Department of Biological Chemistry, University of Michigan, Ann Arbor, MI 48109, USA.
Promega Corporation, Madison, WI 53711, USA.
Nucleic Acids Res. 2018 Jan 9;46(1):362-386. doi: 10.1093/nar/gkx1120.
Human Pumilio proteins, PUM1 and PUM2, are sequence specific RNA-binding proteins that regulate protein expression. We used RNA-seq, rigorous statistical testing and an experimentally derived fold change cut-off to identify nearly 1000 target RNAs-including mRNAs and non-coding RNAs-that are functionally regulated by PUMs. Bioinformatic analysis defined a PUM Response Element (PRE) that was significantly enriched in transcripts that increased in abundance and matches the PUM RNA-binding consensus. We created a computational model that incorporates PRE position and frequency within an RNA relative to the magnitude of regulation. The model reveals significant correlation of PUM regulation with PREs in 3' untranslated regions (UTRs), coding sequences and non-coding RNAs, but not 5' UTRs. To define direct, high confidence PUM targets, we cross-referenced PUM-regulated RNAs with all PRE-containing RNAs and experimentally defined PUM-bound RNAs. The results define nearly 300 direct targets that include both PUM-repressed and, surprisingly, PUM-activated target RNAs. Annotation enrichment analysis reveal that PUMs regulate genes from multiple signaling pathways and developmental and neurological processes. Moreover, PUM target mRNAs impinge on human disease genes linked to cancer, neurological disorders and cardiovascular disease. These discoveries pave the way for determining how the PUM-dependent regulatory network impacts biological functions and disease states.
人 Pumilio 蛋白，PUM1 和 PUM2，是序列特异性的 RNA 结合蛋白，调节蛋白质表达。我们使用 RNA-seq、严格的统计测试和实验衍生的折叠变化截止值来鉴定近 1000 个靶 RNA，包括 mRNA 和非编码 RNA，这些 RNA 受到 PUM 的功能调节。生物信息学分析定义了一个 PUM 反应元件（PRE），在丰度增加的转录本中显著富集，并且与 PUM RNA 结合的共识相匹配。我们创建了一个计算模型，该模型将 PRE 的位置和频率纳入 RNA 中，相对于调节的幅度。该模型显示 PUM 调节与 3'非翻译区（UTR）、编码序列和非编码 RNA 中的 PRE 之间存在显著相关性，但与 5'UTR 没有相关性。为了定义直接的、高可信度的 PUM 靶标，我们将 PUM 调节的 RNA 与所有包含 PRE 的 RNA 和实验定义的 PUM 结合的 RNA 进行交叉引用。结果定义了近 300 个直接靶标，包括 PUM 抑制和令人惊讶的 PUM 激活靶标 RNA。注释富集分析显示，PUM 调节来自多个信号通路和发育及神经过程的基因。此外，PUM 靶标 mRNA 影响与癌症、神经紊乱和心血管疾病相关的人类疾病基因。这些发现为确定 PUM 依赖的调节网络如何影响生物学功能和疾病状态铺平了道路。
