Furthermore, bZIPs and bHLHs can act antagonistically, competing for binding to the same sites, such as the competition for binding to targets shared between the bHLH PHYTOCHROME INTERACTING FACTOR3 (PIF3) and the bZIP ELONGATED HYPOCOTYL5 ( Toledo-Ortiz et al., 2014). Even non-G-box-binding bHLHs and other HLHs can indirectly regulate G-box-regulated genes by competing with G-box-binding bHLHs for dimerization partners ( Hao et al., 2012 Oh et al., 2014). Moreover, both bHLHs and bZIPs bind to DNA as either homodimers or heterodimers, further increasing the possible regulatory combinations. The bZIP family has similarly expanded from four founder genes to over 70 ( Corrêa et al., 2008). Many of the other bHLHs may bind to E-box elements, which retain four nucleotides of the G-box core (ACGT or CANNTG). At least 80 of these bHLHs have the precise amino acid composition in their DNA-binding domain required to bind to G-box elements ( Heim et al., 2003 Carretero-Paulet et al., 2010). However, in plants, these two TF families have expanded massively for example, the bHLH family is now the second largest TF family in plants, with over 100 members in Arabidopsis ( Arabidopsis thaliana), despite having arisen from an estimated 14 founder genes in ancient land plants ( Carretero-Paulet et al., 2010). For instance, the highly conserved G-box motif (CACGTG) is bound by TFs in the basic helix-loop-helix (bHLH) and basic Leu zipper (bZIP) families in organisms ranging from yeasts to humans. Understanding gene regulatory networks in plants is further complicated by the fact that plants have more and larger TF families than animals or fungi ( Shiu et al., 2005) and even larger families than would be expected through whole-genome duplication alone ( Shiu et al., 2005 Rensing, 2014). Therefore, understanding the mechanisms that govern how TFs within large TF families regulate their target genes is an important challenge. This cross talk phenomenon within TF families appears universal within the eukaryotes and has been described in yeast ( Gordân et al., 2013), plants ( Nuruzzaman et al., 2013), and mammalian cancer cell lines ( Altman et al., 2015). Therefore, any change in a TF’s concentration or its spatial or temporal distribution may result in unexpected cross talk within the gene regulatory network a TF may inadvertently affect the expression of gene targets of its other family members. Many transcription factors ( TFs) are part of large families, with many members binding to highly overlapping sets of binding sites. Finally, we present Ara-BOX-cis (), a Web site that provides interactive visualizations of the G-box regulatory network, a useful resource for generating predictions for gene regulatory relations. This network accurately predicts transcriptional patterns and reconstructs known regulatory subnetworks. Therefore, we constructed a gene regulatory network that identifies the set of bZIPs and bHLHs that are most predictive of the expression of genes downstream of perfect G-boxes. We determined that the flanking sequences near G-boxes help determine in vitro specificity but that this is insufficient to predict the transcription pattern of genes near G-boxes. Many TF family members bind to similar or identical sequence motifs, such as G-boxes (CACGTG), so it is difficult to predict regulatory relationships. Plants have significantly more transcription factor ( TF) families than animals and fungi, and plant TF families tend to contain more genes these expansions are linked to adaptation to environmental stressors.
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