MicroRNA miR396, GRF transcription factors and GIF co-regulators: a conserved plant growth regulatory module with potential for breeding and biotechnology

2020 ◽  
Vol 53 ◽  
pp. 31-42 ◽  
Author(s):  
Daniela Liebsch ◽  
Javier F Palatnik
Keyword(s):  
Transcription Factors ◽  
Plant Growth ◽  
Regulatory Module

scholarly journals Light modulates the gravitropic responses through organ-specific PIFs and HY5 regulation ofLAZY4expression inArabidopsis

2020 ◽  
Vol 117 (31) ◽  
pp. 18840-18848 ◽  
Author(s):  
Panyu Yang ◽  
Qiming Wen ◽  
Renbo Yu ◽  
Xue Han ◽  
Xing Wang Deng ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Environmental Factors ◽  
Plant Growth ◽  
Molecular Basis ◽  
Control Plant ◽  
Protein Levels ◽  
Positive Regulator ◽  
Regulatory Module ◽  
Organ Specific ◽  
Negative Gravitropism

Light and gravity are two key environmental factors that control plant growth and architecture. However, the molecular basis of the coordination of light and gravity signaling in plants remains obscure. Here, we report that two classes of transcription factors, PHYTOCHROME INTERACTING FACTORS (PIFs) and ELONGATED HYPOCOTYL5 (HY5), can directly bind and activate the expression ofLAZY4, a positive regulator of gravitropism in both shoots and roots inArabidopsis. In hypocotyls, light promotes degradation of PIFs to reduceLAZY4expression, which inhibits the negative gravitropism of hypocotyls.LAZY4overexpression can partially rescue the negative gravitropic phenotype ofpifqin the dark without affecting amyloplast development. Our identification of the PIFs-LAZY4regulatory module suggests the presence of another role for PIF proteins in gravitropism, in addition to a previous report demonstrating that PIFs positively regulate amyloplast development to promote negative gravitropism in hypocotyls. In roots, light promotes accumulation of HY5 proteins to activate expression ofLAZY4, which promotes positive gravitropism in roots. Together, our data indicate that light exerts opposite regulation ofLAZY4expression in shoots and roots by mediating the protein levels of PIFs and HY5, respectively, to inhibit the negative gravitropism of shoots and promote positive gravitropism of roots inArabidopsis.

The brassinosteroid-regulated transcription factors BZR1/BES1 function as a coordinator in multisignal-regulated plant growth

2018 ◽  
Vol 1861 (6) ◽  
pp. 561-571 ◽  
Author(s):  
Qian-Feng Li ◽  
Jun Lu ◽  
Jia-Wen Yu ◽  
Chang-Quan Zhang ◽  
Jun-Xian He ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Plant Growth

scholarly journals Genome-wide identification and expression profiles of ERF subfamily transcription factors in Zea mays

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9551
Author(s):  
Lidong Hao ◽  
Shubing Shi ◽  
Haibin Guo ◽  
Ming Li ◽  
Pan Hu ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Plant Growth ◽  
Growth And Development ◽  
Expression Profiles ◽  
Vital Role ◽  
Ethylene Response Factor ◽  
Plant Growth And Development ◽  
Element Analysis ◽  
Genome Wide ◽  
Genes Expression

The Ethylene-Response Factor (ERF) subfamily transcription factors (TFs) belong to the APETALA2/Ethylene-Responsive Factor (AP2/ERF) superfamily and play a vital role in plant growth and development. However, identification and analysis of the ERF subfamily genes in maize have not yet been performed at genome-wide level. In this study, a total of 76 ERF subfamily TFs were identified and were found to be unevenly distributed on the maize chromosomes. These maize ERF (ZmERF) TFs were classified into six groups, namely groups B1 to B6, based on phylogenetic analysis. Synteny analysis showed that 50, 54, and 58 of the ZmERF genes were orthologous to those in rice, Brachypodium, and Sorghum, respectively. Cis-element analysis showed that elements related to plant growth and development, hormones, and abiotic stress were identified in the promoter region of ZmERF genes. Expression profiles suggested that ZmERF genes might participate in plant development and in response to salinity and drought stresses. Our findings lay a foundation and provide clues for understanding the biological functions of ERF TFs in maize.

