Why rodent pseudogenes refuse to retire

Long, Manyuan; Zhang, Li

doi:10.1186/gb-2012-13-11-178

Cited by 2 publications

(2 citation statements)

References 8 publications

(16 reference statements)

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“…We found there were one brachypodium relic, two rice relics and two sorghum relics encode different microRNA response elements and could be a plausible target for corresponding microRNAs, implying that they might become ceRNAs and thereby function as microRNA decoys [ 27 , 28 ]. Consistent with the hypothesis [ 4 , 26 , 29 ], we found there were protein-coding genes harbouring the same microRNA response elements in three prime untranslated region and expressing with positive correlation for each of these relics (Table 2 ). Further check showed that there were no out-paralog relationships between these relics and protein-coding genes, thus the sharing of the same microRNA response element is not due to the homology between them, further suggesting the possible ceRNA roles for these transcribed relics.…”

Section: Resultssupporting

confidence: 90%

“…It has been reported that transcripts losing coding potential could function as ceRNAs in rodents [ 4 , 26 ]. We found there were one brachypodium relic, two rice relics and two sorghum relics encode different microRNA response elements and could be a plausible target for corresponding microRNAs, implying that they might become ceRNAs and thereby function as microRNA decoys [ 27 , 28 ].…”

Section: Resultsmentioning

confidence: 99%

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Identification and analysis of unitary loss of long-established protein-coding genes in Poaceae shows evidences for biased gene loss and putatively functional transcription of relics

Zhao

Tang

et al. 2015

BMC Evol Biol

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BackgroundLong-established protein-coding genes may lose their coding potential during evolution (“unitary gene loss”). Members of the Poaceae family are a major food source and represent an ideal model clade for plant evolution research. However, the global pattern of unitary gene loss in Poaceae genomes as well as the evolutionary fate of lost genes are still less-investigated and remain largely elusive.ResultsUsing a locally developed pipeline, we identified 129 unitary gene loss events for long-established protein-coding genes from four representative species of Poaceae, i.e. brachypodium, rice, sorghum and maize. Functional annotation suggested that the lost genes in all or most of Poaceae species are enriched for genes involved in development and response to endogenous stimulus. We also found that 44 mutated genomic loci of lost genes, which we referred as relics, were still actively transcribed, and of which 84% (37 of 44) showed significantly differential expression across different tissues. More interestingly, we found that there were totally five expressed relics may function as competitive endogenous RNA in brachypodium, rice and sorghum genome.ConclusionsBased on comparative genomics and transcriptome data, we firstly compiled a comprehensive catalogue of unitary gene loss events in Poaceae species and characterized a statistically significant functional preference for these lost genes as well showed the potential of relics functioning as competitive endogenous RNAs in Poaceae genomes.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-015-0345-x) contains supplementary material, which is available to authorized users.

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