ArticleGenome research2007
Analysis of overrepresented motifs in human core promoters reveals dual regulatory roles of YY1.
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 79 papers, 1 of them a synthesis that pooled it.
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Who cites it
79 citing papers in PubMed, 1 synthesis or guideline pooled it, 112 citations in OpenAlex.
- Unveiling the Mechanism of Protective Effects of Tanshinone as a New Fighter Against Cardiovascular Diseases: A Systematic Review.Cardiovascular toxicology · 2024Pooled it
- YY1 in hematopoietic stem cells: epigenetic regulation, chromatin architecture, and aging.Current opinion in hematology · 2026Review
- Multiomics analysis of red blood cells reveals thalassemia severity beyond globin gene mutations.Blood advances · 2026Article
- Systematic transcriptome analysis reveals the function of alternative promoters in hematopoietic lineages.Stem cell reports · 2026Article
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- Dissecting thebioRxiv : the preprint server for biology · 2024Article
- Potential Transcriptional Enhancers in Coronaviruses: From Infectious Bronchitis Virus to SARS-CoV-2.International journal of molecular sciences · 2024Article
- Sequence basis of transcription initiation in the human genome.Science (New York, N.Y.) · 2024Article
- Computational identification and experimental characterization of preferred downstream positions in human core promoters.PLoS computational biology · 2021Article
- A lineage-specific requirement for YY1 Polycomb Group protein function in early T cell development.Development (Cambridge, England) · 2021Article
- Knockdown of NIR Suppresses Breast Cancer Cell Proliferation via Promoting FOXO3.OncoTargets and therapy · 2021Article
- Functional regulation of an ancestral RAG transposon ProtoRAG by a trans-acting factor YY1 in lancelet.Nature communications · 2020Article
- Crosstalk between the mTOR and Nrf2/ARE signaling pathways as a target in the improvement of long-term potentiation.Experimental neurology · 2020Review
- Integrative prediction of gene expression with chromatin accessibility and conformation data.Epigenetics & chromatin · 2020Article
- Towards understanding of PRC2 binding to RNA.RNA biology · 2019Review
- Multiple Long-Read Sequencing Survey of Herpes Simplex Virus Dynamic Transcriptome.Frontiers in genetics · 2019Article
- Deep learning sequence-based ab initio prediction of variant effects on expression and disease risk.Nature genetics · 2018Article
- Identification and Functional Analysis of theInternational journal of molecular sciences · 2018Article
- YY1 Upregulates Checkpoint Receptors and Downregulates Type I Cytokines in Exhausted, Chronically Stimulated Human T Cells.iScience · 2018Article
- Nuclear Respiratory Factor 1 (NRF-1) Controls the Activity Dependent Transcription of the GABA-A Receptor Beta 1 Subunit Gene in Neurons.Frontiers in molecular neuroscience · 2018Article
19 more citing papers are in PubMed but not listed here.
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
Abstract
A set of 723 high-quality human core promoter sequences were compiled and analyzed for overrepresented motifs. Beside the two well-characterized core promoter motifs (TATA and Inr), several known motifs (YY1, Sp1, NRF-1, NRF-2, CAAT, and CREB) and one potentially new motif (motif8) were found. Interestingly, YY1 and motif8 mostly reside immediately downstream from the TSS. In particular, the YY1 motif occurs primarily in genes with 5'-UTRs shorter than 40 base pairs (bp) and its locations coincide with the translation start site. We verified that the YY1 motif is bound by YY1 in vitro. We then performed detailed analysis on YY1 chromatin immunoprecipitation data with a whole-genome human promoter microarray (ChIP-chip) and revealed that the thus identified promoters in HeLa cells were highly enriched with the YY1 motif. Moreover, the motif overlapped with the translation start sites on the plus strand of a group of genes, many with short 5'-UTRs, and with the transcription start sites on the minus strand of another distinct group of genes; together, the two groups of genes accounted for the majority of the YY1-bound promoters in the ChIP-chip data. Furthermore, the first group of genes was highly enriched in the functional categories of ribosomal proteins and nuclear-encoded mitochondria proteins. We suggest that the YY1 motif plays a dual role in both transcription and translation initiation of these genes. We also discuss the evolutionary advantages of housing a transcriptional element inside the transcript in terms of the migration of these genes in the human genome.
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Registered trials
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.