The<i>Arabidopsis thaliana</i>TCP transcription factors: A broadening horizon beyond development

Li, Shutian

doi:10.1080/15592324.2015.1044192

Cited by 190 publications

(160 citation statements)

References 130 publications

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“…The most enriched TF motifs were the enhancer box (E-box) and TEOSINTE-BRANCHED CYCLOIDEA/PROLIFERATING CELL FACTOR (TCP/PCF) elements, with 10.5% and 13.2%, respectively. The E-box is targeted by the basic helix-loop-helix TFs (34), and both the E-box and TCP motif are conserved among plants (35) and critical for development, which is reflected in their prevalence in the promoters of genes regulated during seedling development. Additionally, two unidentified motifs were found that have not been reported previously in Arabidopsis (Fig.…”

Section: Significancementioning

confidence: 99%

Nascent RNA sequencing reveals distinct features in plant transcription

Hetzel

Duttke

Benner

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

139

175

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Transcriptional regulation of gene expression is a major mechanism used by plants to confer phenotypic plasticity, and yet compared with other eukaryotes or bacteria, little is known about the design principles. We generated an extensive catalog of nascent and steadystate transcripts in Arabidopsis thaliana seedlings using global nuclear run-on sequencing (GRO-seq), 5′GRO-seq, and RNA-seq and reanalyzed published maize data to capture characteristics of plant transcription. De novo annotation of nascent transcripts accurately mapped start sites and unstable transcripts. Examining the promoters of coding and noncoding transcripts identified comparable chromatin signatures, a conserved "TGT" core promoter motif and unreported transcription factor-binding sites. Mapping of engaged RNA polymerases showed a lack of enhancer RNAs, promoter-proximal pausing, and divergent transcription in Arabidopsis seedlings and maize, which are commonly present in yeast and humans. In contrast, Arabidopsis and maize genes accumulate RNA polymerases in proximity of the polyadenylation site, a trend that coincided with longer genes and CpG hypomethylation. Lack of promoter-proximal pausing and a higher correlation of nascent and steady-state transcripts indicate Arabidopsis may regulate transcription predominantly at the level of initiation. Our findings provide insight into plant transcription and eukaryotic gene expression as a whole.plant transcription | nascent transcripts | RNA polymerase pausing | 5′GRO-seq | GRO-seq G ene expression is a hallmark of life and subject to adaptation in changing environments. Steady-state transcript levels are a result of transcription initiation, elongation, and termination, followed by maturation and decay. Much has been learned about transcriptional mechanisms using yeast and animal models. In contrast, owing to technical difficulties created by plant cell extracts, there remains a large gap in knowledge in plant transcription. Plants and animals diverged more than 1.6 billion years ago. Studying plant transcription therefore not only contributes to a better understanding of the world's largest food source but also the evolution of eukaryotic gene expression.The signals initiating transcription are ultimately integrated at the promoter. Sequence-specific transcription factors (TFs) commonly bind the proximal promoter around −150 to −50 bp upstream of the transcriptional start site (TSS) (1, 2). At the core promoter, located approximately ±50 bp relative to the TSS, basal TFs cooperate with conserved DNA sequence motifs to orchestrate recruitment of the RNA polymerase (RNAP) (1, 3). Transcription has been studied extensively in a number of species (1-3) but not in plant model systems. Studies focusing on promoterenriched sequences were hindered by the lack of precise TSSs (4, 5) but have improved dramatically through techniques such as paired end analysis of transcription start sites (3PEAT) (6) and cap analysis gene expression (CAGE) (7), but both methods are affected by RNA processing and trans...

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Section: Significancementioning

confidence: 99%

Nascent RNA sequencing reveals distinct features in plant transcription

Hetzel

Duttke

Benner

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

139

175

View full text Add to dashboard Cite

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“…Class I members of the teosinte-branched cycloidea PCNA (TCP) protein family encode plant-specific transcription factors (Li et al 2005;Hervé et al 2009;Martín-Trillo and Cubas 2010;Li 2015). Class I TCPs are implicated in the coordination of cell proliferation and development, especially during leaf development, lateral branching, and shoot apical meristem formation in several plant species (Aguilar-Martínez and Sinha 2013; Davière et al 2014).…”

mentioning

confidence: 99%

“…Class I TCPs are implicated in the coordination of cell proliferation and development, especially during leaf development, lateral branching, and shoot apical meristem formation in several plant species (Aguilar-Martínez and Sinha 2013; Davière et al 2014). Loss-of-function mutants in class I TCP genes or EREB factor-associated amphiphilic repression (EAR) motif-fused class I TCP proteins show developmental alterations, suggesting that they are positive regulators of meristem formation (Hervé et al 2009;Kieffer et al 2011;Aguilar-Martínez and Sinha 2013;Li 2015).…”

