The mouse tyrosinase gene. Promoter modulation by positive and negative regulatory elements.

Transcription factors are proteins that directly bind to regulatory sequences of genes to modulate and adjust plants’ responses to different stimuli including biotic and abiotic stresses. Sedentary plant parasitic nematodes, such as beet cyst nematode, Heterodera schachtii, have developed molecular tools to reprogram plant cell metabolism via the sophisticated manipulation of genes expression, to allow root invasion and the induction of a sequence of structural and physiological changes in plant tissues, leading to the formation of permanent feeding sites composed of modified plant cells (commonly called a syncytium). Here, we report on the AtMYB59 gene encoding putative MYB transcription factor that is downregulated in syncytia, as confirmed by RT-PCR and a promoter pMyb59::GUS activity assays. The constitutive overexpression of AtMYB59 led to the reduction in A. thaliana susceptibility, as indicated by decreased numbers of developed females, and to the disturbed development of nematode-induced syncytia. In contrast, mutant lines with a silenced expression of AtMYB59 were more susceptible to this parasite. The involvement of ABA in the modulation of AtMYB59 gene transcription appears feasible by several ABA-responsive cis regulatory elements, which were identified in silico in the gene promoter sequence, and experimental assays showed the induction of AtMYB59 transcription after ABA treatment. Based on these results, we suggest that AtMYB59 plays an important role in the successful parasitism of H. schachtii on A. thaliana roots.

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Brain and muscle creatine kinase genes contain common TA-rich recognition protein-binding regulatory elements.

Molecular and Cellular Biology ◽

10.1128/mcb.10.9.4826 ◽

1990 ◽

Vol 10 (9) ◽

pp. 4826-4836 ◽

Cited By ~ 29

Author(s):

R A Horlick ◽

G M Hobson ◽

J H Patterson ◽

M T Mitchell ◽

P A Benfield

Keyword(s):

Creatine Kinase ◽

Binding Site ◽

Regulatory Element ◽

Gene Promoter ◽

Regulatory Elements ◽

Muscle Creatine Kinase ◽

Enhancer Activity ◽

L6 Myotubes ◽

Recognition Protein ◽

Muscle Creatine

We have previously reported that the rat brain creatine kinase (ckb) gene promoter contains an AT-rich sequence that is a binding site for a protein called TARP (TA-rich recognition protein). This AT-rich segment is a positively acting regulatory element for the ckb promoter. A similar AT-rich DNA segment is found at the 3' end of the 5' muscle-specific enhancer of the rat muscle creatine kinase (ckm) gene and has been shown to be necessary for full muscle-specific enhancer activity. In this report, we show that TARP binds not only to the ckb promoter but also to the AT-rich segment at the 3' end of the muscle-specific ckm enhancer. A second, weaker TARP-binding site was identified in the ckm enhancer and lies at the 5' end of the minimal enhancer segment. TARP was found in both muscle cells (C2 and L6 myotubes) and nonmuscle (HeLa) cells and appeared to be indistinguishable from both sources, as judged by gel retardation and footprinting assays. The TARP-binding sites in the ckm enhancer and the ckb promoter were found to be functionally interchangeable. We propose that TARP is active in both muscle and nonmuscle cells and that it is one of many potential activators that may interact with muscle-specific regulators to determine the myogenic phenotype.

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Distinct regulation of the interleukin-1 and interleukin-6 response elements of the rat haptoglobin gene in rat and human hepatoma cells

Molecular and Cellular Biology ◽

10.1128/mcb.10.11.5967-5976.1990 ◽

1990 ◽

Vol 10 (11) ◽

pp. 5967-5976

Author(s):

H Baumann ◽

K K Morella ◽

G P Jahreis ◽

S Marinković

Keyword(s):

Interleukin 1 ◽

Gene Promoter ◽

Cell Types ◽

Regulatory Elements ◽

Hepatoma Cells ◽

Expression Vectors ◽

Human Hepatoma ◽

Human Hepatoma Cells ◽

Cis Acting ◽

Chloramphenicol Acetyltransferase Gene

The transcription rate of the haptoglobin (Hp) gene is stimulated by interleukin-1 (IL-1), IL-6, and dexamethasone in rat hepatoma (H-35) cells. To identify the cis-acting regulatory elements responsive to these hormones, various lengths of 5' Hp gene-flanking regions, including the promoter, were inserted into chloramphenicol acetyltransferase gene expression vectors and transiently introduced into H-35 cells. The first 4 kb of 5' region mediated a severalfold increase in expression after treatment with IL-6 and dexamethasone. No response to IL-1 was detectable. When, however, upstream sequences were deleted to position -165 relative to the transcription start site, a significant stimulation by IL-1 was gained without appreciably affecting the IL-6 response. With the apparent removal of an inhibitory sequence, the promoter-proximal 165-bp region also displayed a severalfold enhanced response to the combination of dexamethasone, IL-1, and IL-6. The sequence from -165 to -147, termed the A-element, was found to be crucial for all hormone regulatory functions. Two copies of the A-element linked to a heterologous promoter responded to the three hormones, but to a lesser degree than in the Hp gene promoter context. The regulatory elements of the rat Hp gene were similarly active in human hepatoma cells. Optimal regulation by IL-6 in HepG2 cells was, however, independent of the A-element. The A-element functioned in these cells exclusively as an IL-1 response sequence. The results suggest that genomic sequences upstream of the rat Hp gene suppress the regulation by specific cytokines more prominently in transient expression assays than in the normal chromosomal context. Moreover, the functional comparison indicated that specific regulatory regions of the rat Hp gene do not function identically in different hepatic cell types.

