scholarly journals Regulation of rice root development by a retrotransposon acting as a microRNA sponge

eLife ◽  
2017 ◽  
Vol 6 ◽  
Author(s):  
Jungnam Cho ◽  
Jerzy Paszkowski
Keyword(s):  
Gene Regulation ◽  
Transcription Factors ◽  
Root Development ◽  
Binding Sites ◽  
Transcriptional Control ◽  
Specific Expression ◽  
Ability To Act ◽  
Specific Accumulation ◽  
In Trans ◽  
Microrna Sponge

It is well documented that transposable elements (TEs) can regulate the expression of neighbouring genes. However, their ability to act in trans and influence ectopic loci has been reported rarely. We searched in rice transcriptomes for tissue-specific expression of TEs and found them to be regulated developmentally. They often shared sequence homology with co-expressed genes and contained potential microRNA-binding sites, which suggested possible contributions to gene regulation. In fact, we have identified a retrotransposon that is highly transcribed in roots and whose spliced transcript constitutes a target mimic for miR171. miR171 destabilizes mRNAs encoding the root-specific family of SCARECROW-Like transcription factors. We demonstrate that retrotransposon-derived transcripts act as decoys for miR171, triggering its degradation and thus results in the root-specific accumulation of SCARECROW-Like mRNAs. Such transposon-mediated post-transcriptional control of miR171 levels is conserved in diverse rice species.

scholarly journals Tissue-Restricted Expression of the Cardiac α-Myosin Heavy Chain Gene Is Controlled by a Downstream Repressor Element Containing a Palindrome of Two Ets-Binding Sites

1998 ◽  
Vol 18 (12) ◽  
pp. 7243-7258 ◽  
Author(s):  
Madhu Gupta ◽  
Radovan Zak ◽  
Towia A. Libermann ◽  
Mahesh P. Gupta
Keyword(s):  
Gene Regulation ◽  
Myosin Heavy Chain ◽  
Cardiac Myocytes ◽  
Heavy Chain ◽  
Binding Sites ◽  
Cardiac Myocyte ◽  
Specific Expression ◽  
Tissue Specific Expression ◽  
Nonmuscle Cells ◽  
Muscle Gene

ABSTRACT The expression of the α-myosin heavy chain (MHC) gene is restricted primarily to cardiac myocytes. To date, several positive regulatory elements and their binding factors involved in α-MHC gene regulation have been identified; however, the mechanism restricting the expression of this gene to cardiac myocytes has yet to be elucidated. In this study, we have identified by using sequential deletion mutants of the rat cardiac α-MHC gene a 30-bp purine-rich negative regulatory (PNR) element located in the first intronic region that appeared to be essential for the tissue-specific expression of the α-MHC gene. Removal of this element alone elevated (20- to 30-fold) the expression of the α-MHC gene in cardiac myocyte cultures and in heart muscle directly injected with plasmid DNA. Surprisingly, this deletion also allowed a significant expression of the α-MHC gene in HeLa and other nonmuscle cells, where it is normally inactive. The PNR element required upstream sequences of the α-MHC gene for negative gene regulation. By DNase I footprint analysis of the PNR element, a palindrome of two high-affinity Ets-binding sites (CTTCCCTGGAAG) was identified. Furthermore, by analyses of site-specific base-pair mutation, mobility gel shift competition, and UV cross-linking, two different Ets-like proteins from cardiac and HeLa cell nuclear extracts were found to bind to the PNR motif. Moreover, the activity of the PNR-binding factor was found to be increased two- to threefold in adult rat hearts subjected to pressure overload hypertrophy, where the α-MHC gene is usually suppressed. These data demonstrate that the PNR element plays a dual role, both downregulating the expression of the α-MHC gene in cardiac myocytes and silencing the muscle gene activity in nonmuscle cells. Similar palindromic Ets-binding motifs are found conserved in the α-MHC genes from different species and in other cardiac myocyte-restricted genes. These results are the first to reveal a role of the Ets class of proteins in controlling the tissue-specific expression of a cardiac muscle gene.

