A combinatorial cis-regulatory logic restricts color-sensing Rhodopsins to specific photoreceptor subsets in Drosophila

Color vision in Drosophila melanogaster is based on the expression of five different color-sensing Rhodopsin proteins in distinct subtypes of photoreceptor neurons. Promoter regions of less than 300 base pairs are sufficient to reproduce the unique, photoreceptor subtype-specific rhodopsin expression patterns. The underlying cis-regulatory logic remains poorly understood, but it has been proposed that the rhodopsin promoters have a bipartite structure: the distal promoter region directs the highly restricted expression in a specific photoreceptor subtype, while the proximal core promoter region provides general activation in all photoreceptors. Here, we investigate whether the rhodopsin promoters exhibit a strict specialization of their distal (subtype specificity) and proximal (general activation) promoter regions, or if both promoter regions contribute to generating the photoreceptor subtype-specific expression pattern. To distinguish between these two models, we analyze the expression patterns of a set of hybrid promoters that combine the distal promoter region of one rhodopsin with the proximal core promoter region of another rhodopsin. We find that the function of the proximal core promoter regions extends beyond providing general activation: these regions play a previously underappreciated role in generating the non-overlapping expression patterns of the different rhodopsins. Therefore, cis-regulatory motifs in both the distal and the proximal core promoter regions recruit transcription factors that generate the unique rhodopsin patterns in a combinatorial manner. We compare this combinatorial regulatory logic to the regulatory logic of olfactory receptor genes and discuss potential implications for the evolution of rhodopsins.

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Methylation in the Core-promoter Region of the Chondromodulin-I Gene Determines the Cell-specific Expression by Regulating the Binding of Transcriptional Activator Sp3

Journal of Biological Chemistry ◽

10.1074/jbc.m401273200 ◽

2004 ◽

Vol 279 (27) ◽

pp. 28789-28797 ◽

Cited By ~ 32

Author(s):

Tomoki Aoyama ◽

Takeshi Okamoto ◽

Satoshi Nagayama ◽

Koichi Nishijo ◽

Tatsuya Ishibe ◽

...

Keyword(s):

Promoter Region ◽

Core Promoter ◽

Transcriptional Activator ◽

Core Promoter Region ◽

Specific Expression ◽

The Core ◽

I Gene

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The Molecular Characteristics of the FAM13A Gene and the Role of Transcription Factors ACSL1 and ASCL2 in Its Core Promoter Region

Genes ◽

10.3390/genes10120981 ◽

2019 ◽

Vol 10 (12) ◽

pp. 981 ◽

Cited By ~ 3

Author(s):

Chengcheng Liang ◽

Anning Li ◽

Sayed Haidar Abbas Raza ◽

Rajwali Khan ◽

Xiaoyu Wang ◽

...

Keyword(s):

Transcription Factors ◽

Promoter Region ◽

Core Promoter ◽

Expression Patterns ◽

Marker Gene ◽

Molecular Characteristics ◽

Core Promoter Region ◽

Adult Cattle ◽

The Core

The gene family with sequence similarity 13 member A (FAM13A) has recently been identified as a marker gene in insulin sensitivity and lipolysis. In this study, we first analyzed the expression patterns of this gene in different tissues of adult cattle and then constructed a phylogenetic tree based on the FAM13A amino acid sequence. This showed that subcutaneous adipose tissue had the highest expression in all tissues except lung tissue. Then we summarized the gene structure. The promoter region sequence of the gene was successfully amplified, and the −241/+54 region has been identified as the core promoter region. The core promoter region was determined by the unidirectional deletion of the 5’ flanking promoter region of the FAM13A gene. Based on the bioinformatics analysis, we examined the dual luciferase activity of the vector constructed by the mutation site, and the transcription factors ACSL1 and ASCL2 were found as transcriptional regulators of FAM13A. Moreover, electrophoretic mobility shift assay (EMSA) further validated the regulatory role of ACSL1 and ASCL2 in the regulation of FAM13A. ACSL1 and ASCL2 were finally identified as activating transcription factors. Our results provide a basis for the function of the FAM13A gene in bovine adipocytes in order to improve the deposition of fat deposition in beef cattle muscle.

