Figure
![Distribution of TATAWA in plant promoters aligned relative to the TSS. The canonical TATA-box defines the TATAWA-PLM. The distribution model is learned in the [-1000, -300] region where the base line (continuous line) and the upper bound of the confidence interval (dashed line) are estimated and applied to the [-300, 500] region. Distributions are shown for the Arabidopsis thaliana set containing 14927 promoters (A) and for the Oryza sativa set containing 18012 promoters (B). The TATAWA-PLM is preferentially positioned 32 bases upstream of the TSS with a [-39, -26] functional window in both genomes. A. thaliana and O. sativa are characterized by an SMS of 21 and 19 respectively.](profile/Virginie_BERNARD/publication/41909345/figure/fig1/AS:213466875994112@1427905877163/Distribution-of-TATAWA-in-plant-promoters-aligned-relative-to-the-TSS-The-canonical.png)
Distribution of TATAWA in plant promoters aligned relative to the TSS. The canonical TATA-box defines the TATAWA-PLM. The distribution model is learned in the [-1000, -300] region where the base line (continuous line) and the upper bound of the confidence interval (dashed line) are estimated and applied to the [-300, 500] region. Distributions are shown for the Arabidopsis thaliana set containing 14927 promoters (A) and for the Oryza sativa set containing 18012 promoters (B). The TATAWA-PLM is preferentially positioned 32 bases upstream of the TSS with a [-39, -26] functional window in both genomes. A. thaliana and O. sativa are characterized by an SMS of 21 and 19 respectively.
Source publication
![Table 4 Conservation of the three [-39, -26]-PLM classes in orthologous...](profile/Virginie_BERNARD/publication/41909345/figure/tbl4/AS:669682109526024@1536676065349/Conservation-of-the-three-39-26-PLM-classes-in-orthologous-gene-pairs-between-A_Q320.jpg)
The TATA-box and TATA-variants are regulatory elements involved in the formation of a transcription initiation complex. Both have been conserved throughout evolution in a restricted region close to the Transcription Start Site (TSS). However, less than half of the genes in model organisms studied so far have been found to contain either one of thes...
Contexts in source publication
Context 1
... is a particularly well-conserved PLM since it is found in the same promoter region in both plants and animals [30]. Confirming previous results, we found this PLM in both A. thaliana and O. sativa genomes in a preferential position 32 bases upstream of the TSS and strictly located within the [-39, -26] region ( Figure 1). A total of 2606 (17.5%) and 2601 (14.4%) promoters in A. thaliana and O. sativa respectively contained a TATAWA within the [-39, -26] functional window. ...Context 2
... results show that the TC [-39,-26] - PLM exhibits specific characteristics distinguishing it from the other Y-patch motifs. Y-patch motifs show fre- quent occurrence in plant promoters, are present in a wide area around the TSS (see Figure 1) and may be extended from a 6-to a 10-base-long element without decreasing the score associated to their local overrepre- sentation (SMS). Indeed the TC [-39,-26] -PLMs were only observed in a sub-set of 18% of A. thaliana promoters at the TATA-box expected position, were associated with a sharp functional window, were 6-base-long and could not be extended without decreasing their SMS. ...Context 3
... analyses were performed with the R statistical software [66]. We used R for (i) the regression analysis leading to PLM identification ( Figure 1) and the charac- terization of expression categories (Figure 7), and for (ii) motif distributions (Figures 3 and 6). We performed Fisher exact one-sided tests using the Bonferroni correc- tion to compare percentages between two independent samples. ...Similar publications
It is now well known that vertebrates use multiple types of core promoter to accomplish differentiated tasks in Pol II-dependent
transcription. Several transcriptional characteristics are known to be associated with core types, including distribution
patterns of transcription start sites (TSSs) and selection between tissue-specific and constitutive...
Citations
... Research shows that cis-elements play an important role in the transcriptional regulation signal pathway of plants under various biotic and abiotic stresses [40]. There is an antagonistic relationship between BR and ABA in regulating growth and development. ...
