Maize and millet transcription factors annotated using comparative genomic and transcriptomic data
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- 作者：Jinn-Jy Lin (11) (12) (13)
Chun-Ping Yu (14)
Yao-Ming Chang (13)
Sean Chun-Chang Chen (13)
Wen-Hsiung Li (12) (13) (14) (15)
11. Bioinformatics Program ; Taiwan International Graduate Program ; Institute of Information Science ; Academia Sinica ; Taipei ; 115 ; Taiwan
12. Institute of Molecular and Cellular Biology ; National Tsing Hua University ; Hsinchu ; 300 ; Taiwan
13. Biodiversity Research Center ; Academia Sinica ; Taipei ; 115 ; Taiwan
14. Biotechnology Center ; National Chung-Hsing University ; Taichung ; 40227 ; Taiwan
15. Department of Ecology and Evolution ; University of Chicago ; Chicago ; IL ; 60637 ; USA - 关键词：Transcription factor annotation ; Coregulators ; Comparative genomics ; Functional annotation
- 刊名：BMC Genomics
- 出版年：2014
- 出版时间：December 2014
- 年：2014
- 卷：15
- 期：1
- 全文大小：1,639 KB
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- 出版者：BioMed Central
- ISSN：1471-2164
文摘
Background Transcription factors (TFs) contain DNA-binding domains (DBDs) and regulate gene expression by binding to specific DNA sequences. In addition, there are proteins, called transcription coregulators (TCs), which lack DBDs but can alter gene expression through interaction with TFs or RNA Polymerase II. Therefore, it is interesting to identify and classify the TFs and TCs in a genome. In this study, maize (Zea mays) and foxtail millet (Setaria italica), two important species for the study of C4 photosynthesis and kranz anatomy, were selected. Result We conducted a comprehensive genome-wide annotation of TFs and TCs in maize B73 and in two strains of foxtail millet, Zhang gu and Yugu1, and classified them into families. To gain additional support for our predictions, we searched for their homologous genes in Arabidopsis or rice and studied their gene expression level using RNA-seq and microarray data. We identified many new TF and TC families in these two species, and described some evolutionary and functional aspects of the 9 new maize TF families. Moreover, we detected many pseudogenes and transposable elements in current databases. In addition, we examined tissue expression preferences of TF and TC families and identified tissue/condition-specific TFs and TCs in maize and millet. Finally, we identified potential C4-related TF and TC genes in maize and millet. Conclusions Our results significantly expand current TF and TC annotations in maize and millet. We provided supporting evidence for our annotation from genomic and gene expression data and identified TF and TC genes with tissue preference in expression. Our study may facilitate the study of regulation of gene expression, tissue morphogenesis, and C4 photosynthesis in maize and millet. The data we generated in this study are available at http://sites.google.com/site/jjlmmtf.