scholarly journals Comparative transcription analysis of hard and tender fruit spines of cucumber to identify genes involved in morphological development of fruit spines

2020 ◽  
Author(s):  
Duo Lv ◽  
Yao Yu ◽  
Liang-Rong Xiong ◽  
Gang Wang ◽  
Jin-An Pang ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Transcription Factors ◽  
Molecular Mechanism ◽  
Developmental Process ◽  
Expression Patterns ◽  
Gene Families ◽  
Morphological Development ◽  
Wild Type ◽  
Transcription Analysis ◽  
Cucumber Fruit

Abstract Background The trichomes of cucumber on the fruit are also called spines, it not only has important commercial value but also is a classical tissue to study cell division and differentiation mode of multicellular trichomes. Although there have been many researches about the development of unicellular trichomes in model plants, the molecular mechanism of multicellular trichomes formation remains elusive. In this study, we took a pair of cucumber materials defined as hard (Ts, wild-type) and tender spines (ts, mutant) in previous study, the whole developmental process of fruit spines was continuously observed by microscope and SEM, in an attempt to define the development stage of fruit spines, transcriptome profiles at different stages was made to explore the molecular mechanism in the process of spines development. Results With significant phenotypic differences, the developmental process of fruit spines was clearly defined as four stages. Comparion of transcriptome profilings showed a total of 2,788 differential expression genes (DEGs) between the wild-type and mutant at different developmental stages of fruit spines, these genes exhibited different expression patterns at different spines developmental stage. Some DEGs related to cell cycle and meristem had also been identified in transcriptome data. By correlating the expression patterns of several transcription factors that have been reported to be involved in the development of spines, we identified some genes that may be involved in the formation of cucumber fruit spines. The cluster analysis of transcription factors revealed that there were 26 transcription factor families that may be involved in the development of fruit spines, among them, the ERF-ERF, bHLH and WAKY family transcription factor gene families were the top three gene families. Conclusions We defined the four stages of fruit spines development and identified a number of genes that may be involved in the development of multicellular trichomes based on comparative transcription. The results provided a step stone for further analysis of the molecular mechanism in the developmental process of multicellular trichomes.

scholarly journals Comparative transcriptome analysis of hard and tender fruit spines of cucumber to identify genes involved in morphological development of fruit spines

2020 ◽  
Author(s):  
Duo Lv ◽  
Yao Yu ◽  
Liang-Rong Xiong ◽  
Gang Wang ◽  
Jin-An Pang ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Molecular Mechanisms ◽  
Developmental Stages ◽  
Developmental Process ◽  
Stage Iii ◽  
Morphological Development ◽  
Wild Type ◽  
Polar Transport ◽  
Cucumber Fruit ◽  
Auxin Polar Transport

Abstract Background: The trichomes of cucumber fruits are also called spines. Cucumber has important commercial value, and its fruit spines represent a classical tissue with which to study the cell division and differentiation mode of multicellular trichomes. Although there have been many studies on the development of unicellular trichomes in model plants, the molecular mechanism of multicellular trichome formation remains elusive. In this study, we used a pair of cucumber materials defined as having hard (Ts, wild type) or tender (ts, mutant) spines in a previous study. The whole developmental process of fruit spines was continuously observed by microscopy and SEM. In an attempt to define the developmental stages of fruit spines, transcriptome profiles at different stages were determined to explore the molecular mechanisms underlying the process of spine development. Results: According to significant phenotypic differences, the developmental process of fruit spines was clearly defined as involving four stages. Comparison of transcriptome profiles showed that 803 and 722 genes were upregulated in the stalk (stage II and stage III) and base (stage IV) developmental stages of fruit spines, respectively. Functional analysis of differentially expressed genes (DEGs) showed that for all developmental stages of fruit spines, lipid metabolism, amino acid metabolism, and signal transduction were the most noticeable pathways. However, during the development of the stalk, genes related to auxin polar transport and HD-ZIP transcription factors were significantly upregulated. bHLH transcription factors and cytoskeleton-related genes were significantly upregulated during the development of the base. In addition, stage III was the key point for differentiating between the wild type and mutant. We detected 628 DEGs between the wild type and mutant at this stage. These DEGs are mainly involved in calcium signaling of the cytoskeleton and auxin polar transport, indicating that the main reason for the disorder of the fruit spine developmental pattern in the mutant was a change in cell polarity caused by blocked intercellular signal transmission.Conclusions: Our study defines in great detail the developmental stages of cucumber fruit spines. At the same time, transcriptome profiles are used to present the gene regulatory networks at different developmental stages of cucumber fruit spines. In addition, we analyzed transcriptomic data of a wild type and mutant to elucidate the biological pathways involving C-type lectin receptor-like kinase that regulate the development of fruit spines.