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In Silico Analysis of the CST6 Tumor Suppressor Gene

International Journal of Systems Biology and Biomedical Technologies ◽

10.4018/ijsbbt.2013070103 ◽

2013 ◽

Vol 2 (3) ◽

pp. 42-58

Author(s):

Athanasia Pavlopoulou ◽

Georgios Tsaramirsis

Keyword(s):

Tumor Suppressor ◽

Splice Variants ◽

Cpg Island ◽

Mammalian Species ◽

Gene Promoter ◽

In Silico Analysis ◽

Regulatory Elements ◽

Suppressor Gene ◽

Differentially Expressed ◽

Gene Encoding

The gene encoding cystatin E/M, CST6, is a Class II tumor suppressor. Using bioinformatics tools for database mining and virtual gene expression profiling, the authors showed that CST6 is differentially expressed in various types of cancer. Moreover, epigenetic silencing mediated by hypermethylation of the CpG island located at the CST6 promoter was found to be conserved in mammalian species. Comprehensive analyses of animal genomes led to the identification of novel CST6 transcript orthologs and splice variants that enabled us to trace the evolutionary origin of CST6. Moreover, eight novel and potentially regulatory SNPs were identified in CST6 gene. Conserved cancer-relevant regulatory elements were identified in the CST6 gene promoter. In addition, miRNAs that are differentially expressed in human cancers were identified as putative posttranscriptional regulators of CST6. Collectively, the authors suggest that expression of CST6 in normal and cancer cells is coordinately regulated by genomic, transcriptional and post-transcriptional mechanisms.

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The regulatory elements of PLZF gene are not conserved as reveled by molecular cloning and functional characterization of PLZF gene promoter of Clarias batrachus

Gene Reports ◽

10.1016/j.genrep.2019.100402 ◽

2019 ◽

Vol 16 ◽

pp. 100402

Author(s):

Swapnarani Nayak ◽

Lipika Patnaik ◽

Meenati Manjari Soren ◽

V. Chakrapani ◽

Shibani Dutta Mohapatra ◽

...

Keyword(s):

Molecular Cloning ◽

Functional Characterization ◽

Gene Promoter ◽

Regulatory Elements ◽

Clarias Batrachus

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The Role of Insulation in Patterning Gene Expression

Genes ◽

10.3390/genes10100767 ◽

2019 ◽

Vol 10 (10) ◽

pp. 767 ◽

Cited By ~ 3

Author(s):

Özdemir ◽

Gambetta

Keyword(s):

Regulatory Element ◽

Gene Promoter ◽

Regulatory Elements ◽

Spatial And Temporal Patterns ◽

Genetic Studies ◽

Animal Development ◽

Binding Factor ◽

Dna Elements ◽

Biochemical Analyses

Development is orchestrated by regulatory elements that turn genes ON or OFF in precise spatial and temporal patterns. Many safety mechanisms prevent inappropriate action of a regulatory element on the wrong gene promoter. In flies and mammals, dedicated DNA elements (insulators) recruit protein factors (insulator binding proteins, or IBPs) to shield promoters from regulatory elements. In mammals, a single IBP called CCCTC-binding factor (CTCF) is known, whereas genetic and biochemical analyses in Drosophila have identified a larger repertoire of IBPs. How insulators function at the molecular level is not fully understood, but it is currently thought that they fold chromosomes into conformations that affect regulatory element-promoter communication. Here, we review the discovery of insulators and describe their properties. We discuss recent genetic studies in flies and mice to address the question: Is gene insulation important for animal development? Comparing and contrasting observations in these two species reveal that they have different requirements for insulation, but that insulation is a conserved and critical gene regulation strategy.

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Looping of upstream cis-regulatory elements is required for CFTR expression in human airway epithelial cells

Nucleic Acids Research ◽

10.1093/nar/gkaa089 ◽

2020 ◽

Vol 48 (7) ◽

pp. 3513-3524 ◽

Cited By ~ 1

Author(s):

Monali NandyMazumdar ◽

Shiyi Yin ◽

Alekh Paranjapye ◽

Jenny L Kerschner ◽

Hannah Swahn ◽

...

