ArticleGenetics2012
Novel transcript truncating function of Rap1p revealed by synthetic codon-optimized Ty1 retrotransposon.
Article in Genetics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
11 citing papers in PubMed, 13 citations in OpenAlex.
- Pervasive RNA folding is crucial for narnavirus genome maintenance.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- When push comes to shove - RNA polymerase and DNA-bound protein roadblocks.Biophysical reviews · 2023Review
- In vivo structure of the Ty1 retrotransposon RNA genome.Nucleic acids research · 2021Article
- Transcribe this way: Rap1 confers promoter directionality by repressing divergent transcription.Transcription · 2019Review
- Repression of Divergent Noncoding Transcription by a Sequence-Specific Transcription Factor.Molecular cell · 2018Article
- High-resolution transcription maps reveal the widespread impact of roadblock termination in yeast.The EMBO journal · 2018Article
- Bug mapping and fitness testing of chemically synthesized chromosome X.Science (New York, N.Y.) · 2017Article
- Paralog-Specific Functions ofG3 (Bethesda, Md.) · 2017Article
- Co-translational localization of an LTR-retrotransposon RNA to the endoplasmic reticulum nucleates virus-like particle assembly sites.PLoS genetics · 2014Article
- Artificial repressors for controlling gene expression in bacteria.Chemical communications (Cambridge, England) · 2013Article
- Retrotransposon Ty1 RNA contains a 5'-terminal long-range pseudoknot required for efficient reverse transcription.RNA (New York, N.Y.) · 2013Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 2 institutions in 1 country.
Funding
Abstract
Extensive mutagenesis via massive recoding of retrotransposon Ty1 produced a synthetic codon-optimized retrotransposon (CO-Ty1). CO-Ty1 is defective for retrotransposition, suggesting a sequence capable of down-regulating retrotransposition. We mapped this sequence to a critical ~20-bp region within CO-Ty1 reverse transcriptase (RT) and confirmed that it reduced Ty1 transposition, protein, and RNA levels. Repression was not Ty1 specific; when introduced immediately downstream of the green fluorescent protein (GFP) stop codon, GFP expression was similarly reduced. Rap1p mediated this down-regulation, as shown by mutagenesis and chromatin immunoprecipitation. A regular threefold drop is observed in different contexts, suggesting utility for synthetic circuits. A large reduction of RNAP II occupancy on the CO-Ty1 construct was observed 3' to the identified Rap1p site and a novel 3' truncated RNA species was observed. We propose a novel mechanism of transcriptional regulation by Rap1p whereby it serves as a transcriptional roadblock when bound to transcription unit sequences.
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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.