scholarly journals The AML-associated K313 mutation enhances C/EBPα activity by leading to C/EBPα overexpression

2021 ◽  
Vol 12 (7) ◽  
Author(s):  
Ian Edward Gentle ◽  
Isabel Moelter ◽  
Mohamed Tarek Badr ◽  
Konstanze Döhner ◽  
Michael Lübbert ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Culture ◽  
Transcription Factor ◽  
Transcription Factors ◽  
Transcriptional Activity ◽  
Target Gene ◽  
Wild Type ◽  
Elevated Expression ◽  
Factor C ◽  
Acute Myeloid

AbstractMutations in the transcription factor C/EBPα are found in ~10% of all acute myeloid leukaemia (AML) cases but the contribution of these mutations to leukemogenesis is incompletely understood. We here use a mouse model of granulocyte progenitors expressing conditionally active HoxB8 to assess the cell biological and molecular activity of C/EBPα-mutations associated with human AML. Both N-terminal truncation and C-terminal AML-associated mutations of C/EBPα substantially altered differentiation of progenitors into mature neutrophils in cell culture. Closer analysis of the C/EBPα-K313-duplication showed expansion and prolonged survival of mutant C/EBPα-expressing granulocytes following adoptive transfer into mice. C/EBPα-protein containing the K313-mutation further showed strongly enhanced transcriptional activity compared with the wild-type protein at certain promoters. Analysis of differentially regulated genes in cells overexpressing C/EBPα-K313 indicates a strong correlation with genes regulated by C/EBPα. Analysis of transcription factor enrichment in the differentially regulated genes indicated a strong reliance of SPI1/PU.1, suggesting that despite reduced DNA binding, C/EBPα-K313 is active in regulating target gene expression and acts largely through a network of other transcription factors. Strikingly, the K313 mutation caused strongly elevated expression of C/EBPα-protein, which could also be seen in primary K313 mutated AML blasts, explaining the enhanced C/EBPα activity in K313-expressing cells.

scholarly journals Morphological Characterization of Flower Buds Development and Related Gene Expression Profiling at Bud Break Stage in Heterodichogamous Cyclocarya paliurus (Batal.) lljinskaja

Genes ◽  
2019 ◽  
Vol 10 (10) ◽  
pp. 818 ◽  
Author(s):  
Chen ◽  
Mao ◽  
Huang ◽  
Fang
Keyword(s):  
Transcription Factors ◽  
Molecular Mechanism ◽  
Mating Type ◽  
Southern China ◽  
Expression Patterns ◽  
Transcriptional Level ◽  
Bud Break ◽  
Illumina Hiseq ◽  
Cyclocarya Paliurus ◽  
Qrt Pcr