The BES1 transcription factor family was unique and critical in plants. The BES1s played roles in the Brassinosteroid (BR) signaling pathway and participated in the plant’s development, maturation, and stress response process. This study investigated the function of the BES1 gene family of 48 horticultural crops by phylogenetic and genomic colinearity network analysis. In addition, the transcriptional regulatory networks had analyzed the process during biotic stress, abiotic stress, fruit development, and postharvest of kiwifruit and peach. The study illustrated a comprehensive understanding of the phylogenetic relationships of the BES1 family in plant genomes and the prediction of growth and development of kiwifruit and peach fruits and maturation-related BES1 members, laying the foundation for further functional studies of BES1 genes in the future.
... Although, under natural conditions, the DNA zones of higher stability to denaturation are commonly relevant to non-coding regions [82,83], our study showed that even a single 2 H/ 1 H replacement in the III part of IFNA17 creates more n max and n min than their sum after an 2 H-substitution in the promoter (pχ 2 Yates = 0.0013, Table 1, Table 2), which indicates an important role of non-coding gene regions in the regulation of the DNA bubble occurrences in its different parts. Based on this, it can be assumed that regulation of DNA denaturation is a far more complex process than only through classical transcription initiation points (e.g., TC-and TATA-motifs and others [84]). In addition, due to the developed model and new variant of the modified BJ algorithm, after a single 2 H-substitution, it was possible to reveal both the impact of E cr (negative in the diapason from 0.250 to 0.450) and the bubble sizes (positive for the ones 10 bps and less) on the AT/GC ratio in DNA bubbles. ...
The influence of a single 2H/1H replacement on the frequency generation of different-size bubbles in the human interferon alpha-17 gene (IFNA17) under various energies was studied by a developed algorithm and mathematical modeling without simplifications or averaging. This new approach showed the efficacy of researching DNA bubbles and open states both when all hydrogen bonds in nitrogenous base pairs are protium and after an 2H-substitution. After a single deuterium substitution under specific energies, it was demonstrated that the non-coding region of IFNA17 had a more significant regulatory role in bubble generation in the whole gene than the promoter had. It was revealed that a single deuterium substitution for protium has an influence on the frequency generation of DNA bubbles, which also depends on their size and is always higher for the smaller bubbles under the largest number of the studied energies. Wherein, compared to the natural condition under the same critical value of energy, the bigger raises of the bubble frequency occurrence (maximums) were found for 11-30 base pair (bp) bubbles (higher by 319%), 2-4 bp bubbles (higher by 300%), and 31 bp and over ones (higher by 220%); whereas the most significant reductions of the indicators (minimums) were observed for 11-30 bp bubbles (lower by 43%) and bubbles size over 30 bp (lower by 82%). In this study, we also analyzed the impact of several circumstances on the AT/GC ratio in the formation of DNA bubbles, both under natural conditions and after a single hydrogen isotope exchange. Moreover, based on the obtained data, substantial positive and inverse correlations were revealed between the AT/GC ratio and some factors (energy values, size of DNA bubbles). So, this modeling and variant of the modified algorithm, adapted for researching DNA bubbles, can be useful to study the regulation of replication and transcription in the genes under different isotopic substitutions in the nucleobases.
... It has been widely reported that cis-elements in gene promoters play an important role in transcriptional regulation [47,48]. Analysis of cis-elements is helpful to study expression regulation of transcription factors [49]. ...
Background
C2H2 zinc finger proteins (C2H2-ZFPs), one of the largest transcription factors, play a variety of roles in plant development and growth as well as stress response. While, the evolutionary history and expression profile of the C2H2-ZFP genes in Larix kaempferi (LkZFPs) have not been reported so far.
Results
In this study, the whole genome of the LkZFPs was identified and characterized, including physicochemical properties, phylogenetic relationships, conservative motifs, the promoter cis-elements and Gene Ontology (GO) annotation. We identified 47 LkZFPs and divided them into four subfamilies based on phylogenetic analysis and conserved motifs. Subcellular localization prediction showed that most of the LkZFPs were located in the nucleus. Promoter cis-element analysis suggested that the LkZFPs may be involved in the regulation of stress responses. Moreover, Real-time quantitative PCR (RT-qPCR) results showed that Q-type LkZFP genes were involved in the response to abiotic stress, such as salt, drought and hormone stresses. Subcellular localization results showed that LkZFP7 and LkZFP37 were located in the nucleus, LkZFP32 was located in both cytoplasm and nucleus.
