ArticleGenome research2007
Characterization and predictive discovery of evolutionarily conserved mammalian alternative promoters.
Article in Genome research, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 56 papers, 1 of them a synthesis that pooled it.
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Who cites it
56 citing papers in PubMed, 1 synthesis or guideline pooled it.
- A meta-analysis of microarray gene expression in mouse stem cells: redefining stemness.PloS one · 2008Pooled it
- Disease-associated genetic variants can cause missense effects in tissue-specific protein isoforms.Nature communications · 2026Article
- Age-related promoter-switch regulates Runx1 expression in adult rat hearts.BMC cardiovascular disorders · 2023Article
- Reciprocal regulation of flower induction by ELF3α and ELF3β generated via alternative promoter usage.The Plant cell · 2023Article
- Widespread occurrence of hybrid internal-terminal exons in human transcriptomes.Science advances · 2022Article
- Promoter switching in response to changing environment and elevated expression of protein-coding genes overlapping at their 5' ends.Scientific reports · 2021Article
- mountainClimber Identifies Alternative Transcription Start and Polyadenylation Sites in RNA-Seq.Cell systems · 2019Article
- Article
- Selective Activation of AlternativeGenes · 2018Article
- Androgen-dependent alternative mRNA isoform expression in prostate cancer cells.F1000Research · 2018Article
- Relatively frequent switching of transcription start sites during cerebellar development.BMC genomics · 2017Article
- Alternate promoter usage generates two subpopulations of the neuronal RhoGEF Kalirin-7.Journal of neurochemistry · 2017Article
- Ubiquitously expressed genes participate in cell-specific functions via alternative promoter usage.EMBO reports · 2016Article
- Pervasive isoform-specific translational regulation via alternative transcription start sites in mammals.Molecular systems biology · 2016Article
- RUNX1B Expression Is Highly Heterogeneous and Distinguishes Megakaryocytic and Erythroid Lineage Fate in Adult Mouse Hematopoiesis.PLoS genetics · 2016Article
- The intronic region ofBiochemistry and biophysics reports · 2015Article
- Evolution at protein ends: major contribution of alternative transcription initiation and termination to the transcriptome and proteome diversity in mammals.Nucleic acids research · 2014Article
- Ameliorative effects of thyme and calendula extracts alone or in combination against aflatoxins-induced oxidative stress and genotoxicity in rat liver.Cytotechnology · 2014Article
- Genetic disruption of the sh3pxd2a gene reveals an essential role in mouse development and the existence of a novel isoform of tks5.PloS one · 2014Article
- Several cis-regulatory elements control mRNA stability, translation efficiency, and expression pattern of Prrxl1 (paired related homeobox protein-like 1).The Journal of biological chemistry · 2013Article
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Recent studies suggest that surprisingly many mammalian genes have alternative promoters (APs); however, their biological roles, and the characteristics that distinguish them from single promoters (SPs), remain poorly understood. We constructed a large data set of evolutionarily conserved promoters, and used it to identify sequence features, functional associations, and expression patterns that differ by promoter type. The four promoter categories CpG-rich APs, CpG-poor APs, CpG-rich SPs, and CpG-poor SPs each show characteristic strengths and patterns of sequence conservation, frequencies of putative transcription-related motifs, and tissue and developmental stage expression preferences. APs display substantially higher sequence conservation than SPs and CpG-poor promoters than CpG-rich promoters. Among CpG-poor promoters, APs and SPs show sharply contrasting developmental stage preferences and TATA box frequencies. We developed a discriminator to computationally predict promoter type, verified its accuracy through experimental tests that incorporate a novel method for deconvolving mixed sequence traces, and used it to find several new APs. The discriminator predicts that almost half of all mammalian genes have evolutionarily conserved APs. This high frequency of APs, together with the strong purifying selection maintaining them, implies a crucial role in expanding the expression diversity of the mammalian genome.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.