ArticleBMC genomics2007
Frame disruptions in human mRNA transcripts, and their relationship with splicing and protein structures.
Article in BMC genomics, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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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.
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Who cites it
5 citing papers in PubMed.
- Transcribed pseudogene ψPPM1K generates endogenous siRNA to suppress oncogenic cell growth in hepatocellular carcinoma.Nucleic acids research · 2013Article
- pseudoMap: an innovative and comprehensive resource for identification of siRNA-mediated mechanisms in human transcribed pseudogenes.Database : the journal of biological databases and curation · 2013Article
- Back-translation for discovering distant protein homologies in the presence of frameshift mutations.Algorithms for molecular biology : AMB · 2010Article
- Assessing the genomic evidence for conserved transcribed pseudogenes under selection.BMC genomics · 2009Article
- Genomic evidence for non-random endemic populations of decaying exons from mammalian genes.BMC genomics · 2009Article
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundEfforts to gather genomic evidence for the processes of gene evolution are ongoing, and are closely coupled to improved gene annotation methods. Such annotation is complicated by the occurrence of disrupted mRNAs (dmRNAs), harbouring frameshifts and premature stop codons, which can be considered indicators of decay into pseudogenes.
resultsWe have derived a procedure to annotate dmRNAs, and have applied it to human data. Subsequences are generated from parsing at key frame-disruption positions and are required to align significantly within any original protein homology. We find 419 high-quality human dmRNAs (3% of total). Significant dmRNA subpopulations include: zinc-finger-containing transcription factors with long disrupted exons, and antisense homologies to distal genes. We analysed the distribution of initial frame disruptions in dmRNAs with respect to positions of: (i) protein domains, (ii) alternatively-spliced exons, and (iii) regions susceptible to nonsense-mediated decay (NMD). We find significant avoidance of protein-domain disruption (indicating a selection pressure for this), and highly significant overrepresentation of disruptions in alternatively-spliced exons, and 'non-NMD' regions. We do not find any evidence for evolution of novelty in protein structures through frameshifting.
conclusionOur results indicate largely negative selection pressures related to frame disruption during gene evolution.
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