Conclusion
The identification and functional analysis of LkZFPs suggested that some LkZFP genes might play important roles in coping with both biological and abiotic stresses. These results could further increase understanding of the function of the LkZFPs, and provide some research direction and theoretical support.
... Subcellular localization prediction analysis showed that LkNF-YB proteins are mostly found in the nucleus, indicating they are the transcription factors. Studies have shown that many plant TFs promoters have highly conserved cis-elements playing crucial roles in transcriptional regulation signaling pathways when plants are subjected to biological and abiotic stresses [39]. Therefore, cis-acting elements in the promoter region of LkNF-YB genes were analyzed, and it was found that every gene contained at least three elements related to hormonal or biological stress. ...
NF-YB, a subfamily of Nuclear Factor Y (NF-Y) transcription factor, play crucial role in many biological processes of plant growth and development and abiotic stress responses, and they can therefore be good candidate factors for breeding stress-resistant plants. However, the NF-YB proteins have not yet been explored in Larix kaempferi, a tree species with high economic and ecological values in northeast China and other regions, limiting the breeding of anti-stress L. kaempferi. In order to explore the roles of NF-YB transcription factors in L. kaempferi, we identified 20 LkNF-YB family genes from L. kaempferi full-length transcriptome data and carried out preliminary characterization of them through series of analyses on their phylogenetic relationships, conserved motif structure, subcellular localization prediction, GO annotation, promoter cis-acting elements as well as expression profiles under treatment of phytohormones (ABA, SA, MeJA) and abiotic stresses (salt and drought). The LkNF-YB genes were classified into three clades through phylogenetic analysis and belong to non-LEC1 type NF-YB transcription factors. They have 10 conserved motifs; all genes contain a common motif, and their promoters have various phytohormones and abiotic stress related cis-acting elements. Quantitative real time reverse transcription PCR (RT-qPCR) analysis showed that the sensitivity of the LkNF-YB genes to drought and salt stresses was higher in leaves than roots. The sensitivity of LKNF-YB genes to ABA, MeJA, SA stresses was much lower than that to abiotic stress. Among the LkNF-YBs, LkNF-YB3 showed the strongest responses to drought and ABA treatments. Further protein interaction prediction analysis for LkNF-YB3 revealed that LkNF-YB3 interacts with various factors associated with stress responses and epigenetic regulation as well as NF-YA/NF-YC factors. Taken together, these results unveiled novel L. kaempferi NF-YB family genes and their characteristics, providing the basic knowledge for further in-depth studies on their roles in abiotic stress responses of L. kaempferi.
... The eukaryotic core promoter element that was identified first (in Drosophila histone genes) and is best known is the TATA box [48] with the TATAWAAS consensus sequence (where W = A or T, whereas S = G or C according to the IUPAC nomenclature), to which TBP binds and initiates assembly of the preinitiation complex. Although the TATA box is conserved from yeast to humans, it has been detected only in a minority of core promoters in almost all these species: 20% to 46% of core promoters in yeast [49],~10% in humans (24% together with TATA-like sequences) [50], 64% of promoters in Drosophila [51], 27% of promoters in mice [52], and~39% of promoters in A. thaliana [53] (or 29% according to the first genome-wide study by Molina et al. [54]), whereas only~19% of promoters in rice contain a TATA box [55]. Studies on yeast and humans indicate that genes containing the TATA box are usually subject to tissue-specific expression and are mainly regulated by stressful stimuli, whereas genes without TATA are expressed constitutively and are predominantly involved in housekeeping processes [56]. ...