Cyclocarya paliurus (Batal.) Iljinskaja, a unique species growing in southern China, is a multi-function tree species with medicinal, healthcare, material, and ornamental values. So far, sexual reproduction is the main method for extensive cultivation of C. paliurus plantations, but this is limited by low seed plumpness resulted from the character of heterodichogamy. Phenological observations have revealed the asynchronism of flower development in this species. However, its molecular mechanism remains largely unknown. To reveal molecular mechanism of heterodichogamy in C. paliurus, transcriptome of female (F) and male (M) buds from two mating types (protandry, PA; protogyny, PG) at bud break stage were sequenced using Illumina Hiseq 4000 platform. The expression patterns of both 32 genes related to flowering and 58 differentially expressed transcription factors (DETFs) selected from 6 families were divided four groups (PG-F, PG-M, PA-F, and PA-M) into two categories: first flowers (PG-F and PA-M) and later flowers (PA-F and PG-M). The results indicated that genes related to plant hormones (IAA, ABA, and GA) synthesis and response, glucose metabolism, and transcription factors (especially in MIKC family) played significant roles in regulating asynchronism of male and female flowers in the same mating type. The expression of DETFs showed two patterns. One contained DETFs up-regulated in first flowers in comparison to later flowers, and the other was the reverse. Nine genes related to flowering were selected for qRT-PCR to confirm the accuracy of RNA-seq, and generally, the RPKM values of these genes were consistent with the result of qRT-PCR. The results of this work could improve our understanding in asynchronism of floral development within one mating type in C. paliurus at transcriptional level, as well as lay a foundation for further study in heterodichogamous plants.

scholarly journals The transcription factor TAL1 and miR-17-92 create a regulatory loop in hematopoiesis

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Annekarin Meyer ◽  
Stefanie Herkt ◽  
Heike Kunze-Schumacher ◽  
Nicole Kohrs ◽  
Julia Ringleb ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Transcription Factors ◽  
Malignant Disease ◽  
Expression Patterns ◽  
Gene Activation ◽  
Erythroid Differentiation ◽  
Mature Micrornas ◽  
Gene Regulatory ◽  
Regulatory Loop ◽  
Transcriptional Complex

AbstractA network of gene regulatory factors such as transcription factors and microRNAs establish and maintain gene expression patterns during hematopoiesis. In this network, transcription factors regulate each other and are involved in regulatory loops with microRNAs. The microRNA cluster miR-17-92 is located within the MIR17HG gene and encodes six mature microRNAs. It is important for hematopoietic differentiation and plays a central role in malignant disease. However, the transcription factors downstream of miR-17-92 are largely elusive and the transcriptional regulation of miR-17-92 is not fully understood. Here we show that miR-17-92 forms a regulatory loop with the transcription factor TAL1. The miR-17-92 cluster inhibits expression of TAL1 and indirectly leads to decreased stability of the TAL1 transcriptional complex. We found that TAL1 and its heterodimerization partner E47 regulate miR-17-92 transcriptionally. Furthermore, miR-17-92 negatively influences erythroid differentiation, a process that depends on gene activation by the TAL1 complex. Our data give example of how transcription factor activity is fine-tuned during normal hematopoiesis. We postulate that disturbance of the regulatory loop between TAL1 and the miR-17-92 cluster could be an important step in cancer development and progression.

scholarly journals MreA Functions in the Global Regulation of Methanogenic Pathways in Methanosarcina acetivorans

mBio ◽  
2012 ◽  
Vol 3 (4) ◽  
Author(s):  
Matthew J. Reichlen ◽  
Venkata R. Vepachedu ◽  
Katsuhiko S. Murakami ◽  
James G. Ferry
Keyword(s):  
Transcription Factors ◽  
Specific Binding ◽  
Expression Patterns ◽  
Regulation Of Gene Expression ◽  
Methanosarcina Acetivorans ◽  
Wild Type ◽  
Global Regulation ◽  
Altered Expression ◽  
Content Type ◽  
Expression Of Genes

