Identification of diverse target RNAs that are functionally regulated by human Pumilio proteins
Identification of diverse target RNAs that are functionally regulated by human Pumilio proteins
复制标题
DOI：
10.1093/nar/gkx1120
复制
发表时间：
2018-01-09
影响因子：
14.9
通讯作者：
Goldstrohm, Aaron C.
中科院分区：
文献类型：
--
作者：
Bohn, Jennifer A.;Van Etten, Jamie L.;Goldstrohm, Aaron C.
人类Pumilio蛋白PUM1和PUM2是序列特异性rna结合蛋白，调节蛋白表达。我们使用RNA-seq，严格的统计测试和实验推导的折叠变化截止来鉴定近1000种靶rna，包括mrna和非编码rna，这些靶rna在功能上受到PUMs的调节。生物信息学分析定义了一个PUM响应元件（PRE），其转录本显著富集，丰度增加，与PUM rna结合一致。我们创建了一个计算模型，该模型结合了PRE的位置和RNA内相对于调控幅度的频率。该模型显示，PUM调控与3‘非翻译区（UTRs）、编码序列和非编码rna的PREs显著相关，但与5’非翻译区无关。为了定义直接的、高可信度的pumm靶标，我们将pumm调控的rna与所有预含rna和实验定义的pumm结合rna交叉对照。结果确定了近300个直接靶标，包括puma抑制的靶标rna和令人惊讶的puma激活的靶标rna。注释富集分析表明，PUMs可调节多种信号通路和发育及神经过程中的基因。此外，PUM靶向mrna影响与癌症、神经系统疾病和心血管疾病相关的人类疾病基因。这些发现为确定puma依赖性调节网络如何影响生物功能和疾病状态铺平了道路。
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.