Transcription Regulatory Regions Database (TRRD) has been developed for accumulation of experimental information on the structure-function features of regulatory regions of eukaryotic genes. Each entry in TRRD corresponds to a particular gene and contains a description of structure-function features of its regulatory regions (transcription factor binding sites, promoters, enhancers, silencers, etc.) and gene expression regulation patterns. The current release, TRRD 4.2.5, comprises the description of 760 genes, 3403 expression patterns, and >4600 regulatory elements including 3604 transcription factor binding sites, 600 promoters and 152 enhancers. This information was obtained through annotation of 2537 scientific publications. TRRD 4.2.5 is available through the WWW at http://wwwmgs.bionet.nsc.ru/mgs/dbases/trrd4/
Download full-text PDF |
Source |
---|---|
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC102412 | PMC |
http://dx.doi.org/10.1093/nar/28.1.298 | DOI Listing |
BMC Genomics
January 2025
Henan Collaborative Innovation Center of Modern Biological Breeding, College of Agronomy, Henan Institute of Science and Technology, Xinxiang, 453003, China.
Background: The Sec14 domain is an ancient lipid-binding domain that evolved from yeast Sec14p and performs complex lipid-mediated regulatory functions in subcellular organelles and intracellular traffic. The Sec14 family is characterized by a highly conserved Sec14 domain, and is ubiquitously expressed in all eukaryotic cells and has diverse functions. However, the number and characteristics of Sec14 homologous genes in soybean, as well as their potential roles, remain understudied.
View Article and Find Full Text PDFBMC Genomics
January 2025
College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China.
Background: Rex rabbit is famous for its silky and soft fur coat, a characteristic predominantly attributed to its hair follicles. Numerous studies have confirmed the crucial roles of mRNAs and non-coding RNAs (ncRNAs) in regulating key cellular processes such as cell proliferation, differentiation, apoptosis and immunity. However, their involvement in the regulation of the hair cycle in Rex rabbits remains unknown.
View Article and Find Full Text PDFSci Rep
January 2025
Department of Medical Biology, Albert Szent-Györgyi Medical School, University of Szeged, Somogyi u. 4, Szeged, 6720, Hungary.
In our research, we performed temporal transcriptomic profiling of host cells infected with Equid alphaherpesvirus 1 (EHV-1) by utilizing direct cDNA sequencing based on nanopore MinION technology. The sequencing reads were harnessed for transcript quantification at various time points. Viral infection-induced differential gene expression was identified through the edgeR package.
View Article and Find Full Text PDFNat Commun
January 2025
Frontiers Science Center for Molecular Design Breeding, Beijing Key Laboratory of Crop Genetic Improvement, College of Agronomy and Biotechnology, China Agricultural University, Beijing, China.
During cold acclimation in high-latitude and high-altitude regions, japonica rice develops enhanced cold tolerance, but the underlying genetic basis remains unclear. Here, we identify CTB5, a homeodomain-leucine zipper (HD-Zip) transcription factor that confers cold tolerance at the booting stage in japonica rice. Four natural variations in the promoter and coding regions enhance cold response and transcriptional regulatory activity, enabling the favorable CTB5 allele to improve cold tolerance.
View Article and Find Full Text PDFNat Commun
January 2025
Gene Regulation Laboratory, MRC Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, OX3 9DS, Oxford, UK.
Individual enhancers are defined as short genomic regulatory elements, bound by transcription factors, and able to activate cell-specific gene expression at a distance, in an orientation-independent manner. Within mammalian genomes, enhancer-like elements may be found individually or within clusters referred to as locus control regions or super-enhancers (SEs). While these behave similarly to individual enhancers with respect to cell specificity, distribution and distance, their orientation-dependence has not been formally tested.
View Article and Find Full Text PDFEnter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!