Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP.
Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP.
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DOI：
10.1016/j.cell.2010.03.009
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发表时间：
2010-04-02
期刊：
影响因子：
64.5
通讯作者：
Tuschl T
中科院分区：
文献类型：
--
作者：
Hafner M;Landthaler M;Burger L;Khorshid M;Hausser J;Berninger P;Rothballer A;Ascano M Jr;Jungkamp AC;Munschauer M;Ulrich A;Wardle GS;Dewell S;Zavolan M;Tuschl T
RNA转录物受到转录后基因调控，涉及以细胞类型依赖性方式表达的数百种RNA结合蛋白（RBP）和含microRNA的核糖核蛋白复合物（miRNP）。我们开发了一种基于细胞的交联方法，以高分辨率和转录组范围确定细胞RBP和miRNP的结合位点。从4-硫代尿苷处理的细胞的免疫纯化的RNP制备的cDNA中的胸苷到胞苷的转换揭示了交联位点。我们确定了几种深入研究的RBP和miRNP的结合位点和调控结果，包括IGF 2BP 1 -3，AGO/EIF 2C 1 -4和TNRC 6A-C。我们的研究表明，这些因素结合数千个网站含有定义的序列基序，并有不同的偏好外显子与内含子或编码与非翻译转录区域。转录组中结合位点的精确定位对于解释个体之间快速出现的遗传变异数据以及这些变异如何导致复杂的遗传疾病至关重要。
RNA transcripts are subject to post-transcriptional gene regulation involving hundreds of RNA-binding proteins (RBPs) and microRNA-containing ribonucleoprotein complexes (miRNPs) expressed in a cell-type dependent fashion. We developed a cell-based crosslinking approach to determine at high resolution and transcriptome-wide the binding sites of cellular RBPs and miRNPs. The crosslinked sites are revealed by thymidine to cytidine transitions in the cDNAs prepared from immunopurified RNPs of 4-thiouridine-treated cells. We determined the binding sites and regulatory consequences for several intensely studied RBPs and miRNPs, including PUM2, QKI, IGF2BP1-3, AGO/EIF2C1-4 and TNRC6A-C. Our study revealed that these factors bind thousands of sites containing defined sequence motifs and have distinct preferences for exonic versus intronic or coding versus untranslated transcript regions. The precise mapping of binding sites across the transcriptome will be critical to the interpretation of the rapidly emerging data on genetic variation between individuals and how these variations contribute to complex genetic diseases.
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影响因子：
64.8
作者：
Baek, Daehyun;Villen, Judit;Shin, Chanseok;Camargo, Fernando D.;Gygi, Steven P.;Bartel, David P.
通讯作者：
Bartel, David P.
影响因子：
3
作者：
Gaidatzis D;van Nimwegen E;Hausser J;Zavolan M
通讯作者：
Zavolan M
影响因子：
4.5
作者：
Easow, George;Teleman, Aurelio A.;Cohen, Stephen M.
通讯作者：
Cohen, Stephen M.
DOI：
10.1016/s0006-291x(86)80250-9
发表时间：
1986-12-15
影响因子：
3.1
作者：
FAVRE, A;MORENO, G;SALET, C
通讯作者：
SALET, C
DOI：
10.1073/pnas.0509260103
发表时间：
2006-03-21
影响因子：
11.1
作者：
Gerber, AP;Luschnig, S;Herschlag, D
通讯作者：
Herschlag, D