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The −5 A/G single-nucleotide polymorphism in the core promoter region of MT2A and its effect on allele-specific gene expression and Cd, Zn and Cu levels in laryngeal cancer

Toxicology and Applied Pharmacology ◽

10.1016/j.taap.2014.08.016 ◽

2014 ◽

Vol 280 (2) ◽

pp. 256-263 ◽

Cited By ~ 7

Author(s):

Katarzyna Starska ◽

Anna Krześlak ◽

Ewa Forma ◽

Jurek Olszewski ◽

Alina Morawiec-Sztandera ◽

...

Keyword(s):

Gene Expression ◽

Single Nucleotide Polymorphism ◽

Promoter Region ◽

Core Promoter ◽

Specific Gene ◽

Nucleotide Polymorphism ◽

Core Promoter Region ◽

Single Nucleotide ◽

The Core ◽

Allele Specific

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The core promoter region of the tumor necrosis factor alpha gene confers phorbol ester responsiveness to upstream transcriptional activators.

Molecular and Cellular Biology ◽

10.1128/mcb.12.3.1352 ◽

1992 ◽

Vol 12 (3) ◽

pp. 1352-1356 ◽

Cited By ~ 29

Author(s):

D C Leitman ◽

E R Mackow ◽

T Williams ◽

J D Baxter ◽

B L West

Keyword(s):

Transcription Factors ◽

Tumor Necrosis Factor ◽

Promoter Region ◽

Tumor Necrosis ◽

Core Promoter ◽

Core Promoter Region ◽

Necrosis Factor Alpha ◽

The Core ◽

Factor Alpha ◽

Necrosis Factor

Activators of protein kinase C, such as 12-O-tetradecanoylphorbol 13-acetate (TPA), are known to regulate the expression of many genes, including the tumor necrosis factor alpha (TNF) gene, by affecting the level or activity of upstream transcription factors. To investigate the mechanism whereby TPA activates the TNF promoter, a series of 5'-deletion mutants of the human TNF promoter linked to chloramphenicol acetyltransferase was transfected into U937 human promonocytic cells. TPA produced a 7- to 11-fold activation of all TNF promoters tested, even those promoters truncated to contain only the core promoter with no upstream enhancer elements. The proximal TNF promoter containing only 28 nucleotides upstream and 10 nucleotides downstream of the RNA start site confers TPA activation to a variety of unrelated upstream enhancer elements and transcription factors, including Sp1, CTF/NF1, cyclic AMP-response element, GAL-E1a, and GAL-VP16. The level of activation by TPA depends on the TATA box structure, since the TPA response is greater in promoters containing the sequence TATAAA than in those containing TATTAA or TATTTA. These findings suggest that the core promoter region is a target for gene regulation by second-messenger pathways.

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The decapentaplegic core promoter region plays an integral role in the spatial control of transcription.

Molecular and Cellular Biology ◽

10.1128/mcb.15.7.3960 ◽

1995 ◽

Vol 15 (7) ◽

pp. 3960-3968 ◽

Cited By ~ 21

Author(s):

D H Schwyter ◽

J D Huang ◽

T Dubnicoff ◽

A J Courey

Keyword(s):

Expression Pattern ◽

Phase Ii ◽

Promoter Region ◽

Core Promoter ◽

Critical Role ◽

Regulatory Elements ◽

Drosophila Embryo ◽

Phase Iii ◽

Core Promoter Region ◽

Flanking Region

The Drosophila melanogaster decapentaplegic (dpp) gene encodes a transforming growth factor beta-related cell signaling molecule that plays a critical role in dorsal/ventral pattern formation. The dpp expression pattern in the Drosophila embryo is dynamic, consisting of three phases. Phase I, in which dpp is expressed in a broad dorsal domain, depends on elements in the dpp second intron that interact with the Dorsal transcription factor to repress transcription ventrally. In contrast, phases II and III, in which dpp is expressed first in broad longitudinal stripes (phase II) and subsequently in narrow longitudinal stripes (phase III), depend on multiple independent elements in the dpp 5'-flanking region. Several aspects of the normal dpp expression pattern appear to depend on the unique properties of the dpp core promoter. For example, this core promoter (extending from -22 to +6) is able to direct a phase II expression pattern in the absence of additional upstream or downstream regulatory elements. In addition, a ventral-specific enhancer in the dpp 5'-flanking region that binds the Dorsal factor activates the heterologous hsp70 core promoter but not the dpp core promoter. Thus, the dpp core promoter region may contribute to spatially regulated transcription both by interacting directly with spatially restricted activators and by modifying the activity of proteins bound to enhancer elements.

