ArticleNucleic acids research2010
Functional analysis and identification of cis-regulatory elements of human chromosome 21 gene promoters.
Article in Nucleic acids research, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed, 19 citations in OpenAlex.
- Differentially Expressed Genes Related to Flowering Transition between Once- and Continuous-Flowering Roses.Biomolecules · 2021Article
- Computational annotation of miRNA transcription start sites.Briefings in bioinformatics · 2021Review
- Transcriptional interference by small transcripts in proximal promoter regions.Nucleic acids research · 2018Article
- Identification of novel long non-coding RNA biomarkers for prognosis prediction of papillary thyroid cancer.Oncotarget · 2017Article
- Resveratrol compounds inhibit human holocarboxylase synthetase and cause a lean phenotype in Drosophila melanogaster.The Journal of nutritional biochemistry · 2015Article
- Novel roles of holocarboxylase synthetase in gene regulation and intermediary metabolism.Nutrition reviews · 2014Review
- Three promoters regulate the transcriptional activity of the human holocarboxylase synthetase gene.The Journal of nutritional biochemistry · 2013Article
- Cytosine methylation in miR-153 gene promoters increases the expression of holocarboxylase synthetase, thereby increasing the abundance of histone H4 biotinylation marks in HEK-293 human kidney cells.The Journal of nutritional biochemistry · 2012Article
- MicroSCALE screening reveals genetic modifiers of therapeutic response in melanoma.Science signaling · 2012Article
- Effects of single-nucleotide polymorphisms in the human holocarboxylase synthetase gene on enzyme catalysis.European journal of human genetics : EJHG · 2012Article
- Transcription factor binding predictions using TRAP for the analysis of ChIP-seq data and regulatory SNPs.Nature protocols · 2011Article
- The BTB and CNC homology 1 (BACH1) target genes are involved in the oxidative stress response and in control of the cell cycle.The Journal of biological chemistry · 2011Article
- The role of holocarboxylase synthetase in genome stability is mediated partly by epigenomic synergies between methylation and biotinylation events.Epigenetics · 2011Article
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Authors and funding
13 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Given the inherent limitations of in silico studies relying solely on DNA sequence analysis, the functional characterization of mammalian promoters and associated cis-regulatory elements requires experimental support, which demands cloning and analysis of putative promoter regions. Focusing on human chromosome 21, we cloned 182 gene promoters of 2500 bp in length and conducted reporter gene assays on transfected-cell arrays. We found 56 promoters that were active in HEK293 cells, while another 49 promoters could be activated by treatment of cells with Trichostatin A or depletion of serum. We observed high correlations between promoter activities and endogenous transcript levels, RNA polymerase II occupancy, CpG islands and core promoter elements. Truncation of a subset of 62 promoters to ∼500 bp revealed that truncation rarely resulted in loss of activity, but rather in loss of responses to external stimuli, suggesting the presence of cis-regulatory response elements within distal promoter regions. In these regions, we found a strong enrichment of transcription factor binding sites that could potentially activate gene expression in the presence of stimuli. This study illustrates the modular functional architecture of chromosome 21 promoters and helps to reveal the complex mechanisms governing transcriptional regulation.
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