Cement gland-specific activation of the Xag1 promoter is regulated by co-operation of putative Ets and ATF/CREB transcription factors

Development ◽  
2002 ◽  
Vol 129 (19) ◽  
pp. 4387-4397
Author(s):  
Fiona C. Wardle ◽  
Daniel H. Wainstock ◽  
Hazel L. Sive
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Transcription Factors ◽  
Binding Site ◽  
Reporter Gene ◽  
Binding Sites ◽  
Cement Gland ◽  
Specific Expression ◽  
Necessary And Sufficient ◽  
Do So

The cement gland marks the extreme anterior ectoderm of the Xenopus embryo, and is determined through the overlap of several positional domains. In order to understand how these positional cues activate cement gland differentiation, the promoter of Xag1, a marker of cement gland differentiation, was analyzed. Previous studies have shown that Xag1 expression can be activated by the anterior-specific transcription factor Otx2, but that this activation is indirect. 102 bp of upstream genomic Xag1 sequence restricts reporter gene expression specifically to the cement gland. Within this region, putative binding sites for Ets and ATF/CREB transcription factors are both necessary and sufficient to drive cement gland-specific expression, and cooperate to do so. Furthermore, while the putative ATF/CREB factor is activated by Otx2, a factor acting through the putative Ets-binding site is not. These results suggest that Ets-like and ATF/CREB-like family members play a role in regulating Xag1 expression in the cement gland, through integration of Otx2 dependent and independent pathways.

scholarly journals Different Functional Gene Clusters in Yeast have Different Spatial Distributions of the Transcription Factor Binding Sites

2011 ◽  
Vol 5 ◽  
pp. BBI.S6362 ◽  
Author(s):  
Wei-Sheng Wu
Keyword(s):  
Gene Regulation ◽  
Transcription Factor ◽  
Spatial Distribution ◽  
Transcription Factors ◽  
Binding Sites ◽  
Transcription Factor Binding Sites ◽  
Gene Clusters ◽  
Functional Gene ◽  
Spatial Distributions ◽  
Factor Binding

Transcription factors control gene expression by binding to short specific DNA sequences, called transcription factor binding sites (TFBSs), in the promoter of a gene. Thus, studying the spatial distribution of TFBSs in the promoters may provide insights into the molecular mechanisms of gene regulation. I developed a method to construct the spatial distribution of TFBSs for any set of genes of interest. I found that different functional gene clusters have different spatial distributions of TFBSs, indicating that gene regulation mechanisms may be very different among different functional gene clusters. I also found that the binding sites for different transcription factors (TFs) may have different spatial distributions: a sharp peak, a plateau or no dominant single peak. The spatial distributions of binding sites for many TFs derived from my analyses are valuable prior information for TFBS prediction algorithm because different regions of a promoter can assign different possibilities for TFBS occurrence.

C/EBPalpha Is a Key Transcriptional Regulator of the Triggering Receptor on Myeloid Cells-2 Gene

Blood ◽  
2008 ◽  
Vol 112 (11) ◽  
pp. 4762-4762
Author(s):  
Maria Michela Mancarelli ◽  
Lily Catherine Frusciante ◽  
Gabrielle Francoise Cauvi ◽  
Charles De Rossi ◽  
Bruce Edward Torbett
Keyword(s):  
Gene Regulation ◽  
Binding Site ◽  
Binding Sites ◽  
Transcriptional Control ◽  
Transcriptional Activity ◽  
Myeloid Cells ◽  
Myeloid Cell ◽  
Fold Increase ◽  
Full Length ◽  
And Function

