scholarly journals FUNCTIONAL ANALYSIS OF THE PERSICARIA MINOR SESQUITERPENE SYNTHASE GENE PROMOTER IN TRANSGENIC ARABIDOPSIS THALIANA

2019 ◽  
Vol 81 (4) ◽  
Author(s):  
Aimi Farehah Omar ◽  
Ismanizan Ismail
Keyword(s):  
Arabidopsis Thaliana ◽  
Drought Stress ◽  
Promoter Activity ◽  
Regulatory Element ◽  
Regulatory Elements ◽  
Sesquiterpene Synthase ◽  
Functional Region ◽  
Cis Element ◽  
Specific Manner ◽  
Persicaria Minor

Sesquiterpene synthase is an enzyme involved in sesquiterpene biosynthesis which catalyzed sesquiterpene formation from farnesyl diphosphate (FDP). In this research, the sesquiterpene synthase promoter (PmSS) was isolated from Persicaria minor (P.minor) to identify the functional region of the promoter and possible cis - regulatory element involved in the regulation of sesquiterpene synthase gene. Various putative cis - regulatory element involved in environmental stress and hormones were identified on PmSS promoter. The PmSS promoter and three series of deletion promoter were fused to β-glucuronidase (gus) gene and transformed into Arabidopsis thaliana. This study showed PmSS promoter was regulated in a developmental -specific manner and response to wounding, drought, heat, abscisic acid (ABA) and methyl jasmonate (MeJa) treatment. The results revealed the existence of cis regulatory elements that control the regulation of promoter activity in a developmental specific manner at -1758 to -1078 promoter sequences. The presence of cis-element acting as a repressor is expected to be present at the promoter between -1540 to -1078 bp. The region from -1078 to -855 was critical for maximal PmSS promoter activity. Deletion of promoter region from -1758 to -855 induced regulation of promoter in an organ-specific manner. Drought stress treatment did not induced GUS activity in deleted ABRE motif construct, suggested that ABRE motif is essential cis element during drought stress.  

scholarly journals Transcriptional Activation of the Decidual/Trophoblast Prolactin-Related Protein Gene1

Endocrinology ◽  
1999 ◽  
Vol 140 (9) ◽  
pp. 4032-4039 ◽  
Author(s):  
Kyle E. Orwig ◽  
Michael J. Soares
Keyword(s):  
Transcriptional Activation ◽  
Promoter Activity ◽  
Mutational Analysis ◽  
Regulatory Element ◽  
Gene Activation ◽  
Cell Formation ◽  
Regulatory Elements ◽  
Related Protein ◽  
Trophoblast Cells ◽  
Decidual Cells

Abstract The decidual/trophoblast PRL-related protein (d/tPRP) is dually expressed by decidual and trophoblast cells during pregnancy. We have characterized the proximal d/tPRP promoter responsible for directing d/tPRP expression in decidual and trophoblast cells. We have demonstrated that the proximal 93 bp of d/tPRP 5′-flanking DNA are sufficient to direct luciferase gene expression in primary decidual and Rcho-1 trophoblast cells, but not in fibroblast, undifferentiated uterine stromal cells or trophoblast cells of a labyrinthine lineage. The 93-bp d/tPRP promoter was also sufficient to direct differentiation-dependent expression in trophoblast giant cells. Mutational analysis demonstrated the differential importance of activating protein-1 and Ets regulatory elements (located within the proximal 93 bp of d/tPRP 5′-flanking DNA) for activation of the d/tPRP promoter in decidual vs. trophoblast cells. Disruption of the activating protein-1 regulatory element inhibited d/tPRP promoter activity by more than 95% in decidual cells, and approximately 80% trophoblast cells. Disruption of the Ets regulatory element reduced d/tPRP promoter activity by approximately 50% in decidual cells, while inactivating the d/tPRP promoter in trophoblast cells. Protein interactions with the trophoblast Ets regulatory element were shown to be cell type specific and to change during trophoblast giant cell formation. In conclusion, a 93-bp region of the d/tPRP promoter is shown to contain regulatory elements sufficient for gene activation in decidual and trophoblast cells.

