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

Abstract

BackgroundTranscription 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.ResultWe 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.ConclusionsOur 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.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-818) contains supplementary material, which is available to authorized users.

Transcriptome dynamics of developing maize leaves and genomewide prediction ofciselements and their cognate transcription factors

“…Thus, in general, the two methods give consistent predictions. Removing the overlaps between the two methods, we obtained 253 new TF-TFBS pairs in maize, which represent 29 of the 64 maize TF families (71). Hereafter, we refer to this method as "Method 2.…”

“…We used three sources of known TF-TFBS interactions: (i) The TF databases TRANSFAC (2), JASPAR (3), and AthaMap (1); (ii) the set of 63 Arabidopsis TFs and their TFBSs that were identified using the proteinbinding microarray (PBM) technique (68); and (iii) the set of 240 Arabidopsis TFs (254 TFBSs) and 23 rice TFs (25 TFBSs) in CIS-BP (69), in which the selected TF-TFBS pairs were determined directly by PBM or Systematic Evolution of Ligands by Exponential (SELEX) enrichment approaches. Because for each TFBS in these sources the cognate TF was known, we obtained 8,432 cognate TF sequences and used them to search for their maize homologs in a set of 5,246 maize TF sequences (71) with BLAST E-value <10 −7 . To reduce the false identification rate, the gene-expression profile of maize putative cognate TF(s) of a pTFBS was required to be correlated (PCC >0.85) with the mean profile of the gene set from which the pTFBS was obtained.…”

In silico identification of transcription factors associated with the biosynthesis of carotenoids in corn ( Zea mays L. )

“…Homeodomain leucine zipper (HD-Zip) proteins are plant specific transcription factors and have been categorized into four distinct classes (HDZip I-IV) based on a sequence analysis (Ariel et al, 2007). The corn HD-ZIP TF family comprises approximately 65 members (Lin et al, 2014). According to Kubo and coworkers (1999), HD-Zip IV proteins play significant roles during anthocyanin accumulation, differentiation of epidermal cells, trichome formation and root development in Arabidopsis (Kubo et al, 1999).…”

“…A comprehensive genome-wide transcription factor (TF) annotation and classification has been conducted in corn B73, leading to the prediction of 2538 genes as TFs, which were classified into 64 families (Lin et al, 2014). However, to the best of our knowledge, only a few transcription factors implicated in the regulation of accumulation of carotenoids in corn have been reported.…”

Insights into C 4 metabolism from comparative deep sequencing

“…However, comparative transcriptomics has now identified candidate regulators for the C 4 cycle in maize [24,25,35,36,37 ], Setaria [26,38], Flaveria [13] and Gynandropsis gynandra (formerly known as Cleome gynandra) [23,34 ]. Interestingly, independent lineages of C 4 plants appear to have up-regulated homologous transcriptional regulators in either M or BS cells.…”