Abstract Triggering receptor on myeloid cells-2 (TREM-2) is a member of the innate immune signaling receptor TREM family. After differentiation of monocytes, TREM-2 is expressed on the cell surface of macrophages, monocyte-derived dendritic cells, microglia, and osteoclasts. TREM-2 is necessary for modulation of cellular activation and function, and loss of TREM-2 results in the decrease of phagocytosis of apoptotic neurons and cells and an increase in inflammation response of macrophage-lineage cells. To better understand TREM-2 gene regulation during monocyte differentiation we isolated and then analyzed the putative human TREM-2 promoter to identify transcriptional control. The 1131 bp TREM- 2 promoter contains binding sites for C/EBPα and PU.1 transcription factors, known for regulation of myeloid cell differentiation and function. A series of 5 promoter reporter deletion mutants were generated to dissect transcription regulation. We progressively deleted the full-length promoter, −1002/+129, of HIF1, STAT5, GATA1, YY1F, C/EBPα binding sites generating −866/+129, −632/+129, −526/+129, −258/+129, +37/+129 promoter reporters, respectively. All TREM-2 promoter reporters showed minimal transcriptional activity when transfected in 293T-HEK cells. In contrast, C/EBPα was necessary and sufficient for TREM-2 promoter reporter activity in co-transfection studies, demonstrating a 5-fold induction of transcriptional activity as compared to controls. Consistent with the TREM-2 reporter findings showing C/EBPα mediated activity, EMSA assays demonstrated specific C/EBPα binding to sites within the TREM-2 promoter. To determine if both C/EBPα binding sites in TREM-2 were necessary for activity we generated loss of C/EBPα binding site reporters and observed that only the −43/−28 C/EBPα binding site was essential for activity. To clarify if +73/+93 PU.1 binding site had a role in TREM-2 regulation, we co-transfected the full-length promoter with PU.1 and C/EBPα and observed a 10-fold increase of induction of TREM-2 transcriptional activity. However, PU.1 alone did not activate the full-length TREM-2 promoter or bind to the PU.1 consensus site, and loss of the PU.1 binding site did not alter transcriptional activity. These results suggest a key role for direct C/EBPα and indirect PU.1 participation in regulation of TREM-2. Studies are underway to precisely understand TREM-2 gene regulation and how TREM-2 controls macrophage-mediated phagocytosis and inflammation.

Role of SCL/Tal-1, GATA, and Ets transcription factor binding sites for the regulation of Flk-1 expression during murine vascular development

Blood ◽  
2000 ◽  
Vol 96 (9) ◽  
pp. 3078-3085 ◽  
Author(s):  
Andreas Kappel ◽  
Thorsten M. Schlaeger ◽  
Ingo Flamme ◽  
Stuart H. Orkin ◽  
Werner Risau ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Transcription Factors ◽  
Blood Vessel ◽  
Tumor Angiogenesis ◽  
Binding Sites ◽  
Mutational Analysis ◽  
Vascular Development ◽  
Regulatory Elements ◽  
Specific Expression ◽  
Ets Transcription Factors

The receptor tyrosine kinase Flk-1 is essential for embryonic blood vessel development and for tumor angiogenesis. To identify upstream transcriptional regulators of Flk-1, the gene regulatory elements that mediate endothelium-specific expression in mouse embryos were characterized. By mutational analysis, binding sites for SCL/Tal-1, GATA, and Ets transcription factors located in theFlk-1 enhancer were identified as critical elements for the endothelium-specific Flk-1 gene expression in transgenic mice. c-Ets1, a transcription factor that is coexpressed withFlk-1 during embryonic development and tumor angiogenesis, activated the Flk-1 promoter via 2 binding sites. One of these sites was required for Flk-1 promoter function in the embryonic vasculature. These results provide the first evidence that SCL/Tal-1, GATA, and Ets transcription factors act upstream ofFlk-1 in a combinatorial fashion to determine embryonic blood vessel formation and are key regulators not only of the hematopoietic program, but also of vascular development.

scholarly journals Expression analysis of NAC genes during the growth and ripening of apples

2018 ◽  
Vol 45 (No. 1) ◽  
pp. 1-10 ◽  
Author(s):  
Gijing Zhang ◽  
Tong Li ◽  
Lijie zhang ◽  
Wenxuan dong ◽  
Aide Wang
Keyword(s):  
Gene Regulation ◽  
Transcription Factors ◽  
Stress Response ◽  
Sequence Analysis ◽  
Fruit Ripening ◽  
Ethylene Production ◽  
Expression Patterns ◽  
Specific Expression ◽  
Nac Transcription Factors ◽  
Differential Tissue