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 Age-dependent FOXO regulation of p27Kip1 expression via a conserved binding motif in rat muscle precursor cells

2008 ◽  
Vol 295 (5) ◽  
pp. C1238-C1246 ◽  
Author(s):  
Simon J. Lees ◽  
Tom E. Childs ◽  
Frank W. Booth
Keyword(s):  
Promoter Activity ◽  
Regulatory Element ◽  
Treatment Strategies ◽  
Regulatory Elements ◽  
Precursor Cells ◽  
Binding Motif ◽  
Muscle Precursor ◽  
Age Related ◽  
Age Dependent ◽  
Muscle Precursor Cells

Previously, we have demonstrated that forkhead box O3a (FOXO3a) overexpression increased p27Kip1 promoter activity and protein expression, whereas it decreased proliferation in muscle precursor cells (MPCs). The objectives of the present study were to 1) locate and identify FOXO regulatory elements in the rat p27Kip1 promoter using deletion analysis of a promoter/reporter construct and 2) determine if age-related differences exist in FOXO-induced p27Kip1 expression. The full-length (−4.0/+0.4 kb) rat p27Kip1 promoter construct revealed that both FOXO1 and FOXO3a induced an increase in transcriptional activity. Interestingly, MPCs isolated from old animals exhibited an increased FOXO3a-induced p27Kip1 promoter activity compared with MPCs isolated from young animals. Deletion of a 253-bp portion of the 5′-untranslated region (UTR) resulted in a significant decrease in FOXO-induced p27Kip1 promoter expression. Site-specific mutation of a daf-16 family protein-binding element (DBE) within this 253-bp portion of the 5′-UTR also demonstrated a decrease in FOXO-induced p27Kip1 promoter expression. These data suggest that a putative FOXO regulatory element located in the 5′-UTR of the rat p27 Kip1 gene plays a role in the age-dependent differences in FOXO3a-dependent p27Kip1 promoter expression. These findings have implications for developing treatment strategies aimed at increasing the proliferation of MPCs and regenerative capacity of aged skeletal muscle.

scholarly journals The cis-regulatory codes of response to combined heat and drought stress in Arabidopsis thaliana

2020 ◽  
Author(s):  
Christina B. Azodi ◽  
John P. Lloyd ◽  
Shin-Han Shiu
Keyword(s):  
Arabidopsis Thaliana ◽  
Transcription Factors ◽  
Drought Stress ◽  
Transcriptional Response ◽  
Regulatory Elements ◽  
Chromatin Accessibility ◽  
Combined Stress ◽  
Binding Motifs ◽  
Powerful Approach ◽  
The Individual

ABSTRACTPlants respond to their environment by dynamically modulating gene expression. A powerful approach for understanding how these responses are regulated is to integrate information about cis-regulatory elements (CREs) into models called cis-regulatory codes. Transcriptional response to combined stress is typically not the sum of the responses to the individual stresses. However, cis-regulatory codes underlying combined stress response have not been established. Here we modeled transcriptional response to single and combined heat and drought stress in Arabidopsis thaliana. We grouped genes by their pattern of response (independent, antagonistic, synergistic) and trained machine learning models to predict their response using putative CREs (pCREs) as features (median F-measure = 0.64). We then developed a deep learning approach to integrate additional omics information (sequence conservation, chromatin accessibility, histone modification) into our models, improving performance by 6.2%. While pCREs important for predicting independent and antagonistic responses tended to resemble binding motifs of transcription factors associated with heat and/or drought stress, important synergistic pCREs resembled binding motifs of transcription factors not known to be associated with stress. These findings demonstrate how in silico approaches can improve our understanding of the complex codes regulating response to combined stress and help us identify prime targets for future characterization.

Regulatory elements mediating transcription from the Drosophila melanogaster actin 5C proximal promoter

1990 ◽  
Vol 10 (1) ◽  
pp. 206-216
Author(s):  
Y T Chung ◽  
E B Keller
Keyword(s):  
Drosophila Melanogaster ◽  
Transient Expression ◽  
Promoter Activity ◽  
Regulatory Element ◽  
Regulatory Elements ◽  
Proximal Promoter ◽  
Base Pairs ◽  
Chloramphenicol Acetyltransferase Gene ◽  
Constitutive Synthesis

