Ribosome elongating footprints denoised by wavelet transform comprehensively characterize dynamic cellular translation events.
Ribosome elongating footprints denoised by wavelet transform comprehensively characterize dynamic cellular translation events.
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小波变换去噪的核糖体延伸足迹全面表征动态细胞翻译事件
DOI：
10.1093/nar/gky533
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发表时间：
2018-10-12
影响因子：
14.9
通讯作者：
Lu ZJ
中科院分区：
文献类型：
--
作者：
Xu Z;Hu L;Shi B;Geng S;Xu L;Wang D;Lu ZJ
翻译在细胞发育和应激反应中受到动态调节。为了检测主动翻译的开放阅读框架（ORF）和动态细胞翻译事件，我们开发了一种计算方法RiboWave，用于处理核糖体分析数据。RiboWave利用小波变换对原始信号进行去噪，提取核糖体的3-nt周期性，并精确定位其足迹，称为周期性足迹P位点（Periodic Footprint P-site，PF P-site）。这种高分辨率的足迹被发现捕获的积极延长核糖体，翻译景观可以明确的特点，从完整的轨道。我们将RiboWave与几种已发表的方法（如RiboTaper，ORFscore和RibORF）进行了比较，发现在定义主动翻译的ORF时，RiboWave在准确性和使用率方面都优于它们。此外，我们表明，由RiboWave衍生的PF P-位点在表征细胞翻译组的动态性和复杂性方面表现出上级性能，通过准确估计蛋白质水平的丰度，评估差异翻译和识别动态翻译移码。
Abstract Translation is dynamically regulated during cell development and stress response. In order to detect actively translated open reading frames (ORFs) and dynamic cellular translation events, we have developed a computational method, RiboWave, to process ribosome profiling data. RiboWave utilizes wavelet transform to denoise the original signal by extracting 3-nt periodicity of ribosomes and precisely locate their footprint denoted as Periodic Footprint P-site (PF P-site). Such high-resolution footprint is found to capture the full track of actively elongating ribosomes, from which translational landscape can be explicitly characterized. We compare RiboWave with several published methods, like RiboTaper, ORFscore and RibORF, and found that RiboWave outperforms them in both accuracy and usage when defining actively translated ORFs. Moreover, we show that PF P-site derived by RiboWave shows superior performance in characterizing the dynamics and complexity of cellular translatome by accurately estimating the abundance of protein levels, assessing differential translation and identifying dynamic translation frameshift.
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影响因子：
3.7
作者：
Cho CP;Lin SC;Chou MY;Hsu HT;Chang KY
通讯作者：
Chang KY
影响因子：
7
作者：
Harrow J;Frankish A;Gonzalez JM;Tapanari E;Diekhans M;Kokocinski F;Aken BL;Barrell D;Zadissa A;Searle S;Barnes I;Bignell A;Boychenko V;Hunt T;Kay M;Mukherjee G;Rajan J;Despacio-Reyes G;Saunders G;Steward C;Harte R;Lin M;Howald C;Tanzer A;Derrien T;Chrast J;Walters N;Balasubramanian S;Pei B;Tress M;Rodriguez JM;Ezkurdia I;van Baren J;Brent M;Haussler D;Kellis M;Valencia A;Reymond A;Gerstein M;Guigó R;Hubbard TJ
通讯作者：
Hubbard TJ
DOI：
10.1073/pnas.82.11.3616
发表时间：
1985-01-01
影响因子：
11.1
作者：
CRAIGEN, WJ;COOK, RG;CASKEY, CT
通讯作者：
CASKEY, CT
影响因子：
48
作者：
Gonzalez-Perez A;Perez-Llamas C;Deu-Pons J;Tamborero D;Schroeder MP;Jene-Sanz A;Santos A;Lopez-Bigas N
通讯作者：
Lopez-Bigas N
影响因子：
7.4
作者：
Du, Ruijun;Zhu, Lina;Liu, Baohong
通讯作者：
Liu, Baohong