Both male and female gamete generating cells produce processed pseudogenes in the human genome

Maranda, Vincent; Sunstrum, Frédérick G.; Drouin, Guy

doi:10.1016/j.gene.2018.10.061

Cited by 5 publications

(2 citation statements)

References 29 publications

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“…The former is caused by unequal crossing‐over events during cell division, causing functional genes to be duplicated in the genome (Khurana et al, 2010; Milligan et al, 2016). The latter occurs by the insertion into the genome of reverse‐transcribed mRNA which has a structure similar to that of intron‐less cDNA (Kazazian, 2014; Maranda et al, 2019).…”

Section: Introductionmentioning

confidence: 99%

Identification of processed pseudogenes in the genome of Thoroughbred horses: Possibility of gene‐doping detection considering the presence of pseudogenes

et al. 2022

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Processed pseudogenes, also known as retrocopy genes, are copies of messenger RNAs that have been reverse transcribed into DNA and inserted into the genome. In this study, we identified 62 processed pseudogene candidates as intron‐less genes from whole‐genome sequencing (WGS) data of Thoroughbred horses using delly structural variation software. The 62 processed pseudogene candidates were confirmed by PCR amplification of intron‐less products. A total of 11 processed pseudogenes were confirmed in the genome of all 23 analysed horses, whereas three processed pseudogenes with structures of ATP11B, DPH3 and RPL17 were detected in only one of 115 horses by PCR amplification of intron‐less products. Currently, most of the gene doping tests proposed in human and horse sports are adapted PCR‐based methods using hydrolysis probes to detect exon/exon junctions in transgenes because the operation is simple and economical. However, when the pseudogene is present in the host genome, the PCR‐based methods may have a potential risk of detecting false positives. In this study, because processed pseudogenes that exist less frequently in the horse genome may affect PCR‐based transgene detection in gene‐doping tests, we propose and demonstrate that PCR amplification and sequencing using primers designed on transgene and promotors and/or polyadenylation signal for gene expression are useful for gene‐doping detection as an additional confirmatory test to prevent false positives.

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Section: Introductionmentioning

confidence: 99%

Identification of processed pseudogenes in the genome of Thoroughbred horses: Possibility of gene‐doping detection considering the presence of pseudogenes

et al. 2022

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“…Formation of processed pseudogenes is ongoing (Maranda et al, 2019) and more than 40 polymorphic processed pseudogenes have been reported in the human genome (Ewing et al, 2013).…”

Section: Impact Of Processed Pseudogenes On Gene Regulationmentioning

confidence: 99%

Role of Transposable Elements in Gene Regulation in the Human Genome

Ali¹,

Han²,

Liang³

2020

Preprint

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Transposable elements (TEs), also known as mobile elements (MEs), are interspersed repeats that constitute a major fraction of the genomes of higher organisms. As one of their important functional impacts on gene function and genome evolution, TEs participate in regulating the expression of genes nearby and even far away at transcriptional and post-transcriptional levels. There are two principal ways by which TEs regulate expression of genes in the human genome. First, TEs provide cis-regulatory sequences in the genome. TEs’ intrinsic regulatory properties for their own expression make them potential factors for regulating the expression of the host genes. TE-derived cis-regulatory sites are found in promoter and enhancer elements, providing binding sites for a wide range of trans-acting factors. Second, TEs encode for regulatory RNAs. TEs sequences have been revealed to be present in a substantial fraction of miRNAs and long non-coding RNAs (lncRNAs), indicating their TE origin. Furthermore, TEs sequences were found to be critical for regulatory functions of these RNAs including binding to the target mRNA. TEs thus provide crucial regulatory roles by being part of cis-regulatory and regulatory RNA sequences. Moreover, both TE-derived cis-regulatory sequences and TE-derived regulatory RNAs, have been implicated to provide evolutionary novelty to gene regulation. These TE-derived regulatory mechanisms also tend to function in tissue-specific fashion. In this review, we aim to comprehensively cover the studies regarding these two aspects of TE-mediated gene regulation, mainly focusing on the mechanisms, contribution of different types of TEs, differential roles among tissue types, and lineage specificity, based on data mostly in humans.

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Gonadal microRNA Expression Profiles and Their Potential Role in Sex Differentiation and Gonadal Maturation of Mud Crab Scylla paramamosain

et al. 2019

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Both male and female gamete generating cells produce processed pseudogenes in the human genome

Cited by 5 publications

References 29 publications

Identification of processed pseudogenes in the genome of Thoroughbred horses: Possibility of gene‐doping detection considering the presence of pseudogenes

Identification of processed pseudogenes in the genome of Thoroughbred horses: Possibility of gene‐doping detection considering the presence of pseudogenes

Role of Transposable Elements in Gene Regulation in the Human Genome

Gonadal microRNA Expression Profiles and Their Potential Role in Sex Differentiation and Gonadal Maturation of Mud Crab Scylla paramamosain

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