For transcription initiation by RNA polymerase II (Pol II), all eukaryotes require assembly of basal transcription machinery on the core promoter, a region located approximately in the locus spanning a transcription start site (−50; +50 bp). Although Pol II is a complex multi-subunit enzyme conserved among all eukaryotes, it cannot initiate transcription without the participation of many other proteins. Transcription initiation on TATA-containing promoters requires the assembly of the preinitiation complex; this process is triggered by an interaction of TATA-binding protein (TBP, a component of the general transcription factor TFIID (transcription factor II D)) with a TATA box. The interaction of TBP with various TATA boxes in plants, in particular Arabidopsis thaliana, has hardly been investigated, except for a few early studies that addressed the role of a TATA box and substitutions in it in plant transcription systems. This is despite the fact that the interaction of TBP with TATA boxes and their variants can be used to regulate transcription. In this review, we examine the roles of some general transcription factors in the assembly of the basal transcription complex, as well as functions of TATA boxes of the model plant A. thaliana. We review examples showing not only the involvement of TATA boxes in the initiation of transcription machinery assembly but also their indirect participation in plant adaptation to environmental conditions in responses to light and other phenomena. Examples of an influence of the expression levels of A. thaliana TBP1 and TBP2 on morphological traits of the plants are also examined. We summarize available functional data on these two early players that trigger the assembly of transcription machinery. This information will deepen the understanding of the mechanisms underlying transcription by Pol II in plants and will help to utilize the functions of the interaction of TBP with TATA boxes in practice.
... We found 47 different CAREs upstream of these genes and grouped them into different functional categories, as shown in Fig. 2. Most located CAREs were light-responsive (LR) elements which we excluded from the results to spotlight more specific CAREs. The promoter and enhancer elements, including TATA-Box, CAT-Box, AT-Rich element, GC-Motif, and a-Box, formed (Bernard et al. 2010). Following the development of functional assays, mutations in TATA boxes were found to reduce transcription initiation and prevent the proper positioning of transcription factors (Smale 2001). ...
Steviol glycosides are non-caloric sweeteners found in high concentrations in the leaves of the Paraguayan perennial herb S. rebaudiana rebaudiana. In the present study, an attempt has been made to analyze promoter regions of SG-related biosynthesis genes of S. rebaudiana rebaudiana and Helianthus annuus. The close relationship between H. annuus, S. rebaudiana, and the SGs biosynthesis genes in the H. annuus genome provides a remarkable opportunity for SGs production in the H. annuus leaves. Several cis-acting regulatory elements associated with plant development, plant hormonal regulation, and stress response were identified and found in varying frequencies within the two kbp of 5′ regulatory regions, including A-box, MYB, MSB, ABRE, LTR, ERE, STRE, ABA, ARE, DRE, MBSI, TC-RICH REPEATS, WUN-MOTIF, MYC, MYB. The number of cis-elements in both plants is equal. However, S. rebaudiana's UGT genes have significantly more elements than H. annuus. These results suggest that the lack of H. annuus SGs is related to the plant's cis-elements of UGT genes. This finding indicates the potential cis-acting regulatory factors involved in the expression and regulation of the SG gene in H. annuus and S. rebaudiana during cellular development or environmental stress situations. Further, tandem repeats and CPG islands were detected in the promoter regions. RT-PCR analysis of seven SG biosynthesis key genes, including CDPS, KS, KO, KAH, and three glucosyltransferases, namely UGT85C2, UGT74G1, and UGT76G1, revealed that only KS and KO genes are expressed in H. annuus leaves. Futuristically, this data will be a helpful resource for upgrading H. annuus leaves to S. rebaudiana sweeteners producers and understanding the regulation of SG-related genes.
... First, the 254 bp fragment inserted into the third intron of BADH-A1a contains a TATA-box and W-box. A TATA-box is the core promoter element that initiates gene transcription and participates in the formation of the transcription initiation complex (Bernard et al., 2010). The WRKY transcription factors can bind to W-box, while most of the WRKY transcription factors of known function are negative regulators, with only a few of those (Bollier et al., 2018). ...
