Isoform-Level Interpretation of High-Throughput Proteomics Data Enabled by Deep Integration with RNA-seq.
Isoform-Level Interpretation of High-Throughput Proteomics Data Enabled by Deep Integration with RNA-seq.
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通过与RNA-Seq深入集成，对高通量蛋白质组学数据的同工型级解释。
DOI：
10.1021/acs.jproteome.8b00310
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发表时间：
2018-10-05
影响因子：
4.4
通讯作者：
Nairn AC
中科院分区：
文献类型：
--
作者：
Carlyle BC;Kitchen RR;Zhang J;Wilson RS;Lam TT;Rozowsky JS;Williams KR;Sestan N;Gerstein MB;Nairn AC
细胞对基因表达的控制是一个复杂的过程，受到多种水平的调控，但最终决定细胞生物合成状态的是产生的蛋白质。细胞可以调节每个基因的蛋白质输出的一种方式是通过表达具有不同氨基酸序列的不同异构体。这些异构体可能在定位和结合相互作用方面表现出差异，这可能具有深刻的功能含义。高通量液相色谱串联质谱蛋白质组学(LC-MS/MS)依赖于酶消化，与RNA-seq等转录组分谱方法相比，具有覆盖率和灵敏度低的特点。消化会导致蛋白质的可预见的碎裂，这会限制能够区分不同亚型的多肽的产生。在这里，我们利用RNA-seq的转录水平表达来设置先前的可能性，并使蛋白质异构体丰度能够直接从LC-MS/MS中估计，这种方法源于大多数基因似乎在给定的细胞类型或组织中以单一的显性异构体表达的原理。通过对同一样品的RNA-seq和LC-MS/MS数据的深度整合，我们发现在同源HEK293细胞培养中80%以上的基因产物和复杂人脑组织中检测到的70%以上的蛋白质中都可以鉴定出主要的异构体。我们证明，结合核糖体图谱中的翻译组数据可以进一步完善这一过程。在匹配的RNA-seq/Translatome和蛋白质组数据的实验中定义异构体增加了这些数据集的功能相关性，并将进一步拓宽我们对基因表达的多水平控制的理解。
Cellular control of gene expression is a complex process that is subject to multiple levels of regulation, but ultimately it is the protein produced that determines the biosynthetic state of the cell. One way that a cell can regulate the protein output from each gene is by expressing alternate isoforms with distinct amino acid sequences. These isoforms may exhibit differences in localization and binding interactions that can have profound functional implications. High-throughput liquid-chromatography tandem mass-spectrometry proteomics (LC-MS/MS) relies on enzymatic digestion and has lower coverage and sensitivity than transcriptomic profiling methods such as RNA-seq. Digestion results in predictable fragmentation of a protein, which can limit generation of peptides capable of distinguishing between isoforms. Here we exploit transcript-level expression from RNA-seq to set prior likelihoods and enable protein isoform abundances to be directly estimated from LC-MS/MS, an approach derived from the principal that most genes appear to be expressed as a single dominant isoform in a given cell-type or tissue. Through this deep integration of RNA-seq and LC-MS/MS data from the same sample, we show that a principal isoform can be identified in over 80% of gene products in homogenous HEK293 cell culture and over 70% of proteins detected in complex human brain tissue. We demonstrate that incorporation of translatome data from ribosome profiling further refines this process. Defining isoforms in experiments with matched RNA-seq/translatome and proteomic data increases the functional relevance of such datasets and will further broaden our understanding of multi-level control of gene expression.
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影响因子：
2.8
作者：
Krastins, Bryan;Prakash, Amol;Lopez, Mary F.
通讯作者：
Lopez, Mary F.
影响因子：
12.3
作者：
Gonzàlez-Porta M;Frankish A;Rung J;Harrow J;Brazma A
通讯作者：
Brazma A
影响因子：
16.6
作者：
Ebrahim, Ali;Brunk, Elizabeth;Tan, Justin;O'Brien, Edward J.;Kim, Donghyuk;Szubin, Richard;Lerman, Joshua A.;Lechner, Anna;Sastry, Anand;Bordbar, Aarash;Feist, Adam M.;Palsson, Bernhard O.
通讯作者：
Palsson, Bernhard O.
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
影响因子：
9.9
作者：
Lange, Vinzenz;Picotti, Paola;Domon, Bruno;Aebersold, Ruedi
通讯作者：
Aebersold, Ruedi