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To come to a better understanding of the evolution and function of the SBP-box transcription factor family in plants, we identified, isolated and characterized 13 of its members from the moss Physcomitrella patens. For the majority of the moss SBP-box genes, clear orthologous relationships with family members of flowering plants could be established by phylogenetic analysis based on the conserved...
SBP-box proteins are plant-specific putative transcription factors, which contain highly conserved SBP domain and could bind specifically to promoters of the floral meristem identity gene SQUAMOSA and its orthologous genes to regulate their expressions. In this study, 17 non-redundant SBP-box genes in Arabidopsis genome and 19 in rice genome were identified by using the known SBP domain sequences...
In recent times, the focus of research in polycystic ovary syndrome (PCOS) has shifted from candidate gene(s) approach to whole genome analysis for deciphering its molecular pathophysiology. In this regard, several microarray studies have been published, showing differential expression of genes between normal and PCOS states. Co-expression of genes as obtained in microarray experiments can also imply...
Insulin-like growth factors (IGFs) belong to a family of growth factors with structural homology to proinsulin. Up till now, no specific details regarding the transcriptional regulation by autocrine, paracrine or endocrine effector molecules in vivo have been described for the IGF-II gene. This is in big contrast to IGF-I gene transcription which has been studied more extensively. To better understand...
Cux (Cut homeobox) genes are present in all metazoans. Early reports described many phenotypes caused by cut mutations in Drosophila melanogaster. In vertebrates, CUX1 was originally characterized as the CCAAT-displacement protein (CDP). Another line of investigation revealed the presence of CUX1 within a multi-protein complex called the histone nuclear factor D (HiNF-D). Recent studies led to the...
The EGF-TM7 receptor CD97 shows different features of expression and function in muscle cells compared to hematopoetic and tumor cells. Since the molecular function and regulation of CD97 are poorly understood, this study aimed at defining its basal transcriptional regulation in smooth muscle cells (SMCs).The computational analysis of the CD97 5′-flanking region revealed that the TATA box-lacking...
The hypoxia-inducible factor-1 alpha (HIF-1α) protein is the major regulator of oxygen-dependent gene expression and a member of the bHLH–PAS family of transcription factors. In this study we compared and contrasted the rate and mode of HIF-1α molecular evolution between teleost fishes and mammals, as well as within teleost fishes and mammals. Various likelihood methods for estimating codon substitutions...
We present herein a new model for the structure of the Drosophila kayak gene as well as preliminary data on the functional differences of its various isoforms. kayak is a homolog of the human proto-oncogene, c-fos. kayak has three different starts of transcription, and therefore promoters (P)kay-α, (P)kay-β and (P)kay-γ. These three promoters lead to four different transcripts: kay-α, kay sro...
Soil salinity severely affects plant growth and agricultural productivity. AtbZIP24 encodes a bZIP transcription factor that is induced by salt stress in Arabidopsis thaliana but suppressed in the salt-tolerant relative Lobularia maritima. Transcriptional repression of AtbZIP24 using RNA interference improved salt tolerance in A. thaliana. Under non-stress growth conditions, transgenic A. thaliana...
Eph/ephrin signaling is pivotal in prenatal angiogenesis. Although their role in these processes has been extensively studied the mechanisms controlling eph/ephrin expression is not fully understood. To better understand the transcriptional regulation of arteriogenesis we have cloned and characterized the promoter of ephrin-B2 and its regulatory elements. The transcription start site was identified...
By microarray analysis and real-time RT-PCR, we identified 28 soybean flower-enriched transcription factors such as MADS-box proteins, zinc finger proteins, and MYB proteins. Among them, one MADS-box protein GmSEP1 was chosen for further analysis. GmSEP1 contains 8 exons and 7 introns, showing similar exon–intron structure with Arabidopsis SEP genes. Phylogenetic analysis also suggested that GmSEP1...
Matrix Gla protein (MGP) is an extracellular mineral-binding protein expressed in several tissues but it only accumulates in bone and calcified cartilage under physiological conditions. Available evidence indicates that it acts as a physiological inhibitor of mineralization. Runx2 is a transcription factor essential for bone formation in mammals, affecting osteoblast and chondrocyte differentiation...
The MYB DNA-binding domain is conserved in vertebrates, plants, and fungi. This domain mediates the DNA-binding activity of proteins (that have transcription factor activity) in a sequence-specific manner and is also used for the protection of telomeric regions. The MYB DNA-binding domain contains three imperfect conserved repeats of 52 amino acids (R1, R2, and R3). Within each repeat, there are three...
Human alcohol dehydrogenase 4 (ADH4) is one of the key enzymes involved in the metabolism of alcohol. ADH4 is highly expressed in the liver, and previous studies have revealed several cis-acting elements in the proximal promoter region. In this study we have identified a distal upstream enhancer, 4E, of ADH4. In HepG2 human hepatoma cells, 4E increased the activity of an ADH4 basal promoter by 50-fold...
Among modern western pigs, Duroc (high meat fat ratio) and Pietrain (low meat fat ratio) breeds extensively utilized in commercial pork production differ extremely for their muscle phenotypes. The molecular mechanism, especially the epigenetic mechanism, underlying these breed-specific differences is poorly known. Myogenic factor 6 (MYF6) is the most abundantly expressed myogenic factor in adult muscle...
Amyloid-β peptide (Aβ) plaque in the brain is the primary (post mortem) diagnostic criterion of Alzheimer's disease (AD). The physiological role(s) of Aβ are poorly understood. We have previously determined an Aβ interacting domain (AβID) in the promoters of AD-associated genes (Maloney and Lahiri, 2011. Gene. 15,doi:10.1016/j.gene.2011.06.004. epub ahead of print.). This AβID interacts in a DNA sequence-specific...
Deposition of extracellular plaques, primarily consisting of amyloid β peptide (Aβ), in the brain is the confirmatory diagnostic of Alzheimer's disease (AD); however, the physiological and pathological role of Aβ is not fully understood. Herein, we demonstrate novel Aβ activity as a putative transcription factor upon AD-associated genes. We used oligomers from 5′-flanking regions of the apolipoprotein...
The enzymes 3β-hydroxysteroid dehydrogenase (3βHSD) and 17β-hydroxysteroid dehydrogenase (17βHSD) regulate the steroid metabolism in mammals. In this study, we aimed to characterize the steroid related transcription factors at the 5′ flanking region of these two genes. A series of 5′ deletions of approximately 1kb of 5′-flanking region on both genes were fused to a pGL3 basic vector containing firefly...
Sp1 is a ubiquitously expressed transcription factor involved in the regulation of a large number of genes including housekeeping genes as well as actively regulated genes. Although Sp1 was discovered nearly three decades ago, its functional diversity is still not completely understood. One of the ways that make Sp1 versatile in transcriptional regulation is its post-transcriptional modification,...
Several cis-acting elements play critical roles in maintaining circadian expression of clock and clock-controlled genes. Using in silico analysis, we identified 10 sequence motifs that are correlated with the circadian phases of gene expression in the cartilage. One of these motifs, an E-box-like clock-related element (EL-box; GGCACGAGGC), can mediate BMAL1/CLOCK-induced transcription, which is typically...
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