Systematic functional interrogation of human pseudogenes using CRISPRi.
Systematic functional interrogation of human pseudogenes using CRISPRi.
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DOI：
10.1186/s13059-021-02464-2
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发表时间：
2021-08-23
期刊：
影响因子：
12.3
通讯作者：
Chen Y
中科院分区：
文献类型：
--
作者：
Sun M;Wang Y;Zheng C;Wei Y;Hou J;Zhang P;He W;Lv X;Ding Y;Liang H;Hon CC;Chen X;Xu H;Chen Y
人类基因组编码超过14，000个假基因，这些假基因是蛋白质编码基因的进化遗迹，通常被认为是无功能的。新出现的证据表明，一些假基因可能发挥重要的功能。然而，人类假基因在多大程度上与功能相关仍不清楚。由于技术上的挑战，包括假基因和亲本基因之间的高序列相似性，以及转录起始位点的注释不佳，一直没有大规模的假基因功能表征。为了克服这些技术障碍，我们开发了一个集成的计算管道来设计第一个靶向人类假基因启动子近端区域的CRISPR干扰（CRISPRi）单向导RNA（sgRNA）的全基因组文库。我们在luminal A乳腺癌细胞中进行了第一次以假基因为中心的CRISPRi筛选，并揭示了大约70个影响乳腺癌细胞适应性的假基因。在最热门的命中，我们确定了一个癌症睾丸单一的假基因，MGAT 4 EP，这是主要定位在细胞核和相互作用的FOXA 1，一个关键的调节器在管腔A乳腺癌。通过增强FOXA 1的启动子结合，MGAT 4 EP上调致癌转录因子FOXM 1的表达。来自癌症基因组图谱（TCGA）的多组学数据的综合分析揭示了许多单一假基因，其表达显著失调和/或与不同癌症类型中患者的总体/无复发生存期相关。我们的研究代表了第一个大规模的研究特征的假基因功能。我们的研究结果表明，单一的假基因的核功能的重要性，并强调其在人类疾病中未被充分认识的作用。这些功能基因组资源的开发将极大地促进人类假基因功能的研究。在线版本包含补充材料，可通过10.1186/s13059-021-02464-2获得。
The human genome encodes over 14,000 pseudogenes that are evolutionary relics of protein-coding genes and commonly considered as nonfunctional. Emerging evidence suggests that some pseudogenes may exert important functions. However, to what extent human pseudogenes are functionally relevant remains unclear. There has been no large-scale characterization of pseudogene function because of technical challenges, including high sequence similarity between pseudogene and parent genes, and poor annotation of transcription start sites. To overcome these technical obstacles, we develop an integrated computational pipeline to design the first genome-wide library of CRISPR interference (CRISPRi) single-guide RNAs (sgRNAs) that target human pseudogene promoter-proximal regions. We perform the first pseudogene-focused CRISPRi screen in luminal A breast cancer cells and reveal approximately 70 pseudogenes that affect breast cancer cell fitness. Among the top hits, we identify a cancer-testis unitary pseudogene, MGAT4EP, that is predominantly localized in the nucleus and interacts with FOXA1, a key regulator in luminal A breast cancer. By enhancing the promoter binding of FOXA1, MGAT4EP upregulates the expression of oncogenic transcription factor FOXM1. Integrative analyses of multi-omic data from the Cancer Genome Atlas (TCGA) reveal many unitary pseudogenes whose expressions are significantly dysregulated and/or associated with overall/relapse-free survival of patients in diverse cancer types. Our study represents the first large-scale study characterizing pseudogene function. Our findings suggest the importance of nuclear function of unitary pseudogenes and underscore their underappreciated roles in human diseases. The functional genomic resources developed here will greatly facilitate the study of human pseudogene function. The online version contains supplementary material available at 10.1186/s13059-021-02464-2.
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影响因子：
46.9
作者：
Doench JG;Fusi N;Sullender M;Hegde M;Vaimberg EW;Donovan KF;Smith I;Tothova Z;Wilen C;Orchard R;Virgin HW;Listgarten J;Root DE
通讯作者：
Root DE
DOI：
10.1093/bioinformatics/btu638
发表时间：
2015-01-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Anders S;Pyl PT;Huber W
通讯作者：
Huber W
影响因子：
16
作者：
Bosson, Andrew D.;Zamudio, Jesse R.;Sharp, Phillip A.
通讯作者：
Sharp, Phillip A.
影响因子：
28.1
作者：
Kim, Hui Kwon;Lee, Sungtae;Kim, Hyongbum Henry
通讯作者：
Kim, Hyongbum Henry
影响因子：
14.9
作者：
Dwane L;Behan FM;Gonçalves E;Lightfoot H;Yang W;van der Meer D;Shepherd R;Pignatelli M;Iorio F;Garnett MJ
通讯作者：
Garnett MJ