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Pseudofam: the pseudogene families database
- Page 11 of 11 Database, Vol. 2014, Article ID bau009, doi:10.1093/database/bau009 Original article
, 2009
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Characterization of Human Pseudogene-Derived Non-Coding RNAs for Functional Potential
"... Thousands of pseudogenes exist in the human genome and many are transcribed, but their functional potential remains elusive and understudied. To explore these issues systematically, we first developed a computational pipeline to identify transcribed pseudogenes from RNA-Seq data. Applying the pipeli ..."
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Thousands of pseudogenes exist in the human genome and many are transcribed, but their functional potential remains elusive and understudied. To explore these issues systematically, we first developed a computational pipeline to identify transcribed pseudogenes from RNA-Seq data. Applying the pipeline to datasets from 16 distinct normal human tissues identified,3,000 pseudogenes that could produce non-coding RNAs in a manner of low abundance but high tissue specificity under normal physiological conditions. Cross-tissue comparison revealed that the transcriptional profiles of pseudogenes and their parent genes showed mostly positive correlations, suggesting that pseudogene transcription could have a positive effect on the expression of their parent genes, perhaps by functioning as competing endogenous RNAs (ceRNAs), as previously suggested and demonstrated with the PTEN pseudogene, PTENP1. Our analysis of the ENCODE project data also found many transcriptionally active pseudogenes in the GM12878 and K562 cell lines; moreover, it showed that many human pseudogenes produced small RNAs (sRNAs) and some pseudogene-derived sRNAs, especially those from antisense strands, exhibited evidence of interfering with gene expression. Further integrated analysis of transcriptomics and epigenomics data, however, demonstrated that trimethylation of histone 3 at lysine 9 (H3K9me3), a posttranslational modification typically associated with gene repression and heterochromatin, was enriched at many transcribed pseudogenes in a transcription-level dependent manner in the two cell lines. The H3K9me3 enrichment was more
analysis of transcription, and evolution Pseudogenes in the ENCODE regions: Consensus annotation, Open Access
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SHORT REVIEW Heredity (2007), 1–9
"... www.nature.com/hdy Evaluating the role of natural selection in the evolution of gene regulation ..."
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www.nature.com/hdy Evaluating the role of natural selection in the evolution of gene regulation
Non-Variable and Functional
"... One of the iconic (yet enigmatic) arguments for human-ape common ancestry has been the �-globin pseudogene (HBBP1). Evolutionists originally speculated that apparent mutations in HBBP1 were shared mutational mistakes derived from a human-chimpanzee common ancestor. However, others noted that if the ..."
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One of the iconic (yet enigmatic) arguments for human-ape common ancestry has been the �-globin pseudogene (HBBP1). Evolutionists originally speculated that apparent mutations in HBBP1 were shared mutational mistakes derived from a human-chimpanzee common ancestor. However, others noted that if the gene was indeed non-functional, then it should have mutated markedly in the past 3 to 6 million years of human evolution due to a lack of selective constraint on the region. Recent research con�firms that the HBBP1 region of the 6-gene �-globulin cluster is highly non-variable compared to the other �-globin genes based on large-scale DNA diversity assessment within both humans and chimpanzees. Highlighting the lack of HBBP1 sequence variability is genetic data from three different reports that link point mutations in the HBBP1 gene with β-thalassemia disease pathologies. Biochemical evidence for functionality is indicated by multiple categories of functional genomics data showing that the HBBP1 gene is transcriptionally active and a key interactive component of the �-globin gene network. In brief, the HBBP1 gene encodes two consensus regulatory RNAs that are alternatively transcribed and/or post-transcriptionally spliced. This functional complexity produces at least 16 different exon variant transcripts and 42 different intron variant transcripts. Two major regulatory regions in the HBBP1 locus contain active transcription factor binding sites that overlap multiple categorical regions of epigenetic data for functionally active chromatin. The HBBP1 gene also has the most regulatory associations with active and open chromatin within the entire �-globin cluster and its transcripts are expressed in at least 251 different human cell and/or tissue types. Instead of being a useless genomic fossil according to evolutionary predictions, the HBBP1 gene appears to be a highly functional and cleverly integrated feature of the human genome that is intolerant of mutation.
“Orphan ” Retrogenes in the Human Genome
"... Gene duplicates generated via retroposition were long thought to be pseudogenized and consequently decayed. However, a significant number of these genes escaped their evolutionary destiny and evolved into functional genes. Despite multiple studies, the number of functional retrogenes in human and ot ..."
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Gene duplicates generated via retroposition were long thought to be pseudogenized and consequently decayed. However, a significant number of these genes escaped their evolutionary destiny and evolved into functional genes. Despite multiple studies, the number of functional retrogenes in human and other genomes remains unclear. We performed a comparative analysis of human, chicken, and worm genomes to identify “orphan ” retrogenes, that is, retrogenes that have replaced their progenitors. We located 25 such candidates in the human genome. All of these genes were previously known, and the majority has been intensively studied. Despite this, they have never been recognized as retrogenes. Analysis revealed that the phenomenon of replacing parental genes with their retrocopies has been taking place over the entire span of animal evolution. This process was often species specific and contributed to interspecies differences. Surprisingly, these retrogenes, which should evolve in a more relaxed mode, are subject to a very strong purifying selection, which is, on average, two and a half times stronger than other human genes. Also, for retrogenes, they do not show a typical overall tendency for a testis-specific expression. Notably, seven of them are associated with human diseases. Recognizing them as “orphan ” retrocopies, which have different regulatory machinery than their parents, is important for any disease studies in model organisms, especially when discoveries made in one species are transferred to humans. Key words: retrogene, gene duplication, gene expression, human genetic disease.
de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP)
, 2013
"... constraints and expression pattern of the ataxin-3 like 1 retrogene ..."
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p1 Estimating the Relative Contributions of New Genes from Retrotransposition and Segmental Duplication Events During Mammalian Evolution
"... Gene duplication has long been recognized as a major force in genome evolution and has recently been recognized as an important source of individual variation. For many years the origin of functional gene duplicates was assumed to be whole or partial genome duplication events, but recently retrotran ..."
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Gene duplication has long been recognized as a major force in genome evolution and has recently been recognized as an important source of individual variation. For many years the origin of functional gene duplicates was assumed to be whole or partial genome duplication events, but recently retrotransposition has also been shown to contribute new functional protein coding genes and siRNA’s. Here we present a method for the identification and classification of retrotransposed and segmentally duplicated genes and pseudogenes based on local synteny. Using the results of this approach we compare the rates of segmental duplication and retrotransposition in five mammalian genomes and estimate the rate of new functional protein coding gene formation by each mechanism. We find that retrotransposition occurs at a much higher and temporally more variable rate than segmental duplication, and gives rise to many more duplicated sequences over time. While the chance that retrotransposed copies become functional is much lower than that of their segmentally duplicated counterparts, the higher rate of retrotransposition events leads to nearly equal contributions of new genes by each mechanism. 1.
