Genome-wide identification and predictive modeling of polyadenylation sites in eukaryotes
文献类型： 外文期刊
作者： Ji, Guoli 1 ; Guan, Jinting 1 ; Zeng, Yong 1 ; Li, Qingshun Q. 3 ; Wu, Xiaohui 1 ;
作者机构： 1.Xiamen Univ, Dept Automat, Xiamen 361005, Fujian, Peoples R China
2.Xiamen Univ, Innovat Ctr Cell Biol, Xiamen 361005, Fujian, Peoples R China
3.Xiamen Univ, Coll Environm & Ecol, Minist Educ Coastal & Wetland Ecosyst, Key Lab, Xiamen 361005, Fujian, Peoples R China
4.Miami Univ, Dept Biol, Oxford, OH 45056 USA
5.Fujian Acad Agr Sci, Rice Res Inst, Fuzhou, Fujian, Peoples R China
关键词： poly(A) site;poly(A) signal;alternative polyadenylation;high-throughput technology;predictive modeling
期刊名称：BRIEFINGS IN BIOINFORMATICS （ 影响因子：11.622； 五年影响因子：10.288 ）
ISSN：
年卷期：
页码：
收录情况： SCI
摘要： Polyadenylation [poly(A)] is a vital step in post-transcriptional processing of pre-mRNA. Alternative polyadenylation is a widespread mechanism of regulating gene expression in eukaryotes. Defining poly(A) sites contributes to the annotation of transcripts' ends and the study of gene regulatory mechanisms. Here, we survey methods for collecting poly(A) sites using high-throughput sequencing technologies and summarize the general processes for genome-wide poly(A) site identifications. We also compare the performances of various poly(A) site prediction models and discuss the relationship between poly(A) site identification from sequencing projects and predictive modeling. Moreover, we attempt to address some potential problems in current researches and propose future directions related to polyadenylation research.
- 相关文献
作者其他论文 更多>>
-
Analysis of a rice blast resistance gene Pita-Fuhui2663 and development of selection marker
作者：He, Niqing;Huang, Fenghuang;Yu, Mingxiang;Zhu, Yebao;Li, Qingshun Q.;Yang, Dewei;Li, Qingshun Q.
关键词：
-
Differential alternative polyadenylation contributes to the developmental divergence between two rice subspecies, japonica and indica
作者：Zhou, Qian;Fu, Haihui;Ye, Congting;Lin, Juncheng;Li, Qingshun Quinn;Zhou, Qian;Li, Qingshun Quinn;Yang, Dewei;Ye, Xinfu;Li, Qingshun Quinn;Zhu, Sheng;Ye, Wenbin;Ji, Guoli;Wu, Xiaohui;Fu, Haihui;Fu, Haihui;Fu, Haihui
关键词：alternative polyadenylation; 3 ' end formation; environmental adaptation; post-transcriptional regulation; rice subspecies; RNA processing; transcriptome analysis
-
Interplay between Alternative Splicing and Alternative Polyadenylation Defines the Expression Outcome of the Plant Unique OXIDATIVE TOLERANT-6 Gene
作者：Li, Qingshun Q.;Li, Qingshun Q.;Lu, Wenjia;Li, Qingshun Q.;Liu, Zhaoyang;Liu, Man;Li, Qingshun Q.;Liu, Zhaoyang
关键词：
-
Genome-wide characterization of intergenic polyadenylation sites redefines gene spaces in Arabidopsis thaliana
作者：Wu, Xiaohui;Zeng, Yong;Guan, Jinting;Ji, Guoli;Huang, Rongting;Li, Qingshun Q.;Li, Qingshun Q.;Li, Qingshun Q.;Ji, Guoli
关键词：Alternative polyadenylation;RNA processing;Genome annotation;Intergenic region;3 '-UTR
-
Integration of Developmental and Environmental Signals via a Polyadenylation Factor in Arabidopsis
作者：Liu, Man;Xu, Ruqiang;Li, Qingshun Q.;Merrill, Carrie;Von Lanken, Carol;Hunt, Arthur G.;Hong, Liwei;Li, Qingshun Q.;Li, Qingshun Q.
关键词：
-
Bioinformatics Analysis of Alternative Polyadenylation in Green Alga Chlamydomonas reinhardtii Using Transcriptome Sequences from Three Different Sequencing Platforms
作者：Zhao, Zhixin;Wu, Xiaohui;Kumar, Praveen Kumar Raj;Dong, Min;Li, Qingshun Quinn;Liang, Chun;Wu, Xiaohui;Dong, Min;Ji, Guoli;Li, Qingshun Quinn;Li, Qingshun Quinn;Li, Qingshun Quinn
关键词：poly(A) signals;alternative polyadenylation;alternative splicing;intron retention;sequencing platforms;Chlamydomonas reinhardtii
-
Genome-wide determination of poly(A) sites in Medicago truncatula: evolutionary conservation of alternative poly(A) site choice
作者：Wu, Xiaohui;Gaffney, Bobby;Hunt, Arthur G.;Li, Qingshun Q.;Li, Qingshun Q.;Li, Qingshun Q.
关键词：Alternative polyadenylation;RNA processing;Antisense;Evolutionary conservation;Legume;Medicago truncatula