ABSTRACT Results are presented supporting a regulatory role for the product of the MA3302 gene locus (designated MreA) previously annotated as a hypothetical protein in the methanogenic species Methanosarcina acetivorans of the domain Archaea. Sequence analysis of MreA revealed identity to the TrmB family of transcription factors, albeit the sequence is lacking the sensor domain analogous to TrmBL2, abundant in nonmethanogenic species of the domain Archaea. Transcription of mreA was highly upregulated during growth on acetate versus methylotrophic substrates, and an mreA deletion (ΔmreA) strain was impaired for growth with acetate in contrast to normal growth with methylotrophic substrates. Transcriptional profiling of acetate-grown cells identified 280 genes with altered expression in the ΔmreA strain versus the wild-type strain. Expression of genes unique to the acetate pathway decreased whereas expression of genes unique to methylotrophic metabolism increased in the ΔmreA strain relative to the wild type, results indicative of a dual role for MreA in either the direct or indirect activation of acetate-specific genes and repression of methylotrophic-specific genes. Gel shift experiments revealed specific binding of MreA to promoter regions of regulated genes. Homologs of MreA were identified in M. acetivorans and other Methanosarcina species for which expression patterns indicate roles in regulating methylotrophic pathways. IMPORTANCE Species in the domain Archaea utilize basal transcription machinery resembling that of the domain Eukarya, raising questions addressing the role of numerous putative transcription factors identified in sequenced archaeal genomes. Species in the genus Methanosarcina are ideally suited for investigating principles of archaeal transcription through analysis of the capacity to utilize a diversity of substrates for growth and methanogenesis. Methanosarcina species switch pathways in response to the most energetically favorable substrate, metabolizing methylotrophic substrates in preference to acetate marked by substantial regulation of gene expression. Although conversion of the methyl group of acetate accounts for most of the methane produced in Earth’s biosphere, no proteins involved in the regulation of genes in the acetate pathway have been reported. The results presented here establish that MreA participates in the global regulation of diverse methanogenic pathways in the genus Methanosarcina. Finally, the results contribute to a broader understanding of transcriptional regulation in the domain Archaea.

scholarly journals Cytokine-mediated increases in fetal hemoglobin are associated with globin gene histone modification and transcription factor reprogramming

Blood ◽  
2009 ◽  
Vol 114 (11) ◽  
pp. 2299-2306 ◽  
Author(s):  
Orapan Sripichai ◽  
Christine M. Kiefer ◽  
Natarajan V. Bhanu ◽  
Toshihiko Tanno ◽  
Seung-Jae Noh ◽  
...  
Keyword(s):  
Signal Transduction ◽  
Transcription Factor ◽  
Transcription Factors ◽  
Protein Expression ◽  
Histone Modification ◽  
Globin Gene ◽  
Expression Patterns ◽  
Fetal Hemoglobin ◽  
Transcriptome Profiling ◽  
Globin Genes

Abstract Therapeutic regulation of globin genes is a primary goal of translational research aimed toward hemoglobinopathies. Signal transduction was used to identify chromatin modifications and transcription factor expression patterns that are associated with globin gene regulation. Histone modification and transcriptome profiling were performed using adult primary CD34+ cells cultured with cytokine combinations that produced low versus high levels of gamma-globin mRNA and fetal hemoglobin (HbF). Embryonic, fetal, and adult globin transcript and protein expression patterns were determined for comparison. Chromatin immunoprecipitation assays revealed RNA polymerase II occupancy and histone tail modifications consistent with transcriptional activation only in the high-HbF culture condition. Transcriptome profiling studies demonstrated reproducible changes in expression of nuclear transcription factors associated with high HbF. Among the 13 genes that demonstrated differential transcript levels, 8 demonstrated nuclear protein expression levels that were significantly changed by cytokine signal transduction. Five of the 8 genes are recognized regulators of erythropoiesis or globin genes (MAFF, ID2, HHEX, SOX6, and EGR1). Thus, cytokine-mediated signal transduction in adult erythroid cells causes significant changes in the pattern of globin gene and protein expression that are associated with distinct histone modifications as well as nuclear reprogramming of erythroid transcription factors.