Keyword(s):

Epithelial Cells ◽

Molecular Mechanisms ◽

Gene Promoter ◽

Regulatory Elements ◽

Airway Epithelial Cells ◽

Control Mechanisms ◽

Airway Epithelial ◽

Cell Type ◽

Long Range Interactions ◽

Cell Type Specific

Abstract The CFTR gene lies within an invariant topologically associated domain (TAD) demarcated by CTCF and cohesin, but shows cell-type specific control mechanisms utilizing different cis-regulatory elements (CRE) within the TAD. Within the respiratory epithelium, more than one cell type expresses CFTR and the molecular mechanisms controlling its transcription are likely divergent between them. Here, we determine how two extragenic CREs that are prominent in epithelial cells in the lung, regulate expression of the gene. We showed earlier that these CREs, located at −44 and −35 kb upstream of the promoter, have strong cell-type-selective enhancer function. They are also responsive to inflammatory mediators and to oxidative stress, consistent with a key role in CF lung disease. Here, we use CRISPR/Cas9 technology to remove these CREs from the endogenous locus in human bronchial epithelial cells. Loss of either site extinguished CFTR expression and abolished long-range interactions between these sites and the gene promoter, suggesting non-redundant enhancers. The deletions also greatly reduced promoter interactions with the 5′ TAD boundary. We show substantial recruitment of RNAPII to the −35 kb element and identify CEBPβ as a key activator of airway expression of CFTR, likely through occupancy at this CRE and the gene promoter.

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beta-Casein mRNA sequesters a single-stranded nucleic acid-binding protein which negatively regulates the beta-casein gene promoter.

Molecular and Cellular Biology ◽

10.1128/mcb.14.9.6004 ◽

1994 ◽

Vol 14 (9) ◽

pp. 6004-6012 ◽

Cited By ~ 33

Author(s):

S Altiok ◽

B Groner

Keyword(s):

Epithelial Cells ◽

Untranslated Region ◽

Mammary Epithelial Cells ◽

Gene Promoter ◽

Regulatory Elements ◽

Hormonal Control ◽

Mammary Epithelial ◽

Casein Gene ◽

Lactogenic Hormone ◽

Beta Casein

beta-Casein gene expression in mammary epithelial cells is under the control of the lactogenic hormones, glucocorticoids, insulin, and prolactin. The hormonal control affects gene transcription, and several regulatory elements in the beta-casein gene promoter between positions -80 and -221 have previously been identified. A region located in the promoter between positions -170 and -221 contains overlapping sequences for negative and positive regulatory elements. A sequence-specific single-stranded DNA-binding factor (STR), composed of two proteins with molecular masses of 35 and 54 kDa, recognizes the upper strand of this region and has a repressing role in transcription. High-level STR binding activity was observed in nuclear extracts from mammary glands of pregnant and postlactating mice and from noninduced HC11 mammary epithelial cells, cells with a low level of transcriptional activity of the beta-casein gene. STR activity is downregulated in mammary epithelial cells during lactation of the animals and after lactogenic hormone induction of HC11 cells in culture. These cells strongly transcribe the beta-casein gene. We investigated the mechanism of downregulation and found that a lactogenic-hormone-induced molecule (I-STR) inhibits STR from binding to its DNA target. I-STR is composed of RNA. STR is sequestered into the cytoplasm by I-STR after lactogenic hormone induction of mammary epithelial cells and remains present in an RNA-bound form. A high-affinity STR binding site was found in the 5' untranslated region of beta-casein mRNA. We propose that beta-casein mRNA can function as I-STR. beta-Casein mRNA may positively regulate its own transcription by translocating STR from the nucleus to the cytoplasm. The beta-casein STR binding sequence increases expression of a transfected beta-galactosidase gene when it is placed into the 5' untranslated region sequence of the mRNA. STR may have a positive role in posttranscriptional regulation.

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Interaction between two different regulatory elements activates the murine alpha A-crystallin gene promoter in explanted lens epithelia.

Molecular and Cellular Biology ◽

10.1128/mcb.7.5.1807 ◽

1987 ◽

Vol 7 (5) ◽

pp. 1807-1814 ◽

Cited By ~ 32

Author(s):

A B Chepelinsky ◽

B Sommer ◽

J Piatigorsky

Keyword(s):

Dna Sequences ◽

Gene Promoter ◽

Regulatory Elements ◽

Regulatory Sequences ◽

Base Pairs ◽

Hybrid Gene ◽

Promoter Sequences ◽

Hybrid Genes ◽

Cat Gene ◽

Cat Expression

Previous experiments have indicated that 5' flanking DNA sequences (nucleotides-366 to +46) are capable of regulating the lens-specific transcription of the murine alpha A-crystallin gene. Here we have analyzed these 5' regulatory sequences by transfecting explanted embryonic chicken lens epithelia with different alpha A-crystallin-CAT (chloramphenicol acetyltransferase) hybrid genes (alpha A-crystallin promoter sequences fused to the bacterial CAT gene in the pSVO-CAT expression vector). The results indicated the presence of a proximal (-88 to +46) and a distal (-111 to -88) domain which must interact for promoter function. Deletion experiments showed that the sequence between -88 and -60 was essential for function of the proximal domain in the explanted epithelia. A synthetic oligonucleotide containing the sequence between -111 and -84 activated the proximal domain when placed in either orientation 57 base pairs upstream from position -88 of the alpha A-crystallin-CAT hybrid gene.

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