ArticleGenome research2011
Core promoter T-blocks correlate with gene expression levels in C. elegans.
Article in Genome research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed, 40 citations in OpenAlex.
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- Transcript accumulation rates in the earlyScience advances · 2023Article
- An updated C. elegans nuclear body muscle transcriptome for studies in muscle formation and function.Skeletal muscle · 2023Article
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- A novel in vitro Caenorhabditis elegans transcription system.BMC molecular and cell biology · 2020Article
- Evolutionary Dynamics of the SKN-1 → MED → END-1,3 Regulatory Gene Cascade inG3 (Bethesda, Md.) · 2020Article
- Chromatin accessibility and the regulatory epigenome.Nature reviews. Genetics · 2019Review
- Genome-wide discovery of active regulatory elements and transcription factor footprints inGenome research · 2017Article
- Widespread adenine N6-methylation of active genes in fungi.Nature genetics · 2017Article
- Nucleosome fragility is associated with future transcriptional response to developmental cues and stress in C. elegans.Genome research · 2017Article
- Fine-Scale Crossover Rate Variation on the Caenorhabditis elegans X Chromosome.G3 (Bethesda, Md.) · 2016Article
- Mutagenesis of GATA motifs controlling the endoderm regulator elt-2 reveals distinct dominant and secondary cis-regulatory elements.Developmental biology · 2016Article
- Bilaterian-like promoters in the highly compact Amphimedon queenslandica genome.Scientific reports · 2016Article
- MED GATA factors promote robust development of the C. elegans endoderm.Developmental biology · 2015Article
- H3K36 methylation promotes longevity by enhancing transcriptional fidelity.Genes & development · 2015Article
- Comparative RNA-Seq analysis reveals pervasive tissue-specific alternative polyadenylation in Caenorhabditis elegans intestine and muscles.BMC biology · 2015Article
- The impact of sequence length and number of sequences on promoter prediction performance.BMC bioinformatics · 2015Article
Corrections and comments
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Core promoters mediate transcription initiation by the integration of diverse regulatory signals encoded in the proximal promoter and enhancers. It has been suggested that genes under simple regulation may have low-complexity permissive promoters. For these genes, the core promoter may serve as the principal regulatory element; however, the mechanism by which this occurs is unclear. We report here a periodic poly-thymine motif, which we term T-blocks, enriched in occurrences within core promoter forward strands in Caenorhabditis elegans. An increasing number of T-blocks on either strand is associated with increasing nucleosome eviction. Strikingly, only forward strand T-blocks are correlated with expression levels, whereby genes with ≥6 T-blocks have fivefold higher expression levels than genes with ≤3 T-blocks. We further demonstrate that differences in T-block numbers between strains predictably affect expression levels of orthologs. Highly expressed genes and genes in operons tend to have a large number of T-blocks, as well as the previously characterized SL1 motif involved in trans-splicing. The presence of T-blocks thus correlates with low nucleosome occupancy and the precision of a trans-splicing motif, suggesting its role at both the DNA and RNA levels. Collectively, our results suggest that core promoters may tune gene expression levels through the occurrences of T-blocks, independently of the spatio-temporal regulation mediated by the proximal promoter.
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