ArticleNucleic acids research2000
Statistical analysis of yeast genomic downstream sequences reveals putative polyadenylation signals.
Article in Nucleic acids research, 2000. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 73 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
73 citing papers in PubMed, 144 citations in OpenAlex.
- Review
- Effect ofPeerJ · 2024Article
- Functional characterization of the Komagataella phaffii 1033 gene promoter and transcriptional terminator.World journal of microbiology & biotechnology · 2023Article
- Development of Terminator-Promoter Bifunctional Elements for Application inInternational journal of molecular sciences · 2023Article
- RSAT 2022: regulatory sequence analysis tools.Nucleic acids research · 2022Article
- Xrn1 influence on gene transcription results from the combination of general effects on elongating RNA pol II and gene-specific chromatin configuration.RNA biology · 2021Article
- The identification of novel promoters and terminators for protein expression and metabolic engineering applications inMetabolic engineering communications · 2021Article
- Advances in linking polyketides and non-ribosomal peptides to their biosynthetic gene clusters in Fusarium.Current genetics · 2019Review
- DeeReCT-PolyA: a robust and generic deep learning method for PAS identification.Bioinformatics (Oxford, England) · 2019Article
- Modeling of Genome-Wide Polyadenylation Signals inFrontiers in genetics · 2019Article
- RSAT 2018: regulatory sequence analysis tools 20th anniversary.Nucleic acids research · 2018Article
- Article
- Enhancement of protein production via the strong DIT1 terminator and two RNA-binding proteins in Saccharomyces cerevisiae.Scientific reports · 2016Article
- Defects in the NC2 repressor affect both canonical and non-coding RNA polymerase II transcription initiation in yeast.BMC genomics · 2016Article
- The chromatin environment shapes DNA replication origin organization and defines origin classes.Genome research · 2015Article
- RSAT 2015: Regulatory Sequence Analysis Tools.Nucleic acids research · 2015Article
- Chromatin-dependent regulation of RNA polymerases II and III activity throughout the transcription cycle.Nucleic acids research · 2015Article
- Inducible, tightly regulated and growth condition-independent transcription factor in Saccharomyces cerevisiae.Nucleic acids research · 2014Article
- Analysis of pattern overlaps and exact computation of P-values of pattern occurrences numbers: case of Hidden Markov Models.Algorithms for molecular biology : AMB · 2014Article
- DNA damage induces targeted, genome-wide variation of poly(A) sites in budding yeast.Genome research · 2013Article
13 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The study of a few genes has permitted the identification of three elements that constitute a yeast polyadenyl-ation signal: the efficiency element (EE), the positioning element and the actual site for cleavage and poly-adenyl-ation. In this paper we perform an analysis of oligonucleotide composition on the sequences located downstream of the stop codon of all yeast genes. Several oligonucleotide families appear over-represented with a high significance (referred to herein as 'words'). The family with the highest over-representation includes the oligonucleotides shown experimentally to play a role as EEs. The word with the highest score is TATATA, followed, among others, by a series of single-nucleotide variants (TATGTA, TACATA, TAAATA.) and one-letter shifts (ATATAT). A position analysis reveals that those words have a high preference to be in 3' flanks of yeast genes and there they have a very uneven distribution, with a marked peak around 35 bp after the stop codon. Of the predicted ORFs, 85% show one or more of those sequences. Similar results were obtained using a data set of EST sequences. Other clusters of over-represented words are also detected, namely T- and A-rich signals. Using these results and previously known data we propose a general model for the 3' trailers of yeast mRNAs.
Indexed as
Identifiers
What OpenQuestion holds
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.