The major cytoskeletal actin gene of Drosophila melanogaster, the actin 5C gene, has two promoters, the proximal one of which controls constitutive synthesis of actin in all growing tissues. To locate regulatory elements required for constitutive activity of the proximal promoter, mutants of this promoter were fused to the bacterial chloramphenicol acetyltransferase gene and assayed for transient expression activity in cultured Drosophila embryonic Schneider line 2 cells. An essential regulatory element has been located 313 base pairs upstream from the cap site. Deletion of this element lowered expression to one-third of the wild-type level. The element has the sequence AAGTTGTAGTTG, as shown by protein-binding footprinting with the reagent methidiumpropyl-EDTA-Fe(II). This element is probably not a general one, since it was not detected in a search of the published 5'-flanking sequences of 27 Drosophila genes. In addition to this regulatory element, there are five GAGA elements in the actin 5C proximal promoter, some or all of which are essential for the promoter activity as shown by an in vivo competition assay. Although this promoter has no classical TATA element, there is an essential promoter region about 35 base pairs upstream from the cap site that could be a TATA surrogate. The promoter also shows sequences homologous to the alcohol dehydrogenase factor 1-binding site and to the core of the vertebrate serum response element, but mutations of these sites did not affect promoter activity in transient expression assays.

scholarly journals Characterization of cell-specific modulatory element in the murine ornithine decarboxylase promoter

1996 ◽  
Vol 316 (3) ◽  
pp. 993-998 ◽  
Author(s):  
Jorma J. PALVIMO ◽  
Maija PARTANEN ◽  
Olli A. JÄNNE
Keyword(s):  
Ornithine Decarboxylase ◽  
Transcriptional Activation ◽  
Binding Proteins ◽  
Protein Complexes ◽  
Regulatory Element ◽  
Regulatory Elements ◽  
Nuclear Proteins ◽  
Promoter Strength ◽  
Cell Type ◽  
Specific Manner

The promoter of the murine ornithine decarboxylase (ODC) gene contains, adjacent to the TATA box, a cAMP response element (CRE)-like motif that interacts with specific nuclear proteins. Here we examine the role of this CRE-like element (CREL) in ODC promoter activation in proliferating cells. Mutations that abolished binding of nuclear proteins to CREL influenced only marginally the cAMP induction of the reporter constructs driven by 1.6 kb of the ODC promoter. Instead, these mutations altered the basal promoter function in a cell-specific manner, in that they reduced the promoter activity in CV-1 cells, but increased it in NIH/3T3, CHO and HeLa cells. Thus, depending on the cell type, the CREL motif is able to confer either repression or activation on ODC gene transcription. In contrast with 1.6 kb promoter constructs, the same mutations in the context of a shorter sequence (proximal 133 nt) reduced the promoter strength in all cell types studied. The ability of the CREL element to attenuate transcription seems to be connected with the function of some upstream regulatory elements. Differences in nuclear proteins binding to CREL, as studied by electrophoretic mobility shift assays (EMSAs), did not explain the findings on cell-type specificity in transcriptional activation, as mutations in CREL abrogated formation of specific CREL–protein complexes in all cell lines examined. The protein complexes interacting with CREL were not recognized by antibodies specific for CRE-binding proteins CREB-1 and CREB-2, or activating transcription factors ATF-1, ATF-2 and ATF-3. EMSA experiments also demonstrated co-operative interactions between the CREL motif-binding proteins and other nuclear proteins, such as Sp1, interacting with CG-rich sequences of the promoter. In conclusion, the proximal ODC promoter contains a well-conserved regulatory element, which is clearly different from the CRE/ATF element. This motif acts in concert with other distal and proximal elements in a complex cell-specific manner.

scholarly journals Transcriptional regulation of MHC class I gene expression in rat oligodendrocytes

1998 ◽  
Vol 330 (1) ◽  
pp. 155-161 ◽  
Author(s):  
Georgia MAVRIA ◽  
T. Kersten HALL ◽  
A. Richard JONES ◽  
G. Eric BLAIR
Keyword(s):  
Mhc Class I ◽  
Promoter Activity ◽  
Regulatory Element ◽  
Regulatory Elements ◽  
Class I ◽  
Cell Leukaemia ◽  
Type I ◽  
Down Regulation ◽  
Leukaemia Virus ◽  
Negative Regulatory Element