Plant-specific NAC transcription factors (TFs) play crucial roles in various pathways related to the stress response. However, to date, little information regarding NAC gene regulation during fruit ripening is available for the apple (Malus domestica). Here, we report that 13 out of 182 MdNAC genes were differentially expressed during the stages of fruit growth and ripening. Sequence analysis indicates that these 13 MdNAC genes harbour distinct structures and potentially diverse functions. The expression of both MdNAC1a and MdNAC78 was repressed by ethylene and induced by 1-MCP during storage. MdNAC2, MdNAC26, MdNAC41, MdNAC57, MdNAC80, MdNAC91, MdNAC119 and MdNAC141 were up-regulated by ethylene and their transcription mirrored ethylene production rates during storage. MdNAC1, MdNAC16 and MdNAC32 did not respond to 1-MCP exposure. Additionally, the 13 MdNAC genes identified displayed differential tissue-specific expression patterns. These results suggest that NAC TFs play an important role in the regulation of apple development via both ethylene-dependent and -independent mechanisms.

scholarly journals Tissue-specific transcriptome analyses reveal candidate genes for stilbene, flavonoid and anthraquinone biosynthesis in the medicinal plant Polygonum cuspidatum

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Xiaowei Wang ◽  
Hongyan Hu ◽  
Zhijun Wu ◽  
Haili Fan ◽  
Guowei Wang ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Medicinal Plant ◽  
Expression Patterns ◽  
Phenylpropanoid Pathway ◽  
Polygonum Cuspidatum ◽  
Specific Expression ◽  
Tissue Specific ◽  
Factors Associated ◽  
Specific Accumulation ◽  
Different Tissues

Abstract Background Polygonum cuspidatum Sieb. et Zucc. is a well-known medicinal plant whose pharmacological effects derive mainly from its stilbenes, anthraquinones, and flavonoids. These compounds accumulate differentially in the root, stem, and leaf; however, the molecular basis of such tissue-specific accumulation remains poorly understood. Because tissue-specific accumulation of compounds is usually associated with tissue-specific expression of the related biosynthetic enzyme genes and regulators, we aimed to clarify and compare the transcripts expressed in different tissues of P. cuspidatum in this study. Results High-throughput RNA sequencing was performed using three different tissues (the leaf, stem, and root) of P. cuspidatum. In total, 80,981 unigenes were obtained, of which 40,729 were annotated, and 21,235 differentially expressed genes were identified. Fifty-four candidate synthetase genes and 12 transcription factors associated with stilbene, flavonoid, and anthraquinone biosynthetic pathways were identified, and their expression levels in the three different tissues were analyzed. Phylogenetic analysis of polyketide synthase gene families revealed two novel CHS genes in P. cuspidatum. Most phenylpropanoid pathway genes were predominantly expressed in the root and stem, while methylerythritol 4-phosphate and isochorismate pathways for anthraquinone biosynthesis were dominant in the leaf. The expression patterns of synthase genes were almost in accordance with metabolite profiling in different tissues of P. cuspidatum as measured by high-performance liquid chromatography or ultraviolet spectrophotometry. All predicted transcription factors associated with regulation of the phenylpropanoid pathway were expressed at lower levels in the stem than in the leaf and root, but no consistent trend in their expression was observed between the leaf and the root. Conclusions The molecular knowledge of key genes involved in the biosynthesis of P. cuspidatum stilbenes, flavonoids, and anthraquinones is poor. This study offers some novel insights into the biosynthetic regulation of bioactive compounds in different P. cuspidatum tissues and provides valuable resources for the potential metabolic engineering of this important medicinal plant.