scholarly journals Basic Helix-Loop-Helix (bHLH) Transcription Factors Regulate a Wide Range of Functions in Arabidopsis

2021 ◽  
Vol 22 (13) ◽  
pp. 7152
Author(s):  
Yaqi Hao ◽  
Xiumei Zong ◽  
Pan Ren ◽  
Yuqi Qian ◽  
Aigen Fu
Keyword(s):  
Transcription Factor ◽  
Transcription Factors ◽  
Target Genes ◽  
Gene Families ◽  
Bhlh Transcription Factor ◽  
Basic Helix Loop Helix ◽  
Helix Loop Helix ◽  
Wide Range ◽  
Range Of Functions ◽  
Eukaryotic Organisms

The basic helix-loop-helix (bHLH) transcription factor family is one of the largest transcription factor gene families in Arabidopsis thaliana, and contains a bHLH motif that is highly conserved throughout eukaryotic organisms. Members of this family have two conserved motifs, a basic DNA binding region and a helix-loop-helix (HLH) region. These proteins containing bHLH domain usually act as homo- or heterodimers to regulate the expression of their target genes, which are involved in many physiological processes and have a broad range of functions in biosynthesis, metabolism and transduction of plant hormones. Although there are a number of articles on different aspects to provide detailed information on this family in plants, an overall summary is not available. In this review, we summarize various aspects of related studies that provide an overview of insights into the pleiotropic regulatory roles of these transcription factors in plant growth and development, stress response, biochemical functions and the web of signaling networks. We then provide an overview of the functional profile of the bHLH family and the regulatory mechanisms of other proteins.

scholarly journals Transcriptome profilings reveal the candidate genes, pathways and transcription factors related to nitrogen utilization and excessive nitrogen stress in perennial ryegrass.

2020 ◽  
Author(s):  
Yinruizhi Li ◽  
Mengdi Wang ◽  
Ke Teng ◽  
Di Dong ◽  
Zhuocheng Liu ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Transcription Factors ◽  
Perennial Ryegrass ◽  
Expression Patterns ◽  
Enrichment Analysis ◽  
Nitrogen Utilization ◽  
Utilization Rate ◽  
Nitrogen Stress ◽  
Molecular Response ◽  
Stress Effect

Abstract Background：Lolium perenne L. is a kind of high quality forage grass, which can provide a good nutritional basis for herbivorous livestock. However, how to improve the nitrogen utilization rate of ryegrass and avoid the nitrate toxicity caused by excessive nitrogen has been troubling people for a long time. Up to now, the molecular response mechanism of ryegrass to nitrogen is not clear, especially under the condition of excessive nitrogen. Based on this, we tried to obtain a new insight into molecular response of ryegrass in nitrogen utilization and excessive nitrogen stress, providing the molecular theoretical basis for solving this problem.Results: In this study, the transcription of perennial ryegrass at different nitrogen levels was identified by high-throughput next-generation DNA sequencing. Phenotypic characterizations investigated that ryegrass in treatment N0.5 has a better growth state than the other three groups. The treatment N1 and N10 contained excessive nitrogen, which had a stress effect on plant growth. Analysis of differentially expressed genes indicated that 345, 105 genes are considered to involve in the regulation of nitrogen utilization and excessive nitrogen stress, respectively. GO enrichment analysis revealed that plant response to nitrogen mainly enrich in two categories, including “biological process” and “molecular function”. KEGG enrichment analysis suggested that “Photosynthesis-antenna proteins” may respond positively to nitrogen under appropriate nitrogen conditions, whereas “steroid biosynthesis”, “carotenoid biosynthesis” and “C5-branched dibasic acid metabolism” had been identified as top significant enrichment pathways response to excessive nitrogen. Transcription factors analysis showed that 21 TFs related to nitrogen utilization were classified into 10 transcription factor families, especially AP2-EREBP and MYB TF families. 4 TFs related to excessive nitrogen stress were identified, which belonged to 4 transcription factor families including LOB, NAC, AP2-EREBP and HB. The expression patterns of these selected genes above were also analyzed. Conclusions: These results made a contribution to comprehend the molecular mechanism of perennial ryegrass response to nitrogen. It provides new ideas for guiding the production practice and variety improvement of forage and even food crops from the perspective of molecular biology.

