Computational and Experimental Modeling of Alternative Polyadenylation

项目总结/摘要 选择性多聚腺苷酸化（阿帕）在人类大部分基因转录后调控中起重要作用， 基因.阿帕的广泛重要性通过改变NUDT 21的表达得到很好的例证，NUDT 21是一个关键的阿帕 我们在第一轮拨款中报告的调节剂，在胶质母细胞瘤，特发性肺 纤维化和神经精神疾病。最近，我们的工作揭示了一种新的机制，通过这种机制， UTR缩短可以抑制肿瘤抑制基因（例如，PTEN）通过干扰竞争性 内源性RNA（ceRNA）串扰，而不是通过诱导癌基因顺式。除了这几个 例如，阿帕在广泛的人类特征和疾病中的流行和功能仍然存在， 大部分未知。大多数人类特征/疾病已被发现与数十万种 非编码单核苷酸多态性（SNPs）在许多全基因组关联研究（GWAS）。 然而，这些SNP的功能解释仍然是一个重大的挑战，因为GWAS数据不 展示SNPs是如何工作的为了更好地理解它们的作用，表达数量性状基因座（eQTL）已经被应用于 已被广泛用于将GWAS SNP与基因表达联系起来。尽管在阐明eQTL方面付出了巨大努力， 许多GWAS SNPs的功能仍然无法解释。一个重要原因是eQTL不考虑阿帕 调控我们最近构建了第一个人类3′UTR阿帕数量性状基因座（3′ aQTL）， 包含约40万个与靶基因阿帕相关的SNP，使用约8，000个GTEx v7 RNA-seq样本 46种组织类型（Nature Genetics，2021年接受）。这些3′ aQTL可以解释约16.1%的GWAS SNPs在15个常见性状/疾病中存在，与eQTL和剪接QTL有很大区别。基于 这些令人兴奋的初步数据，我们假设阿帕的计算和实验建模将 大大促进了对阿帕监管重要的许多GWAS SNP的解释， 在3′ UTR和基因下游区域富集。因此，我们建议发展创新的生物信息学 以及鉴定3′ aQTL和提名APA连锁疾病/性状易感基因的实验方法 在各种各样的细胞类型和环境因素中，随后使用 我们独特的CRISPR工程系统。我们期望将阿帕确立为一种新兴的重要分子 表型来解释GWAS风险SNP的大部分，导致对GWAS风险SNP的重要新生物学见解。 阿帕和APA连锁易感基因的遗传基础，在广泛的人类特征和疾病。

Project Summary / Abstract Alternative polyadenylation (APA) plays an important role in the post-transcriptional regulation of most human genes. The broad importance of APA is well exemplified by the altered expression of NUDT21, a key APA regulator that we reported in the first cycle of this grant, in diseases such as glioblastoma, diopathic pulmonary fibrosis, and neuropsychiatric disorders. More recently, our work has revealed a novel mechanism by which 3ʹ- UTR shortening can repress tumor suppressor genes (e.g., PTEN) in trans by disrupting competing endogenous RNA (ceRNA) crosstalk, rather than by inducing oncogenes in cis. Aside from these few examples, the prevalence and functions of APA in a wide spectrum of human traits and diseases remain largely unknown. Most human traits/diseases have been found as associated with hundreds of thousands of noncoding single-nucleotide polymorphisms (SNPs) in numerous genome-wide association studies (GWASs). However, functional interpretation of these SNPs remains a significant challenge because GWAS data do not show how the SNPs work. To better understand their effects, expression quantitative trait loci (eQTLs) have been widely used to link GWAS SNPs to gene expression. Despite massive efforts on elucidating eQTLs, the functions of many GWAS SNPs remain unexplained. An important reason is that eQTLs do not consider APA regulation. We have recently constructed the first human 3′UTR APA quantitative trait loci (3′aQTLs), which contain ~0.4 million SNPs associated with APA of target genes, using ~8,000 GTEx v7 RNA-seq samples across 46 tissue types (Nature Genetics, accepted in 2021). These 3′aQTLs can explain ~16.1% of GWAS SNPs in 15 common traits/diseases, and they are largely distinct from eQTLs and splicing QTLs. Based on these exciting preliminary data, we hypothesize that computational and experimental modeling of APA will substantially facilitate the interpretation of numerous GWAS SNPs important for APA regulation, which are enriched in 3′UTRs and gene downstream regions. Hence, we propose to develop innovative bioinformatics and experimental methods for identifying 3′aQTLs and nominating APA-linked disease/trait susceptibility genes in a wide variety of cell types and environmental factors, followed by in vivo functional characterization using our unique CRISPR engineering system. We expect to establish APA as an emerging and important molecular phenotype to explain a large fraction of GWAS risk SNPs, leading to significant novel biological insights into the genetic basis of APA and APA-linked susceptibility genes in a wide spectrum of human traits and diseases.