ArticleGenome biology2008
Evidence for common short natural trans sense-antisense pairing between transcripts from protein coding genes.
Article in Genome biology, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 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
13 citing papers in PubMed, 22 citations in OpenAlex.
- Non-coding Transcripts from Enhancers: New Insights into Enhancer Activity and Gene Expression Regulation.Genomics, proteomics & bioinformatics · 2017Review
- Alu-miRNA interactions modulate transcript isoform diversity in stress response and reveal signatures of positive selection.Scientific reports · 2016Article
- Aberrant expression of miR-153 is associated with overexpression of hypoxia-inducible factor-1α in refractory epilepsy.Scientific reports · 2016Article
- Trm9-Catalyzed tRNA Modifications Regulate Global Protein Expression by Codon-Biased Translation.PLoS genetics · 2015Article
- Macrophage infiltration promotes invasiveness of breast cancer cells via activating long non-coding RNA UCA1.International journal of clinical and experimental pathology · 2015Article
- The association between MMP-12 82 A/G polymorphism and susceptibility to various malignant tumors: a meta-analysis.International journal of clinical and experimental medicine · 2015Article
- TRIM29 functions as an oncogene in gastric cancer and is regulated by miR-185.International journal of clinical and experimental pathology · 2015Article
- Enhanced expression of stem cell markers and drug resistance in sphere-forming non-small cell lung cancer cells.International journal of clinical and experimental pathology · 2015Article
- Association between plasma homocysteine and progression of early nephropathy in type 2 diabetic patients.International journal of clinical and experimental medicine · 2015Article
- Regulatory Roles for Long ncRNA and mRNA.Cancers · 2013Article
- Heat shock factor binding in Alu repeats expands its involvement in stress through an antisense mechanism.Genome biology · 2011Article
- Locating protein-coding sequences under selection for additional, overlapping functions in 29 mammalian genomes.Genome research · 2011Article
- The long arm of long noncoding RNAs: roles as sensors regulating gene transcriptional programs.Cold Spring Harbor perspectives in biology · 2011Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors at 6 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThere is increasing realization that regulation of genes is done partly at the RNA level by sense-antisense binding. Studies typically concentrate on the role of non-coding RNAs in regulating coding RNA. But the majority of transcripts in a cell are likely to be coding. Is it possible that coding RNA might regulate other coding RNA by short perfect sense-antisense binding? Here we compare all well-described human protein coding mRNAs against all others to identify sites 15-25 bp long that could potentially perfectly match sense-antisense.
resultsFrom 24,968 protein coding mRNA RefSeq sequences, none failed to find at least one match in the transcriptome. By randomizations generating artificial transcripts matched for G+C content and length, we found that there are more such trans short sense-antisense pairs than expected. Several further features are consistent with functionality of some of the putative matches. First, transcripts with more potential partners have lower expression levels, and the pair density of tissue specific genes is significantly higher than that of housekeeping genes. Further, the single nucleotide polymorphism density is lower in short pairing regions than it is in flanking regions. We found no evidence that the sense-antisense pairing regions are associated with small RNAs derived from the protein coding genes.
conclusionsOur results are consistent with the possibility of common short perfect sense-antisense pairing between transcripts of protein coding genes.
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.