Drought and salt stress can strongly affect the growth and development of wheat. Wheat adapts to drought and salt stress through osmotic regulation. Betaine aldehyde dehydrogenase (BADH) is a key enzyme in the synthesis of betaine, an osmotic regulator. We cloned a region of the TaBADH-A1 promoter and genomic DNA that included the introns and exons, from four Chinese wheat cultivars. Following the analysis of TaBADH-A1 genomic DNA and promoter sequence polymorphisms of 4 cloned and 15 cultivars from the database, 7 haplotypes of TaBADH-A1 gene were identified. We divided the 7 haplotypes with a 254 bp insertion or deletion (indel) into two main alleles, BADH-A1a and BADH-A1b. Meanwhile, a molecular marker was developed based on the 254 bp indel of the third intron of TaBADH-A1 gene. Expression levels of BADH-A1b were found to be significantly higher than those of BADH-A1a under drought and salt stress conditions. Betaine accumulation was significantly higher in wheat containing BADH-A1b compared to BADH-A1a under drought and salt stress. We also identified that the average relative germination and survival rates of wheat with the BADH-A1b allele were significantly higher than wheat with the BADH-A1a allele. The results reveal that wheat containing BADH-A1b has stronger drought and salt tolerance than wheat with BADH-A1a. Meanwhile, the geographic distribution and frequency of the TaBADH-A1 locus alleles indicate that BADH-A1a has been preferred in Chinese wheat breeding programs, while BADH-A1b, associated with favorable stress tolerance, has been neglected. The results of this study provide evidence for an excellent candidate allele for marker-assisted selection of new wheat cultivars with increased salt tolerance and drought resistance.
... The presence of TC microsatellite and TC-rich sequences in the 5′ flanking region of EgCAD2 (Fig. 5) prompts us to speculate that these TC-rich sequences might play a role like TATA-box in the initiation of transcription when those TSSs that lack a TATA-box at their 5′ upstream regions are used during transcription. This agrees with the findings reported by several previous studies (Bernard et al. 2010;Francki et al. 2009;Yamamoto et al. 2007;Zuo and Li 2011;Tokizawa et al. 2017). ...
Cinnamyl alcohol dehydrogenase (CAD) is the key enzyme for lignin biosynthesis in plants. In this study, genome-wide analysis was performed to identify CAD genes in oil palm (Elaeis guineensis). Phylogenetic analysis was then conducted to select the bona fide EgCADs. The bona fide EgCAD genes and their respective 5' flanking regions were cloned and analysed. Their expression profiles were evaluated in various organs using RT-PCR. Seven EgCAD genes (EgCAD1-7) were identified and divided into four phylogenetic groups. EgCAD1 and EgCAD2 display high sequence similarities with other bona fide CADs and possess all the signature motifs of the bona fide CAD. They also display similar 3D protein structures. Gene expression analysis showed that EgCAD1 was expressed most abundantly in the root tissues, while EgCAD2 was expressed constitutively in all the tissues studied. EgCAD1 possesses only one transcription start site, while EgCAD2 has five. Interestingly, a TC microsatellite was found in the 5' flanking region of EgCAD2. The 5' flanking regions of EgCAD1 and EgCAD2 contain lignin-associated regulatory elements i.e. AC-elements, and other defence-related motifs, including W-box, GT-1 motif and CGTCA-motif. Altogether, these results imply that EgCAD1 and EgCAD2 are bona fide CAD involved in lignin biosynthesis during the normal development of oil palm and in response to stresses. Our findings shed some light on the roles of the bona fide CAD genes in oil palm and pave the way for manipulating lignin content in oil palm through a genetic approach.
Supplementary information:
The online version contains supplementary material available at 10.1007/s13205-022-03208-0.
... Generally, the TATA-box is the core promoter element that initiates gene transcription and participates in the formation of the transcription initiation complex. It provides the basis for the transcription of the three newly formed transcription initiation sites in the promoter region of TaHDZ-A34 (Bernard et al. 2010;Xu et al. 2019). The CAAT-box is a common cis-acting element with enhancer activity in promoters, which might enhance the Hap-A expression level (Gao et al. 2019;Xu et al. 2019). ...
