Comparison of TRIBE and STAMP for identifying targets of RNA binding proteins in human and Drosophila cells.
Comparison of TRIBE and STAMP for identifying targets of RNA binding proteins in human and Drosophila cells.
复制标题
DOI：
10.1261/rna.079608.123
复制
发表时间：
2023-08
期刊：
影响因子：
--
通讯作者：
中科院分区：
文献类型：
--
作者：
RNA结合蛋白(RBPs)具有多种功能，与多种神经系统疾病有关。为了在少数细胞中识别限制性商业惯例的靶点，我们开发了TRIBE，其中RNA编辑酶ADAR(ADARcd)的催化结构域与RBP融合。当RBP与mRNA结合时，ADAR催化目标mRNA中的A到G修饰，这在标准RNA测序中很容易识别。在STAMP中，除了ADARcd被RNA编辑酶APOBEC取代外，概念是相同的。在这里，我们比较了人类和果蝇细胞中的部落和STAMP。目标是了解每种方法的优缺点，以便研究人员可以选择最适合他们的RBP和系统的方法。在人类细胞中，使用RBP TDP-43进行部落和STAMP。虽然他们都识别了TDP-43靶标mRNAs，但结合这两种方法更成功地识别了高置信度靶标。在果蝇细胞中，RBP-APOBEC融合只产生了少量的编辑位点，与对照编辑的水平相当。Hrp48和Thor(果蝇eIF4E-BP)这两种不同的限制性商业惯例也是如此，这表明STAMP在果蝇中不起作用。
RNA binding proteins (RBPs) perform a myriad of functions and are implicated in numerous neurological diseases. To identify the targets of RBPs in small numbers of cells, we developed TRIBE, in which the catalytic domain of the RNA editing enzyme ADAR (ADARcd) is fused to an RBP. When the RBP binds to an mRNA, ADAR catalyzes A to G modifications in the target mRNA that can be easily identified in standard RNA sequencing. In STAMP, the concept is the same except the ADARcd is replaced by the RNA editing enzyme APOBEC. Here we compared TRIBE and STAMP side-by-side in human and Drosophila cells. The goal is to learn the pros and cons of each method so that researchers can choose the method best suited to their RBP and system. In human cells, TRIBE and STAMP were performed using the RBP TDP-43. Although they both identified TDP-43 target mRNAs, combining the two methods more successfully identified high-confidence targets. In Drosophila cells, RBP–APOBEC fusions generated only low numbers of editing sites, comparable to the level of control editing. This was true for two different RBPs, Hrp48 and Thor (Drosophila EIF4E-BP), indicating that STAMP does not work well in Drosophila.
登录
查看更多内容
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：
64.8
作者：
Komor AC;Kim YB;Packer MS;Zuris JA;Liu DR
通讯作者：
Liu DR
影响因子：
5.8
作者：
Biswas, Jeetayu;Rahman, Reazur;Singer, Robert H.
通讯作者：
Singer, Robert H.
影响因子：
64.5
作者：
Hallegger M;Chakrabarti AM;Lee FCY;Lee BL;Amalietti AG;Odeh HM;Copley KE;Rubien JD;Portz B;Kuret K;Huppertz I;Rau F;Patani R;Fawzi NL;Shorter J;Luscombe NM;Ule J
通讯作者：
Ule J
影响因子：
10.5
作者：
Flamand, Mathieu N.;Ke, Ke;Tamming, Renee;Meyer, Kate D.
通讯作者：
Meyer, Kate D.