tModBase: deciphering the landscape of tRNA modifications and their dynamic changes from epitranscriptome data.
tModBase: deciphering the landscape of tRNA modifications and their dynamic changes from epitranscriptome data.
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tModBase：从表观转录组数据中解读 tRNA 修饰的概况及其动态变化
DOI：
10.1093/nar/gkac1087
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发表时间：
2023-01-06
影响因子：
14.9
通讯作者：
Zheng, Ling-Ling
中科院分区：
文献类型：
--
作者：
Lei, Hao-Tian;Wang, Zhang-Hao;Li, Bin;Sun, Yang;Mei, Shi-Qiang;Yang, Jian-Hua;Qu, Liang-Hu;Zheng, Ling-Ling
tRNA molecules contain dense, abundant modifications that affect tRNA structure, stability, mRNA decoding and tsRNA formation. tRNA modifications and related enzymes are responsive to environmental cues and are associated with a range of physiological and pathological processes. However, there is a lack of resources that can be used to mine and analyse these dynamically changing tRNA modifications. In this study, we established tModBase (https://www.tmodbase.com/) for deciphering the landscape of tRNA modification profiles from epitranscriptome data. We analysed 103 datasets generated with second- and third-generation sequencing technologies and illustrated the misincorporation and termination signals of tRNA modification sites in ten species. We thus systematically demonstrate the modification profiles across different tissues/cell lines and summarize the characteristics of tRNA-associated human diseases. By integrating transcriptome data from 32 cancers, we developed novel tools for analysing the relationships between tRNA modifications and RNA modification enzymes, the expression of 1442 tRNA-derived small RNAs (tsRNAs), and 654 DNA variations. Our database will provide new insights into the features of tRNA modifications and the biological pathways in which they participate.
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影响因子：
14.9
作者：
Dixit S;Kessler AC;Henderson J;Pan X;Zhao R;D'Almeida GS;Kulkarni S;Rubio MAT;Hegedűsová E;Ross RL;Limbach PA;Green BD;Paris Z;Alfonzo JD
通讯作者：
Alfonzo JD
影响因子：
14.9
作者：
Chan PP;Lowe TM
通讯作者：
Lowe TM
影响因子：
46.9
作者：
Hu JF;Yim D;Ma D;Huber SM;Davis N;Bacusmo JM;Vermeulen S;Zhou J;Begley TJ;DeMott MS;Levine SS;de Crécy-Lagard V;Dedon PC;Cao B
通讯作者：
Cao B
影响因子：
14.9
作者：
Fleming, Brittany A.;Blango, Matthew G.;Rousek, Alexis A.;Kincannon, William M.;Tran, Alexander;Lewis, Adam J.;Russell, Colin W.;Zhou, Qin;Baird, Lisa M.;Barber, Amelia E.;Brannon, John R.;Beebout, Connor J.;Bandarian, Vahe;Hadjifrangiskou, Maria;Howard, Michael T.;Mulvey, Matthew A.
通讯作者：
Mulvey, Matthew A.
影响因子：
14.9
作者：
Boccaletto P;Stefaniak F;Ray A;Cappannini A;Mukherjee S;Purta E;Kurkowska M;Shirvanizadeh N;Destefanis E;Groza P;Avşar G;Romitelli A;Pir P;Dassi E;Conticello SG;Aguilo F;Bujnicki JM
通讯作者：
Bujnicki JM