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Identification and Characterization of the Potential Promoter Regions of 1031 Kinds of Human Genes

Genome Research ◽

10.1101/gr.164001 ◽

2001 ◽

Vol 11 (5) ◽

pp. 677-684

Author(s):

Yutaka Suzuki ◽

Tatsuhiko Tsunoda ◽

Jun Sese ◽

Hirotoshi Taira ◽

Junko Mizushima-Sugano ◽

...

Keyword(s):

Large Scale ◽

Expression Patterns ◽

Cpg Islands ◽

Genomic Sequences ◽

Cdna Libraries ◽

Promoter Regions ◽

Specific Expression ◽

Link Type ◽

Potential Promoter ◽

E Boxes

To understand the mechanism of transcriptional regulation, it is essential to identify and characterize the promoter, which is located proximal to the mRNA start site. To identify the promoters from the large volumes of genomic sequences, we used mRNA start sites determined by a large-scale sequencing of the cDNA libraries constructed by the “oligo-capping” method. We aligned the mRNA start sites with the genomic sequences and retrieved adjacent sequences as potential promoter regions (PPRs) for 1031 genes. The PPR sequences were searched to determine the frequencies of major promoter elements. Among 1031 PPRs, 329 (32%) contained TATA boxes, 872 (85%) contained initiators, 999 (97%) contained GC box, and 663 (64%) contained CAAT box. Furthermore, 493 (48%) PPRs were located in CpG islands. This frequency of CpG islands was reduced in TATA+/Inr+PPRs and in the PPRs of ubiquitously expressed genes. In the PPRs of the CGM2 gene, the DRA gene, and theTM30pl genes, which showed highly colon specific expression patterns, the consensus sequences of E boxes were commonly observed. The PPRs were also useful for exploring promoter SNPs.[The nucleotide sequences described in this paper have been deposited in the DDBJ, EMBL, and GenBank data libraries under accession nos.AU098358–AU100608.]

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High Frequency of Either Altered Pre-Core Start Codon or Weakened Kozak Sequence in the Core Promoter Region in Hepatitis B Virus A1 Strains from Rwanda

Genes ◽

10.3390/genes10030182 ◽

2019 ◽

Vol 10 (3) ◽

pp. 182 ◽

Cited By ~ 1

Author(s):

Heléne Norder ◽

Theogene Twagirumugabe ◽

Joanna Said ◽

Yarong Tian ◽

Ka-Wei Tang ◽

...

Keyword(s):

Hepatitis B Virus ◽

Hepatitis B ◽

Promoter Region ◽

Core Promoter ◽

Etiologic Agent ◽

Start Codon ◽

Core Promoter Region ◽

Kozak Sequence ◽

The Core ◽

B Virus

Hepatitis B virus (HBV) is endemic in Rwanda and is a major etiologic agent for chronic liver disease in the country. In a previous analysis of HBV strains from Rwanda, the S genes of most strains segregated into one single clade of subgenotype, A1. More than half (55%) of the anti-HBe positive individuals were viremic. In this study, 23 complete HBV genomes and the core promoter region (CP) from 18 additional strains were sequenced. Phylogenetic analysis of complete genomes confirmed that most Rwandan strain formed a single unique clade, within subgenotype A1. Strains from 17 of 22 (77%) anti-HBe positive HBV carriers had either mutated the precore start codon (9 strains with either CUG, ACG, UUG, or AAG) or mutations in the Kozak sequence preceding the pre-core start codon (8 strains). These mutually exclusive mutations were also identified in subgenotypes A1 (70/266; 26%), A2 (12/255; 5%), and A3 (26/49; 53%) sequences from the GenBank. The results showed that previous, rarely described HBV variants, expressing little or no HBeAg, are selected in anti-HBe positive subgenotype Al carriers from Rwanda and that mutations reducing HBeAg synthesis might be unique for a particular HBV clade, not just for a specific genotype or subgenotype.

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