Role of SCL/Tal-1, GATA, and Ets transcription factor binding sites for the regulation of Flk-1 expression during murine vascular development

Blood ◽  
2000 ◽  
Vol 96 (9) ◽  
pp. 3078-3085 ◽  
Author(s):  
Andreas Kappel ◽  
Thorsten M. Schlaeger ◽  
Ingo Flamme ◽  
Stuart H. Orkin ◽  
Werner Risau ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Transcription Factors ◽  
Blood Vessel ◽  
Tumor Angiogenesis ◽  
Binding Sites ◽  
Mutational Analysis ◽  
Vascular Development ◽  
Regulatory Elements ◽  
Specific Expression ◽  
Ets Transcription Factors

Abstract The receptor tyrosine kinase Flk-1 is essential for embryonic blood vessel development and for tumor angiogenesis. To identify upstream transcriptional regulators of Flk-1, the gene regulatory elements that mediate endothelium-specific expression in mouse embryos were characterized. By mutational analysis, binding sites for SCL/Tal-1, GATA, and Ets transcription factors located in theFlk-1 enhancer were identified as critical elements for the endothelium-specific Flk-1 gene expression in transgenic mice. c-Ets1, a transcription factor that is coexpressed withFlk-1 during embryonic development and tumor angiogenesis, activated the Flk-1 promoter via 2 binding sites. One of these sites was required for Flk-1 promoter function in the embryonic vasculature. These results provide the first evidence that SCL/Tal-1, GATA, and Ets transcription factors act upstream ofFlk-1 in a combinatorial fashion to determine embryonic blood vessel formation and are key regulators not only of the hematopoietic program, but also of vascular development.

Methods for studying global patterns of DNA binding by bacterial transcription factors and RNA polymerase

2008 ◽  
Vol 36 (4) ◽  
pp. 754-757 ◽  
Author(s):  
David C. Grainger ◽  
Stephen J.W. Busby
Keyword(s):  
Escherichia Coli ◽  
Gene Regulation ◽  
Transcription Factors ◽  
Dna Binding ◽  
Chromatin Immunoprecipitation ◽  
Binding Sites ◽  
Regulatory Networks ◽  
Major Goal ◽  
Bacterial Transcription ◽  
Global Patterns

A major goal in the study of gene regulation is to untangle the transcription-regulatory networks of Escherichia coli and other ‘simple’ organisms. To do this we must catalogue the binding sites of all transcription factors. ChIP (chromatin immunoprecipitation), combined with DNA microarray analysis, is a powerful tool that permits global patterns of DNA binding to be measured. Here, we discuss the benefits of this approach and the application of this technique to bacterial systems.

scholarly journals Cis-regulatory divergence in gene expression between two thermally divergent yeast species

2016 ◽  
Author(s):  
Xueying C. Li ◽  
Justin C. Fay
Keyword(s):  
Gene Expression ◽  
Gene Regulation ◽  
Binding Sites ◽  
Small Subset ◽  
Regulatory Sequences ◽  
Promoter Regions ◽  
Specific Expression ◽  
Thermal Growth ◽  
Allele Specific ◽  
Regulatory Effects

AbstractGene regulation is a ubiquitous mechanism by which organisms respond to their environment. While organisms are often found to be adapted to the environments they experience, the role of gene regulation in environmental adaptation is not often known. In this study, we examine divergence in cis-regulatory effects between two Saccharomyces species, S. cerevisiae and S. uvarum, that have substantially diverged in their thermal growth profile. We measured allele specific expression (ASE) in the species’ hybrid at three temperatures, the highest of which is lethal to S. uvarum but not the hybrid or S. cerevisiae. We find that S. uvarum alleles can be expressed at the same level as S. cerevisiae alleles at high temperature and most cis-acting differences in gene expression are not dependent on temperature. While a small set of 136 genes show temperature-dependent ASE, we find no indication that signatures of directional cis-regulatory evolution are associated with temperature. Within promoter regions we find binding sites enriched upstream of temperature responsive genes, but only weak correlations between binding site and expression divergence. Our results indicate that temperature divergence between S. cerevisiae and S. uvarum has not caused widespread divergence in cis-regulatory activity, but point to a small subset of genes where the species’ alleles show differences in magnitude or opposite responses to temperature. The difficulty of explaining divergence in cis-regulatory sequences with models of transcription factor binding sites and nucleosome positioning highlights the importance of identifying mutations that underlie cis-regulatory divergence between species.

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