scholarly journals Arabidopsis WRKY46, WRKY54 and WRKY70 Transcription Factors Are Involved in Brassinosteroid-Regulated Plant Growth and Drought Response

2017 ◽  
pp. tpc.00364.2017 ◽  
Author(s):  
Jiani Chen ◽  
Trevor Nolan ◽  
Huaxun Ye ◽  
Mingcai Zhang ◽  
Hongning Tong ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Plant Growth ◽  
Drought Response

scholarly journals A proximal tissue-specific module and a distal negative regulatory module control apolipoprotein(a) gene transcription

2004 ◽  
Vol 379 (1) ◽  
pp. 151-159 ◽  
Author(s):  
Sarita NEGI ◽  
Saurabh K. SINGH ◽  
Nirupma PATI ◽  
Vikas HANDA ◽  
Ruchi CHAUHAN ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Gene Transcription ◽  
Hela Cells ◽  
Hepg2 Cells ◽  
Regulatory Element ◽  
Regulatory Elements ◽  
Tissue Specific ◽  
Apolipoprotein A ◽  
Regulatory Module ◽  
Specific Manner

The apo(a) [apolipoprotein(a)] gene is responsible for variations in plasma lipoprotein(a), high levels of which are a risk factor for atherosclerosis and myocardial infarction. The apo(a) promoter stimulates the expression of reporter genes in HepG2 cells, but not in HeLa cells. In the present study, we demonstrate that the 1.4 kb apo(a) promoter comprises two composite regulatory regions: a distal negative regulatory module (positions −1432 to −716) and a proximal tissue-specific module (−716 to −616). The distal negative regulatory module contains two strong negative regulatory regions [polymorphic PNR (pentanucleotide repeat region) and NREβ (negative regulatory element β)], which sandwich the postive regulatory region PREβ (positive regulatory element β). The PNR was shown to bind to transcription factors in a tissue-specific manner, whereas the ubiquitous transcription factors hepatocyte nuclear factor 3α and GATA binding protein 4 bound to NREβ to repress gene transcription. The proximal tissue-specific module contains two regulatory elements: an activating region (PREα) that activates transcription in HepG2 cells, and NREα, which is responsible for repressing the apo(a) gene in HeLa cells. NREα binds to a HeLa-specific repressor. These multiple regulatory elements might work co-operatively to finely regulate apo(a) gene expression. Although the tissue-specific module is required for apo(a) gene activation and repression in a tissue-specific manner, the combinatorial interplay of the distal and proximal regulators might define the complex pathway(s) of apo(a) gene regulation.

scholarly journals Analysis of Evolution, Expression and Genetic Transformation of TCP Transcription Factors in Blueberry Reveal That VcTCP18 Negatively Regulates the Release of Flower Bud Dormancy

2021 ◽  
Vol 12 ◽  
Author(s):  
Yongqiang Li ◽  
Shuang An ◽  
Qiangqiang Cheng ◽  
Yu Zong ◽  
Wenrong Chen ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Plant Growth ◽  
Gene Family ◽  
Fruit Development ◽  
Germination Rate ◽  
Expression Patterns ◽  
Bud Dormancy ◽  
Dormancy Release ◽  
Flower Bud ◽  
Bud Dormancy Release

Plant-specific TEOSINTE BRANCHED 1, CYCLOIDEA, PROLIFERATING CELL FACTORS (TCP) transcription factors have versatile functions in plant growth, development and response to environmental stress. Despite blueberry’s value as an important fruit crop, the TCP gene family has not been systematically studied in this plant. The current study identified blueberry TCP genes (VcTCPs) using genomic data from the tetraploid blueberry variety ‘Draper’; a total of 62 genes were obtained. Using multiple sequence alignment, conserved motif, and gene structure analyses, family members were divided into two subfamilies, of which class II was further divided into two subclasses, CIN and TB1. Synteny analysis showed that genome-wide or segment-based replication played an important role in the expansion of the blueberry TCP gene family. The expression patterns of VcTCP genes during fruit development, flower bud dormancy release, hormone treatment, and tissue-specific expression were analyzed using RNA-seq and qRT-PCR. The results showed that the TB1 subclass members exhibited a certain level of expression in the shoot, leaf, and bud; these genes were not expressed during fruit development, but transcript levels decreased uniformly during the release of flower bud dormancy by low-temperature accumulation. The further transgenic experiments showed the overexpression of VcTCP18 in Arabidopsis significantly decreased the seed germination rate in contrast to the wild type. The bud dormancy phenomena as late-flowering, fewer rosettes and main branches were also observed in transgenic plants. Overall, this study provides the first insight into the evolution, expression, and function of VcTCP genes, including the discovery that VcTCP18 negatively regulated bud dormancy release in blueberry. The results will deepen our understanding of the function of TCPs in plant growth and development.

