ArticleBMC genomics2010
The spatial distribution of cis regulatory elements in yeast promoters and its implications for transcriptional regulation.
Article in BMC genomics, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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38 citing papers in PubMed, 57 citations in OpenAlex.
- The shape of fitness functions and the distribution of mutational effect sizes jointly limit adaptation by regulatory mutations.Nature ecology & evolution · 2026Article
- Promoter Motif Profiling and Binding Site Distribution Analysis of Transcription Factors Predict Auto- and Cross-Regulatory Mechanisms inInternational journal of molecular sciences · 2025Article
- Combinatorial Alkali-Responsive Hybrid Promoters as Tools for Heterologous Protein Expression in Saccharomyces cerevisiae.Microbial biotechnology · 2025Article
- A four eigen-phase model of multi-omics unveils new insights into yeast metabolic cycle.NAR genomics and bioinformatics · 2025Article
- Article
- Dominant and genome-wide formation of DNA:RNA hybrid G-quadruplexes in living yeast cells.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- A comparative analysis of ENCODE and Cistrome in the context of TF binding signal.BMC genomics · 2024Article
- Transcription of microRNAs is regulated by developmental signaling pathways and transcription factors.Frontiers in cell and developmental biology · 2024Article
- Isolation of 5' regulatory region of3 Biotech · 2023Article
- Comparative Genome Analysis RevealsFrontiers in microbiology · 2022Article
- Systematic identification ofeLife · 2020Article
- YQFC: a web tool to compare quantitative biological features between two yeast gene lists.Database : the journal of biological databases and curation · 2020Article
- Next-Generation Sequencing Profiles of the Methylome and Transcriptome in Peripheral Blood Mononuclear Cells of Rheumatoid Arthritis.Journal of clinical medicine · 2019Article
- Pervasive and dynamic transcription initiation inGenome research · 2019Article
- YeasTSS: an integrative web database of yeast transcription start sites.Database : the journal of biological databases and curation · 2019Article
- Genetics ofeLife · 2018Article
- DNA signals at isoform promoters.Scientific reports · 2016Article
- Positional distribution of transcription factor binding sites in Arabidopsis thaliana.Scientific reports · 2016Article
- Sense and antisense transcription are associated with distinct chromatin architectures across genes.Nucleic acids research · 2015Article
- Truncated Ubiquitin 5' Regulatory Region from Erianthus arundinaceus Drives Enhanced Transgene Expression in Heterologous Systems.Molecular biotechnology · 2015Article
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Authors and funding
5 authors at 3 institutions in 2 countries.
Funding
Abstract
backgroundHow the transcription factor binding sites (TFBSs) are distributed in the promoter region have implications for gene regulation. Previous studies used the translation start codon as the reference point to infer the TFBS distribution. However, it is biologically more relevant to use the transcription start site (TSS) as the reference point. In this study, we reexamined the spatial distribution of TFBSs, investigated various promoter features that may affect the distribution, and studied the effect of TFBS distribution on transcriptional regulation.
resultsWe found a sharp peak for the distribution of TFBSs at ~115 bp upstream of the TSS, but no clear peak when the translation start codon was used as the reference point. Our analysis of sequence variation data among 63 yeast strains revealed very low deletion polymorphisms in the region between the distribution peak and the TSS, suggesting that the distances between TFBSs and the TSS have been selectively constrained in evolution. As in previous studies, we found that the nucleosome occupancy and the presence/absence of TATA-box in the promoter region affect the TFBS distribution pattern. In addition, we found that there exists a correlation between the 5'UTR length and the TFBS distribution pattern and we showed that the TFBS distribution pattern affects gene transcription level and plasticity.
conclusionsThe spatial distribution of TFBSs obtained using the TSS as the reference point shows a much sharper peak than does the distribution obtained using the translation start codon as the reference point. The TFBS distribution pattern is affected by nucleosome occupancy and presence of TATA-box and it affects the transcription level and transcription plasticity of the gene.
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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.