE COMMUNICATIONS
影响因子：
16.6
作者：
Carrasco Pro, Sebastian;Hook, Heather;Bray, David;Berenzy, Daniel;Moyer, Devlin;Yin, Meimei;Labadorf, Adam Thomas;Tewhey, Ryan;Siggers, Trevor;Fuxman Bass, Juan Ignacio
通讯作者：
Fuxman Bass, Juan Ignacio

Rapid profiling of transcription factor-cofactor interaction networks reveals principles of epigenetic regulation.

转录因子-辅因子相互作用网络的快速分析揭示了表观遗传调控的原理。