MHC class I molecules are normally expressed at very low levels in the brain and their up-regulation in response to cytokines and viral infections has been associated with a number of neurological disorders. Here we demonstrate that the down-regulation of surface class I molecules in differentiated primary rat oligodendrocytes was accompanied by reduced steady-state levels of class I heavy-chain mRNA. Transient expression assays were performed in oligodendrocytes and fibroblasts, using a mouse H-2Kb class I promoter chloramphenicol acetyltransferase plasmid termed pH2KCAT (which contained 5ʹ-flanking sequences from -2033 to +5 bp of the H-2Kb gene relative to the transcriptional start site at +1 bp). These assays showed that H-2Kb promoter activity was reduced in oligodendrocytes but not in class I-expressing fibroblasts. H-2Kb promoter activity was up-regulated in oligodendrocytes co-transfected with a plasmid expression vector encoding the transcriptional activator tax of human T-cell leukaemia virus type I, showing that down-regulation of promoter activity was reversible. Deletion mutant analysis of the H-2Kb promoter revealed the presence of negative regulatory elements that were functional in oligodendrocytes at -1.61 to -1.07 kb and -242 to -190 bp. Deletion of sequences in pH2KCAT encompassing the downstream element totally abolished promoter activity in both oligodendrocytes and fibroblasts, whereas a deletion within the upstream negative regulatory element increased promoter activity specifically in oligodendrocytes. The upstream negative regulatory element also down-regulated a linked heterologous herpes simplex virus thymidine kinase promoter in oligodendrocytes, but not in fibroblasts. Gel retardation assays using overlapping DNA probes that spanned the entire -1.61 to -1.07 kb region revealed the presence of a number of DNA-binding activities that were present in oligodendrocyte, but not in fibroblast nuclear extracts.

scholarly journals The cis-regulatory codes of response to combined heat and drought stress in Arabidopsis thaliana

2020 ◽  
Vol 2 (3) ◽  
Author(s):  
Christina B Azodi ◽  
John P Lloyd ◽  
Shin-Han Shiu
Keyword(s):  
Arabidopsis Thaliana ◽  
Transcription Factors ◽  
Drought Stress ◽  
Transcriptional Response ◽  
Regulatory Elements ◽  
Chromatin Accessibility ◽  
Combined Stress ◽  
Binding Motifs ◽  
Powerful Approach ◽  
The Individual

Abstract Plants respond to their environment by dynamically modulating gene expression. A powerful approach for understanding how these responses are regulated is to integrate information about cis-regulatory elements (CREs) into models called cis-regulatory codes. Transcriptional response to combined stress is typically not the sum of the responses to the individual stresses. However, cis-regulatory codes underlying combined stress response have not been established. Here we modeled transcriptional response to single and combined heat and drought stress in Arabidopsis thaliana. We grouped genes by their pattern of response (independent, antagonistic and synergistic) and trained machine learning models to predict their response using putative CREs (pCREs) as features (median F-measure = 0.64). We then developed a deep learning approach to integrate additional omics information (sequence conservation, chromatin accessibility and histone modification) into our models, improving performance by 6.2%. While pCREs important for predicting independent and antagonistic responses tended to resemble binding motifs of transcription factors associated with heat and/or drought stress, important synergistic pCREs resembled binding motifs of transcription factors not known to be associated with stress. These findings demonstrate how in silico approaches can improve our understanding of the complex codes regulating response to combined stress and help us identify prime targets for future characterization.

scholarly journals Gateway cloning and in-planta transformation of drought stress responsive Ecmyb1 gene isolated from Eleusine coracana var.PRM 6107

2021 ◽  
Vol 22 (1) ◽  
pp. 205-211
Author(s):  
Megha Bhatt ◽  
Prafull Salvi ◽  
Pushpa Lohani
Keyword(s):  
Gene Expression ◽  
Arabidopsis Thaliana ◽  
Drought Stress ◽  
Stress Responses ◽  
Anthocyanin Biosynthesis ◽  
Regulatory Protein ◽  
Regulatory Elements ◽  
Growth And Yield ◽  
Yield Potential ◽  
Gateway Cloning

Drought is one of the key abiotic stress that critically influences the crops by restraining their growth and yield potential. Being sessile, plants tackle the detrimental effects of drought stress via modulating the cellular state by changing the gene expression. Such alteration of gene expression is essentially driven by the transcriptional syndicate. Transcription factors (TF) are the key regulatory protein that controls the expression of their target gene by binding to the cis-regulatory elements present in the promoter region. Myb-TFs ubiquitously present in all eukaryotes belong to one of the largest TF family, and play wide array of biological functions in plants including anthocyanin biosynthesis, vasculature system, cell signaling, seed maturation and abiotc stress responses. In the present study the full length Myb TF from Eleusine corocana was subcloned using Gateway cloning system and further transformed into Arabidopsis thaliana through floral dip method. Transgenic Arabidopsis thaliana plants harbouring Ecmyb1 gene were screened and grown in transgenic glasshouse under controlled conditions.

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