Maize and millet transcription factors annotated using comparative genomic and transcriptomic data

Jinn-Jy Lin, Chun-Ping Yu, Yao-Ming Chang, Chun-Chang Chen, Wen-Hsiung Li

Research output: Contribution to journalArticle

12 Citations (Scopus)

Abstract

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. © 2014 Lin et al.; licensee BioMed Central Ltd.
Original languageEnglish
JournalBMC Genomics
Volume15
Issue number1
DOIs
Publication statusPublished - 2014
Externally publishedYes

Fingerprint

Zea mays
Transcription Factors
Setaria Plant
Gene Expression
Photosynthesis
Millets
Genome
Genes
Pseudogenes
DNA Transposable Elements
RNA Polymerase II
DNA
Gene Expression Regulation
Morphogenesis
Arabidopsis
Anatomy
Databases
RNA

Keywords

  • Comparative genomics
  • Coregulators
  • Functional annotation
  • Transcription factor annotation
  • transcription factor
  • Arabidopsis
  • Article
  • C4 plant
  • comparative genomic hybridization
  • controlled study
  • familia
  • foxtail millet
  • gene expression regulation
  • gene function
  • genetic database
  • genome analysis
  • maize
  • microarray analysis
  • molecular evolution
  • nonhuman
  • photosynthesis
  • protein expression
  • pseudogene
  • rice
  • RNA sequence
  • sequence homology
  • tissue growth
  • tissue specificity
  • transcriptomics
  • transposon
  • Zea mays

Cite this

Maize and millet transcription factors annotated using comparative genomic and transcriptomic data. / Lin, Jinn-Jy; Yu, Chun-Ping; Chang, Yao-Ming; Chen, Chun-Chang; Li, Wen-Hsiung.

In: BMC Genomics, Vol. 15, No. 1, 2014.

Research output: Contribution to journalArticle

Lin, Jinn-Jy ; Yu, Chun-Ping ; Chang, Yao-Ming ; Chen, Chun-Chang ; Li, Wen-Hsiung. / Maize and millet transcription factors annotated using comparative genomic and transcriptomic data. In: BMC Genomics. 2014 ; Vol. 15, No. 1.
@article{a97d561ae97a4f4ea0a30467cf0b1fe6,
title = "Maize and millet transcription factors annotated using comparative genomic and transcriptomic data",
abstract = "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. {\circledC} 2014 Lin et al.; licensee BioMed Central Ltd.",
keywords = "Comparative genomics, Coregulators, Functional annotation, Transcription factor annotation, transcription factor, Arabidopsis, Article, C4 plant, comparative genomic hybridization, controlled study, familia, foxtail millet, gene expression regulation, gene function, genetic database, genome analysis, maize, microarray analysis, molecular evolution, nonhuman, photosynthesis, protein expression, pseudogene, rice, RNA sequence, sequence homology, tissue growth, tissue specificity, transcriptomics, transposon, Zea mays",
author = "Jinn-Jy Lin and Chun-Ping Yu and Yao-Ming Chang and Chun-Chang Chen and Wen-Hsiung Li",
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year = "2014",
doi = "10.1186/1471-2164-15-818",
language = "English",
volume = "15",
journal = "BMC Genomics",
issn = "1471-2164",
publisher = "BioMed Central Ltd.",
number = "1",

}

TY - JOUR

T1 - Maize and millet transcription factors annotated using comparative genomic and transcriptomic data

AU - Lin, Jinn-Jy

AU - Yu, Chun-Ping

AU - Chang, Yao-Ming

AU - Chen, Chun-Chang

AU - Li, Wen-Hsiung

N1 - 被引用次數:3 Export Date: 21 March 2016 CODEN: BGMEE 通訊地址: Li, W.-H.; Institute of Molecular and Cellular Biology, National Tsing Hua UniversityTaiwan 參考文獻: Ohme-Takagi, M., Shinshi, H., Ethylene-inducible DNA binding proteins that interact with an ethylene-responsive element (1995) Plant Cell, 7, pp. 173-182. , 160773, 7756828; Nole-Wilson, S., Krizek, B.A., DNA binding properties of the Arabidopsis floral development protein AINTEGUMENTA (2000) Nucleic Acids Res, 28, pp. 4076-4082. , 113152, 11058102; Ulmasov, T., Hagen, G., Guilfoyle, T.J., ARF1, a transcription factor that binds to auxin response elements (1997) Science, 276, pp. 1865-1868. , 9188533; Guilfoyle, T.J., Ulmasov, T., Hagen, G., The ARF family of transcription factors and their role in plant hormone-responsive transcription (1998) Cell Mol Life Sci, 54, pp. 619-627. , 9711229; Mannervik, M., Nibu, Y., Zhang, H., Levine, M., Transcriptional coregulators in development (1999) Science, 284, pp. 606-609. , 10213677; Tiwari, S.B., Wang, X.J., Hagen, G., Guilfoyle, T.J., AUX/IAA proteins are active repressors, and their stability and activity are modulated by auxin (2001) Plant Cell, 13, pp. 2809-2822. , 139490, 11752389; 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PY - 2014

Y1 - 2014

N2 - 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. © 2014 Lin et al.; licensee BioMed Central Ltd.

AB - 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. © 2014 Lin et al.; licensee BioMed Central Ltd.

KW - Comparative genomics

KW - Coregulators

KW - Functional annotation

KW - Transcription factor annotation

KW - transcription factor

KW - Arabidopsis

KW - Article

KW - C4 plant

KW - comparative genomic hybridization

KW - controlled study

KW - familia

KW - foxtail millet

KW - gene expression regulation

KW - gene function

KW - genetic database

KW - genome analysis

KW - maize

KW - microarray analysis

KW - molecular evolution

KW - nonhuman

KW - photosynthesis

KW - protein expression

KW - pseudogene

KW - rice

KW - RNA sequence

KW - sequence homology

KW - tissue growth

KW - tissue specificity

KW - transcriptomics

KW - transposon

KW - Zea mays

U2 - 10.1186/1471-2164-15-818

DO - 10.1186/1471-2164-15-818

M3 - Article

VL - 15

JO - BMC Genomics

JF - BMC Genomics

SN - 1471-2164

IS - 1

ER -