ArticleGenome biology2022
Evolution and function of developmentally dynamic pseudogenes in mammals.
Article in Genome biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed, 38 citations in OpenAlex.
- Multifaceted role ofiScience · 2026Article
- Epigenetic characterization of pseudogenes across human tissues.Genome research · 2026Article
- Divergent Amplification of Y-Linked Dosage-Sensitive Genes Triggers Regulatory Mismatch Underlying Cattle-Yak Male Sterility.Biomolecules · 2026Article
- From Genomic Fossils to Functional Elements: The Evolving Story of Pseudogenes.Advanced genetics (Hoboken, N.J.) · 2025Review
- One Earth-One Health to Combat Antimicrobial Resistance Having a Dual Mutation Pattern, Based on the Robust Self-Regulation and Perpetual Reconstruction of Ecosystems.Antibiotics (Basel, Switzerland) · 2025Article
- Genomic Analysis of Indel and SV Reveals Functional and Adaptive Signatures in Hubei Indigenous Cattle Breeds.Animals : an open access journal from MDPI · 2025Article
- Vitamin C: From Self-Sufficiency to Dietary Dependence in the Framework of Its Biological Functions and Medical Implications.Life (Basel, Switzerland) · 2025Review
- ZNF280AY: a pseudogene on the ovine Y chromosome and its copy number variation associated with testicular size in Hu sheep.Journal of animal science · 2025Article
- Efficient GBA1 editing via HDR with ssODNs by outcompeting pseudogene-mediated gene conversion upon CRISPR/Cas9 cleavage.Frontiers in genome editing · 2025Article
- Proteomics Can Rise to the Challenge of Pseudogenes' Coding Nature.Journal of proteome research · 2024Review
- Zebrafish: unraveling genetic complexity through duplicated genes.Development genes and evolution · 2024Review
- Network-based modelling reveals cell-type enriched patterns of non-coding RNA regulation during human skeletal muscle remodelling.bioRxiv : the preprint server for biology · 2024Article
- Network-based modelling reveals cell-type enriched patterns of non-coding RNA regulation during human skeletal muscle remodelling.NAR molecular medicine · 2024Article
- Novel Candidate Genes Involved in an Initial Stage of White Striping Development in Broiler Chickens.Animals : an open access journal from MDPI · 2024Article
- Loss to gain: pseudogenes in microorganisms, focusing on eubacteria, and their biological significance.Applied microbiology and biotechnology · 2024Review
- Many purported pseudogenes in bacterial genomes are bona fide genes.BMC genomics · 2024Article
- EndoQuad: a comprehensive genome-wide experimentally validated endogenous G-quadruplex database.Nucleic acids research · 2024Article
- Genetic variation in patent foramen ovale: a case-control genome-wide association study.Frontiers in genetics · 2024Article
- The Spatio-Temporal Expression Profiles of Silkworm Pseudogenes Provide Valuable Insights into Their Biological Roles.Evolutionary bioinformatics online · 2024Article
- Interchromosomal Colocalization with Parental Genes Is Linked to the Function and Evolution of Mammalian Retrocopies.Molecular biology and evolution · 2023Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundPseudogenes are excellent markers for genome evolution, which are emerging as crucial regulators of development and disease, especially cancer. However, systematic functional characterization and evolution of pseudogenes remain largely unexplored.
resultsTo systematically characterize pseudogenes, we date the origin of human and mouse pseudogenes across vertebrates and observe a burst of pseudogene gain in these two lineages. Based on a hybrid sequencing dataset combining full-length PacBio sequencing, sample-matched Illumina sequencing, and public time-course transcriptome data, we observe that abundant mammalian pseudogenes could be transcribed, which contribute to the establishment of organ identity. Our analyses reveal that developmentally dynamic pseudogenes are evolutionarily conserved and show an increasing weight during development. Besides, they are involved in complex transcriptional and post-transcriptional modulation, exhibiting the signatures of functional enrichment. Coding potential evaluation suggests that 19% of human pseudogenes could be translated, thus serving as a new way for protein innovation. Moreover, pseudogenes carry disease-associated SNPs and conduce to cancer transcriptome perturbation.
conclusionsOur discovery reveals an unexpectedly high abundance of mammalian pseudogenes that can be transcribed and translated, and these pseudogenes represent a novel regulatory layer. Our study also prioritizes developmentally dynamic pseudogenes with signatures of functional enrichment and provides a hybrid sequencing dataset for further unraveling their biological mechanisms in organ development and carcinogenesis in the future.
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