scholarly journals CmMYB#7, an R3 MYB transcription factor, acts as a negative regulator of anthocyanin biosynthesis in chrysanthemum

2019 ◽  
Vol 70 (12) ◽  
pp. 3111-3123 ◽  
Author(s):  
Lili Xiang ◽  
Xiaofen Liu ◽  
Heng Li ◽  
Xueren Yin ◽  
Donald Grierson ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Transcription Factors ◽  
Binding Site ◽  
Transient Expression ◽  
Regulatory Mechanism ◽  
Anthocyanin Biosynthesis ◽  
Expression Patterns ◽  
Negative Regulator ◽  
Myb Transcription Factor ◽  
Anthocyanin Content

Abstract ‘Jimba’, a well-known white flowered chrysanthemum cultivar, occasionally and spontaneously produces red colored petals under natural cultivation, but there is little information about the molecular regulatory mechanism underlying this process. We analysed the expression patterns of 91 MYB transcription factors in ‘Jimba’ and ‘Turning red Jimba’ and identified an R3 MYB, CmMYB#7, whose expression was significantly decreased in ‘Turning red Jimba’ compared with ‘Jimba’, and confirmed it is a passive repressor of anthocyanin biosynthesis. CmMYB#7 competed with CmMYB6, which together with CmbHLH2 is an essential component of the anthocyanin activation complex, for interaction with CmbHLH2 through the bHLH binding site in the R3 MYB domain. This reduced binding of the CmMYB6–CmbHLH2 complex and inhibited its ability to activate CmDFR and CmUFGT promoters. Moreover, using transient expression assays we demonstrated that changes in the expression of CmMYB#7 accounted for alterations in anthocyanin content. Taken together, our findings illustrate that CmMYB#7 is a negative regulator of anthocyanin biosynthesis in chrysanthemum.

scholarly journals The APETALA2 transcription factor LsAP2 regulates seed shape in lettuce

2020 ◽  
Author(s):  
Chen Luo ◽  
Shenglin Wang ◽  
Kang Ning ◽  
Zijing Chen ◽  
Yixin Wang ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Transcription Factors ◽  
Seed Development ◽  
Regulatory Networks ◽  
Development Process ◽  
Biological Function ◽  
Structural Characteristics ◽  
Wild Type ◽  
Seed Shape ◽  
Significant Function

Abstract Seeds are major vehicles of propagation and dispersal in plants. A number of transcription factors, including APETALA2 (AP2), play crucial roles during the seed development process in various plant species. However, genes essential for seed development and the regulatory networks during seed development remain unclear in lettuce. Here, we identified a lettuce AP2 (LsAP2) gene that was highly expressed at the early stages of seed development. LsAP2 knockout plants obtained by the CRISPR/Cas9 system were used to explore the biological function of LsAP2. Compared with wild-type, the seeds of the Lsap2 mutant plants had increased length and decreased width, and developed an extended tip at the seed top. After further investigating the seed structural characteristics of Lsap2 mutant plants, we proposed a new function of LsAP2 in seed dispersal. Moreover, we identified several interactors of LsAP2. Our results showed that LsAP2 directly interacted with the lettuce homolog of BREVIPEDICELLUS (LsBP) and promoted the expression of LsBP. Transcriptome analysis revealed that LsAP2 might also be involved in brassinosteroid biosynthesis and signaling pathways. Taken together, our data indicate that LsAP2 has a significant function in regulating seed shape in lettuce.

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