mentioning

confidence: 99%

Root stem cell niche organizer specification by molecular convergence of PLETHORA and SCARECROW transcription factor modules

et al. 2018

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Continuous formation of somatic tissues in plants requires functional stem cell niches where undifferentiated cells are maintained. In Arabidopsis thaliana, PLETHORA (PLT) and SCARECROW (SCR) genes are outputs of apicalbasal and radial patterning systems, and both are required for root stem cell specification and maintenance. The WUSCHEL-RELATED HOMEOBOX 5 (WOX5) gene is specifically expressed in and required for functions of a small group of root stem cell organizer cells, also called the quiescent center (QC). PLT and SCR are required for QC function, and their expression overlaps in the QC; however, how they specify the organizer has remained unknown. We show that PLT and SCR genetically and physically interact with plant-specific teosinte-branched cycloidea PCNA (TCP) transcription factors to specify the stem cell niche during embryogenesis and maintain organizer cells post-embryonically. PLT-TCP-SCR complexes converge on PLT-binding sites in the WOX5 promoter to induce expression.

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“…9B), with Csa6G446400 (a putative TCP11) being specifically expressed in the flowering stage (63.2 TPM in the normal ovary and 210.4 TPM in the super ovary; Supplemental Table S7). In Arabidopsis, TCP 11 and TCP7 belong to class I subfamily, whereas TCP4 and TCP2 belong to class II subfamily, and all the four genes positively regulate organ growth through cell proliferation (Viola et al, 2011;Aguilar-Martínez and Sinha, 2013;Li, 2015). Similarly, genes encoding multiple NAC TFs such as NAC062, NAC052, NAC2, and NAC1 were upregulated in the super ovary (Fig.…”

Section: Transcriptomic Differentiation Of the Normal And Super Ovarimentioning

confidence: 93%

Integration of Hormonal and Nutritional Cues Orchestrates Progressive Corolla Opening

Sun

Zhao

et al. 2016

Plant Physiology

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Flower opening is essential for pollination and thus successful sexual reproduction; however, the underlying mechanisms of its timing control remain largely elusive. We identify a unique cucumber (Cucumis sativus) line '6457' that produces normal ovaries when nutrients are under-supplied, and super ovaries (87%) with delayed corolla opening when nutrients are oversupplied. Corolla opening in both normal and super ovaries is divided into four distinct phases, namely the green bud, green-yellow bud, yellow bud, and flowering stages, along with progressive color transition, cytological tuning, and differential expression of 14,282 genes. In the super ovary, cell division and cell expansion persisted for a significantly longer period of time; the expressions of genes related to photosynthesis, protein degradation, and signaling kinases were dramatically upregulated, whereas the activities of most transcription factors and stress-related genes were significantly down-regulated; concentrations of cytokinins (CKs) and gibberellins were higher in accordance with reduced cytokinin conjugation and degradation and increased expression of gibberellin biosynthesis genes. Exogenous CK application was sufficient for the genesis of super ovaries, suggesting a decisive role of CKs in controlling the timing of corolla opening. Furthermore, 194 out of 11,127 differentially expressed genes identified in pairwise comparisons, including critical developmental, signaling, and cytological regulators, contained all three types of cis-elements for CK, nitrate, and phosphorus responses in their promoter regions, indicating that the integration of hormone modulation and nutritional regulation orchestrated the precise control of corolla opening in cucumber. Our findings provide a valuable framework for dissecting the regulatory pathways for flower opening in plants.The flower is the most distinguishing organ in higher plants, and artists and scientists have been attracted to explore the mystery of flower structure and origin for decades. The evolution of flowering plants was greatly accelerated approximately 100 million years ago with the development of flowers, which were essential for recruiting animals to help distribute pollen and seeds (Danielson and Frommer, 2013). Flowers are produced from a specialized structure in the shoot tip called the shoot apical meristem, which consists of a pool of stem cells that continuously divide and replenish themselves (Fletcher et al., 1999). Morphologically, flowers are comprised of four basic structures arranged in concentric whorls: sepals in the outermost whorl 1, petals in whorl 2, stamens in whorl 3, and carpels in the innermost whorl 4. Bisexual flowers possess all four basic structures, while unisexual flowers lack one or more structures, usually the male organ stamen or the female organ carpel (Dellaporta and Calderon-Urrea, 1993). In flowering plants, approximately 90% species produce bisexual flowers, 6% species are dioecious with male and female flowers on separate plants, and 4% species a...

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TheArabidopsis thalianaTCP transcription factors: A broadening horizon beyond development

Cited by 190 publications

References 130 publications

Nascent RNA sequencing reveals distinct features in plant transcription

Nascent RNA sequencing reveals distinct features in plant transcription

Root stem cell niche organizer specification by molecular convergence of PLETHORA and SCARECROW transcription factor modules

Integration of Hormonal and Nutritional Cues Orchestrates Progressive Corolla Opening

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