The availability of high-throughput genomic sequencing has allowed us to construct a more robust characterization of retinoic acid response elements than was possible in the past. We located human, mouse, and rat homologs for each of 51 well-documented, conserved retinoic acid response elements. Mathematical and statistical analyses of these 153 sites, 78 of which are new, shows that 92% of response elements have direct-repeat symmetry, but that only 76% exhibit canonical spacing attributes. While the familiar '(a/g)g(g/t)tca' hexamer motif is upheld, the more relaxed sequence, '(a/g)g(g/t)(g/t)(g/c)a', represents a 10% consensus. Sites are as likely to be on the coding strand as on the non-coding strand, and 86% of them are in upstream locations. From a statistical point of view, DR1 elements are fundamentally different from DR2 and DR5 elements, but this is only evident in the 5' hexamer. While there is considerable variation in core positions, and while no nucleotide can be considered forbidden at any position, variation among species at a fixed locus appears surprisingly constrained once a functional site has been attained.
Download full-text PDF |
Source |
|---|---|
| http://dx.doi.org/10.1016/j.jsbmb.2005.05.005 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Metabolic pathways of eicosanoids-derivatives of arachidonic acid and their significance in skin.
Cell Mol Biol Lett
January 2025
Department of Analytical Chemistry, Medical University of Bialystok, Kilinskiego 1, 15-069, Bialystok, Poland.
The skin is a barrier that protects the human body against environmental factors (physical, including solar radiation, chemicals, and pathogens). The integrity and, consequently, the effective metabolic activity of skin cells is ensured by the cell membrane, the important structural and metabolic elements of which are phospholipids. Phospholipids are subject to continuous transformation, including enzymatic hydrolysis (with the participation of phospholipases A, C, and D) to free polyunsaturated fatty acids (PUFAs), which under the influence of cyclooxygenases (COX1/2), lipoxygenases (LOXs), and cytochrome P450 (CYPs P450) are metabolized to various classes of oxylipins, depending on the type of PUFA being metabolized and the enzyme acting.
View Article and Find Full Text PDFNucleic acid recognition during prokaryotic immunity.
Mol Cell
January 2025
Laboratory of Bacteriology, The Rockefeller University, New York, NY 10065, USA; Howard Hughes Medical Institute, The Rockefeller University, New York, NY 10065, USA. Electronic address:
Parasitic elements often spread to hosts through the delivery of their nucleic acids to the recipient. This is particularly true for the primary parasites of bacteria, bacteriophages (phages) and plasmids. Although bacterial immune systems can sense a diverse set of infection signals, such as a protein unique to the invader or the disruption of natural host processes, phage and plasmid nucleic acids represent some of the most common molecules that are recognized as foreign to initiate defense.
View Article and Find Full Text PDFDecipher syntrophies and adaptive response towards enhancing conversion of propionate to methane under psychrophilic condition.
Water Res
January 2025
Laboratory of Biomass Bio-chemical Conversion, Guang Zhou Institute of Energy Conversion, Chinese Academy of Sciences, Guangzhou 510640, China. Electronic address:
Propionate is a key intermediate in anaerobic digestion (AD) under low operational temperatures, which can destabilize the process. In this study, the supplementation of syntrophic cold-tolerant consortia and trace elements significantly improved the performance of psychrophilic (20 °C) reactor, increasing methane production to 91 % of mesophilic reactor levels and reducing propionate concentrations to less than 2 % of those in untreated psychrophilic reactors. Multi-omics analyses revealed that psychrophilic conditions downregulated the methylmalonyl-CoA and aceticlastic methanogenesis pathways.
View Article and Find Full Text PDFPhosphorus speciation in the hyporheic zone and its response to sediment-water quality-biological activity coupling effect.
J Environ Manage
January 2025
Xi'an Key Laboratory of Environmental Simulation and Ecological Health in the Yellow River Basin, College of Urban and Environmental Sciences, Northwest University, Xi'an, 710127, China; Yellow River Institute of Shaanxi Province, Northwest University, Xi'an, 710127, China.
Different speciation of phosphorus in the hyporheic zone exhibit various release potentials, so as to control the phosphorus content in the overlying water. The process of phosphorus release under the multi-factor coupling of rivers is crucial for understanding the element cycle in complex environments. In this paper, the Weihe River in China was used as a case study to analyze the phosphorus speciation and distribution of overlying water and sediments in the hyporheic zone, and the phosphorus release process of sediments under the coupling of multiple factors.
View Article and Find Full Text PDFGenome-Wide Analysis of the Gene Family in .
Plant Direct
January 2025
Provincial Key Laboratory of Conservation and Utilization of Traditional Chinese Medicine Resources, Institute of Chinese Herbal Medicines Henan Academy of Agricultural Sciences Zhengzhou China.
The superfamily represents a class of transcription factors involved in plant growth, development, and stress responses. ., also known as safflower, is an important plant whose flowers contain carthamin, an expensive aromatic pigment with various medicinal and flavoring properties.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!