scholarly journals A distinct core regulatory module enforces oncogene expression in KMT2A-rearranged leukemia

2021 ◽  
Author(s):  
Taku Harada ◽  
Yaser Heshmati ◽  
Jeremie Kalfon ◽  
Juliana Xavier Ferrucio ◽  
Monika Perez ◽  
...  
Keyword(s):  
Acute Myeloid Leukemia ◽  
Transcription Factors ◽  
Myeloid Leukemia ◽  
Control Cell ◽  
Therapeutic Targeting ◽  
Genome Wide ◽  
Regulatory Module ◽  
Small Set ◽  
Evolving Model ◽  
Acute Myeloid

A small set of lineage-restricted transcription factors (TFs), termed core regulatory circuitry (CRC), control cell identity and malignant transformation. Here, we integrated gene dependency, chromatin architecture and TF perturbation datasets to characterize 31 core TFs in acute myeloid leukemia (AML). Contrary to a widely accepted model, we detected a modular CRC structure with hierarchically organized, partially redundant and only sparsely interconnected modules of core TFs controlling distinct genetic programs. Rapid TF degradation followed by measurement of genome-wide transcription rates revealed that core TFs directly regulate dramatically fewer genes than previously assumed. Leukemias carrying KMT2A (MLL) rearrangements depend on the IRF8/MEF2 axis to directly enforce expression of the key oncogenes MYC, HOXA9 and BCL2. Our datasets provide an evolving model of CRC organization in human cells, and a resource for further inquiries into and therapeutic targeting of aberrant transcriptional circuits in cancer.

scholarly journals Genome-Wide Identification, Characterization and Expression Analysis of TCP Transcription Factors in Petunia

2020 ◽  
Vol 21 (18) ◽  
pp. 6594
Author(s):  
Shuting Zhang ◽  
Qin Zhou ◽  
Feng Chen ◽  
Lan Wu ◽  
Baojun Liu ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Plant Growth ◽  
Gene Family ◽  
Stress Responses ◽  
Expression Profiles ◽  
Expression Patterns ◽  
Leaf Morphogenesis ◽  
Systematic Analysis ◽  
Genome Wide ◽  
A Genome

The plant-specific TCP transcription factors are well-characterized in both monocots and dicots, which have been implicated in multiple aspects of plant biological processes such as leaf morphogenesis and senescence, lateral branching, flower development and hormone crosstalk. However, no systematic analysis of the petunia TCP gene family has been described. In this work, a total of 66 petunia TCP genes (32 PaTCP genes in P. axillaris and 34 PiTCP genes in P. inflata) were identified. Subsequently, a systematic analysis of 32 PaTCP genes was performed. The phylogenetic analysis combined with structural analysis clearly distinguished the 32 PaTCP proteins into two classes—class Ι and class Ⅱ. Class Ⅱ was further divided into two subclades, namely, the CIN-TCP subclade and the CYC/TB1 subclade. Plenty of cis-acting elements responsible for plant growth and development, phytohormone and/or stress responses were identified in the promoter of PaTCPs. Distinct spatial expression patterns were determined among PaTCP genes, suggesting that these genes may have diverse regulatory roles in plant growth development. Furthermore, differential temporal expression patterns were observed between the large- and small-flowered petunia lines for most PaTCP genes, suggesting that these genes are likely to be related to petal development and/or petal size in petunia. The spatiotemporal expression profiles and promoter analysis of PaTCPs indicated that these genes play important roles in petunia diverse developmental processes that may work via multiple hormone pathways. Moreover, three PaTCP-YFP fusion proteins were detected in nuclei through subcellular localization analysis. This is the first comprehensive analysis of the petunia TCP gene family on a genome-wide scale, which provides the basis for further functional characterization of this gene family in petunia.

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