Unlabelled:
A predominant objective in wheat breeding is improving yield-related traits. The homeodomain-leucine zipper (HD-Zip) transcription factor plays a significant role in plant growth and development. In this study, we cloned all homeologs of TaHDZ34, which is a member of the HD-Zip class IV transcription factor family in wheat (Triticum aestivum L.). Sequence polymorphism analysis showed that TaHDZ-A34, TaHDZ-B34, and TaHDZ-D34 formed five, six, and six haplotypes, respectively, and the genes were divided into two main haplotype groups. We also developed functional molecular markers. The TaHDZ34 genes were divided into eight main haplotype combinations. Association analysis and distinct population validation preliminarily indicated that TaHDZ34 genes modulate grain number per spike, effective spikelet number per spike, thousand kernel weight, and flag leaf area per plant in wheat. Hap-ABD was the most effective haplotype combination of TaHDZ34. Subcellular localization showed that TaHDZ-A34 was localized to the nucleus. The interacting proteins of TaHDZ-A34 were involved in protein synthesis/degradation, energy production and transportation, and photosynthesis. Geographic distribution and frequencies of TaHDZ34 haplotype combinations suggested that Hap-Abd and Hap-AbD were preferentially selected in Chinese wheat breeding programs. The high-yield-related haplotype combination Hap-ABD provided beneficial genetic resources for the marker-assisted selection of new wheat cultivars.
Supplementary information:
The online version contains supplementary material available at 10.1007/s11032-022-01298-5.
... These DNA-centered methods have several advantages: they are capable to rapidly analyze a large number of potential TFBSs, identify de novo potential cis-regulatory elements without a priori, produce the highest-resolution footprints of DNA binding sites, and last but not least, are not dependent on experimental conditions. In this regard, PLMdetect (Preferentially Located Motif detection) (20) currently detects known cis-regulatory elements that are over-represented at a specific location relative to the transcription start site (TSS) in A. thaliana and are therefore referred to as preferentially located motifs (PLMs) (21)(22)(23)(24). However, to date, no large-scale functional PLMdetect-based studies have been performed on plant proximal regions, including the 3'untranslated region that also contribute to transcriptional regulation (1,2,25). ...
... By taking into account the preferential position of PLMs, the three-group structure revealed in the two species with distantly related genomes echoes and enriches established knowledge of the 5'-gene-proximal region. Thus, the densities of 5'-uPLMs in both species were higher in the core promoter region corresponding to group 2 and known to be the locus of many regulatory events (21,(43)(44)(45). This result suggests that many 5'-uPLMs might represent potential core promoter players in both species (Figure 8). ...
... Thus, we showed that part of the genes encoding alpha-expansin are characterized by 5'-uPLMs signals localized after the TSS, while part of the genes encoding acyl omega-hydroxylases are characterized by 3'-uPLMs signals localized in group 1 and 2. Functional enrichments also allowed the characterization of group 2 5'-uPLM signals in some genes involved in reactive oxygen metabolic processes. These signals were composed of more than 72% of uPLMs similar to RNA polymerase II binding sites, in agreement with previous observations showing a link between TATA-box and stress response, including the response to H 2 O 2 (21,46,58). Additionally, specific enrichments of the 3'-uPLMscontaining gene sets in group 1 compared to other groups revealed an involvement of these genes in ethylene response in both species. ...
The identification of cis-regulatory elements controlling gene expression is an arduous challenge that is being actively explored to discover the key genetic factors responsible for traits of agronomic interest. In this regard, in silico predictive methods have the advantage of being of high-resolution and independent of experimental conditions. Here, we expanded the preferentially located motif (PLM) detection method to comprehensively analyze the gene-proximal regions of Arabidopsis thaliana and Zea mays. We identified three groups of PLMs in each region for each species and highlighted conserved PLMs in both species, particularly in the 3′-proximal region. Moreover, we showed that PLMs occurred at both transcription factor and microRNA binding sites in each group with specific positional distributions for each region. Although the majority of PLMs were unassigned PLMs, it is noteworthy that some were supported by MNase-defined cistrome occupancy analysis. Enrichment analysis also revealed that unassigned PLMs provide functional predictions distinct from those inferred by the other PLMs. Using PLMs that occured at transcription factor binding sites, we inferred the regulatory network of a poorly characterized Z. mays-specific gene family, paving the way for further characterization of its individual members.
