Evolution and function of developmentally dynamic pseudogenes in mammals

Qian, Sheng Hu; Chen, Lu; Ying, Xiong; Chen, Zhenxia

doi:10.1186/s13059-022-02802-y

Cited by 17 publications

(10 citation statements)

References 99 publications

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“…Complete Loss Events were enriched in sensory or stimulus detection ( fig. 3 and supplementary data, Supplementary Material online), consistent with previous reports that most genes lost in humans are sensory related ( Gilad et al 2003 ; Young and Trask 2007 ; Kawamura and Melin 2017 ; Niimura et al 2018 ; Qian et al 2022 ). Complete Loss Events among different lineages also showed different patterns.…”

Section: Resultssupporting

confidence: 90%

Genome-Wide Identification of Gene Loss Events Suggests Loss Relics as a Potential Source of Functional lncRNAs in Humans

Wen

Kang

Lan

et al. 2023

Molecular Biology and Evolution

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Gene loss is a prevalent source of genetic variation in genome evolution. Calling loss events effectively and efficiently is a critical step for systematically characterizing their functional and phylogenetic profiles genome-wide. Here, we developed a novel pipeline integrating orthologous inference and genome alignment. Interestingly, we identified 33 gene loss events that give rise to evolutionarily novel lncRNAs that show distinct expression features and could be associated with various functions related to growth, development, immunity and reproduction, suggesting loss relics as a potential source of functional lncRNAs in humans. Our data also demonstrated that the rates of protein gene loss are variable among different lineages with distinct functional biases.

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Section: Resultssupporting

confidence: 90%

Genome-Wide Identification of Gene Loss Events Suggests Loss Relics as a Potential Source of Functional lncRNAs in Humans

Wen

Kang

Lan

et al. 2023

Molecular Biology and Evolution

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“…Pseudogenes have been extensively studied for their roles in evolution [ 22 – 24 ]. To our knowledge, this study is the first to examine pseudogenes as artifacts of the sequencing and assembly process.…”

Section: Discussionmentioning

confidence: 99%

Many purported pseudogenes in bacterial genomes are bona fide genes

Cooley,

Wright

2024

BMC Genomics

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Background Microbial genomes are largely comprised of protein coding sequences, yet some genomes contain many pseudogenes caused by frameshifts or internal stop codons. These pseudogenes are believed to result from gene degradation during evolution but could also be technical artifacts of genome sequencing or assembly. Results Using a combination of observational and experimental data, we show that many putative pseudogenes are attributable to errors that are incorporated into genomes during assembly. Within 126,564 publicly available genomes, we observed that nearly identical genomes often substantially differed in pseudogene counts. Causal inference implicated assembler, sequencing platform, and coverage as likely causative factors. Reassembly of genomes from raw reads confirmed that each variable affects the number of putative pseudogenes in an assembly. Furthermore, simulated sequencing reads corroborated our observations that the quality and quantity of raw data can significantly impact the number of pseudogenes in an assembler dependent fashion. The number of unexpected pseudogenes due to internal stops was highly correlated (R2 = 0.96) with average nucleotide identity to the ground truth genome, implying relative pseudogene counts can be used as a proxy for overall assembly correctness. Applying our method to assemblies in RefSeq resulted in rejection of 3.6% of assemblies due to significantly elevated pseudogene counts. Reassembly from real reads obtained from high coverage genomes showed considerable variability in spurious pseudogenes beyond that observed with simulated reads, reinforcing the finding that high coverage is necessary to mitigate assembly errors. Conclusions Collectively, these results demonstrate that many pseudogenes in microbial genome assemblies are actually genes. Our results suggest that high read coverage is required for correct assembly and indicate an inflated number of pseudogenes due to internal stops is indicative of poor overall assembly quality.

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“…First, retrocopy-derived RNAs could function as NATs, lncRNAs, or microRNAs in diverse cellular activities, including regulation of their parental genes (Kubiak and Makałowska 2017). Besides, RNAs transcribed from retrocopies may be processed and translated, and function at the protein level (Qian et al 2022). Second, the action of transcription and the resulting RNAs can orchestrate both intra- and inter- chromosomal chromatin organization (van Steensel and Furlong 2019; Bertero 2021; Quinodoz and Guttman 2021).…”

Section: Discussionmentioning

confidence: 99%

Interchromosomal Colocalization with Parental Genes Is Linked to the Function and Evolution of Mammalian Retrocopies

Yan

Tian

et al. 2023

Preprint

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Retrocopies are gene duplicates arising from reverse transcription of mature mRNA transcripts and their insertion back into the genome. While long being regarded as processed pseudogenes, more and more functional retrocopies have been discovered. How the stripped-down retrocopies recover expression capability and become functional paralogs continually intrigues evolutionary biologists. Here, we investigated the function and evolution of retrocopies in the context of three-dimensional (3D) genome organization. By mapping retrocopy-parent pairs onto the chromatin contact maps of human and mouse cell lines, we found that retrocopies and their parental genes show a higher-than-expected interchromosomal colocalization frequency. The spatial interactions between retrocopies and parental genes occur frequently at loci in active subcompartments and near nuclear speckles. Accordingly, colocalized retrocopies are more actively transcribed and translated, and are more evolutionarily conserved than noncolocalized ones. The active transcription of colocalized retrocopies may result from their permissive epigenetic environment and shared regulatory elements with parental genes. Population genetic analysis on retroposed gene copy number variants (retroCNVs) in human populations revealed that retrocopy insertions are not entirely random in regard to interchromosomal interactions and that colocalized retroCNVs are more likely to reach high frequency, suggesting that both insertion bias and natural selection contribute to the colocalization of retrocopy-parent pairs. Further dissection implies that reduced selection efficacy, rather than positive selection, contributes to the elevated allele frequency of colocalized retroCNVs. Overall, our results hint a role of interchromosomal colocalization in the "resurrection" of initially neutral retrocopies.

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Evolution and function of developmentally dynamic pseudogenes in mammals

Cited by 17 publications

References 99 publications

Genome-Wide Identification of Gene Loss Events Suggests Loss Relics as a Potential Source of Functional lncRNAs in Humans

Genome-Wide Identification of Gene Loss Events Suggests Loss Relics as a Potential Source of Functional lncRNAs in Humans

Many purported pseudogenes in bacterial genomes are bona fide genes

Interchromosomal Colocalization with Parental Genes Is Linked to the Function and Evolution of Mammalian Retrocopies

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