Category Ranking
98%
Total Visits
921
Avg Visit Duration
2 minutes
Citations
20
Article Abstract
We have developed a new method for promoter sequence classification based on a genetic algorithm and the MAHDS sequence alignment method. We have created four classes of human promoters, combining 17,310 sequences out of the 29,598 present in the EPD database. We searched the human genome for potential promoter sequences (PPSs) using dynamic programming and position weight matrices representing each of the promoter sequence classes. A total of 3,065,317 potential promoter sequences were found. Only 1,241,206 of them were located in unannotated parts of the human genome. Every other PPS found intersected with either true promoters, transposable elements, or interspersed repeats. We found a strong intersection between PPSs and Alu elements as well as transcript start sites. The number of false positive PPSs is estimated to be 3 × 10 per nucleotide, which is several orders of magnitude lower than for any other promoter prediction method. The developed method can be used to search for PPSs in various eukaryotic genomes.
Download full-text PDF |
Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC10454140 | PMC |
| http://dx.doi.org/10.3390/ijms241612561 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Low-Density Lipoprotein Receptor-Related Protein 11 Promotes Proliferation in Lung Adenocarcinoma.
Cancer Sci
September 2025
Section of Oncopathology and Morphological Pathology, Department of Pathology, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan.
Low-density lipoprotein receptor-related protein 11 (LRP11) is reported to be overexpressed in various cancers; however, its functional role in lung adenocarcinoma remains poorly understood. This study aimed to elucidate the tumor-promoting function of LRP11 in lung adenocarcinoma. We assessed the expression and function of LRP11 in lung adenocarcinoma cell lines through both silencing and overexpression experiments.
View Article and Find Full Text PDFDnaA regulates stationary phase-specific expression of a AAA family gene in Caulobacter crescentus.
Genes Genet Syst
September 2025
Department of Molecular Biology, Graduate School of Pharmaceutical Sciences, Kyushu University.
In most eubacteria the initiator protein DnaA triggers chromosomal replication by forming an initiation complex at the origin of replication and also functions as a transcriptional regulator, coordinating gene expression with cell cycle progression. While DnaA-regulated genes are relatively well characterized in exponentially growing cells, its role in gene regulation during stationary phase remains insufficiently explored. Here, using an aquatic bacterium Caulobacter crescentus as a model, we show that C.
View Article and Find Full Text PDFInfluence of lactulose as a composition of organic-mineral feed additive on broiler chicken productivity, feed digestibility, and microbiome.
Vet World
July 2025
Federal Research Centre of Biological Systems and Agrotechnologies of the Russian Academy of Sciences, 29, 9 Yanvarya Street, Orenburg, 460000, Russia.
Background And Aim: The global demand for efficient poultry production necessitates alternatives to antibiotic growth promoters. This study aimed to evaluate the effects of a novel four-component organic-mineral feed additive (OMFA), comprising lactulose, arginine, ultrafine silicon dioxide particles, and succinic acid, and a three-component variant (without lactulose) on growth performance, nutrient digestibility, elemental tissue composition, and the cecal microbiota of Arbor Acres broiler chickens.
Materials And Methods: One hundred and five one-day-old broiler chicks were randomly allocated into three groups: Control, Group I (four-component OMFA), and Group II (three-component OMFA).
ONAC005 enhances salt stress tolerance by promoting suberin deposition in root endodermis.
Plant J
September 2025
Plant Genomics and Breeding Institute, Seoul National University, Seoul, South Korea.
Salt stress impairs photosynthetic efficiency and consequently reduces the growth, development, and grain yield of crop plants. The formation of hydrophobic barriers in the root endodermis, including the suberin lamellae and Casparian strips, is a key adaptive strategy for salt stress tolerance. In this study, we identified the role of the rice NAC transcription factor, ONAC005, in salt stress tolerance.
View Article and Find Full Text PDFRNA gradients can guide condensates toward promoters: Implications for enhancer-promoter contacts and condensate-promoter kissing.
J Chem Phys
September 2025
Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.
We study how protein condensates respond to a site of active RNA transcription (i.e., a gene promoter) due to electrostatic protein-RNA interactions.
View Article and Find Full Text PDF