ArticleGenome research2007
Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolution.
Article in Genome research, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 112 papers.
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Who cites it
112 citing papers in PubMed, 224 citations in OpenAlex.
- Functional roles and clinical implications of pseudogenes signatures as emerging biomarkers in cancer.Discover oncology · 2026Review
- A Genome-Wide Pseudogene Map Reveals the Asymmetric Evolution of the A, B, and D Subgenomes in Common Wheat.Plants (Basel, Switzerland) · 2026Article
- Evolutionary patterns of the mitochondrial control region in vertebrates: A large-scale comparative analysis.PloS one · 2026Article
- Identification and structural characterization of pseudogenes in Fusarium graminearum.Scientific reports · 2025Article
- Competing endogenous RNAs network dysregulation in oral cancer: a multifaceted perspective on crosstalk and competition.Cancer cell international · 2024Review
- The reconstruction of evolutionary dynamics of processed pseudogenes indicates deep silencing of "retrobiome" in naked mole rat.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Loss to gain: pseudogenes in microorganisms, focusing on eubacteria, and their biological significance.Applied microbiology and biotechnology · 2024Review
- BORIS/CTCFL epigenetically reprograms clustered CTCF binding sites into alternative transcriptional start sites.Genome biology · 2024Article
- The network structure of hematopoietic cancers.Scientific reports · 2023Article
- The X-factor in ART: does the use of assisted reproductive technologies influence DNA methylation on the X chromosome?Human genomics · 2023Article
- Article
- Functional Attenuation of UCP1 as the Potential Mechanism for a Thickened Blubber Layer in Cetaceans.Molecular biology and evolution · 2022Article
- B Chromosomes' Sequences in Yellow-Necked MiceLife (Basel, Switzerland) · 2021Article
- Structural characterization and duplication modes of pseudogenes in plants.Scientific reports · 2021Article
- Potential of long non-coding RNAs as a therapeutic target and molecular markers in glioblastoma pathogenesis.Heliyon · 2021Review
- RetroScan: An Easy-to-Use Pipeline for Retrocopy Annotation and Visualization.Frontiers in genetics · 2021Article
- Computational Methods for Pseudogene Annotation Based on Sequence Homology.Methods in molecular biology (Clifton, N.J.) · 2021Review
- Re-recognition of pseudogenes: From molecular to clinical applications.Theranostics · 2020Review
- Pseudogene CHIAP2 inhibits proliferation and invasion of lung adenocarcinoma cells by means of the WNT pathway.Journal of cellular physiology · 2019Article
- Origination and Function of Plant Pseudogenes.Plant signaling & behavior · 2019Article
52 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
16 authors at 6 institutions in 5 countries.
Funding
Abstract
Arising from either retrotransposition or genomic duplication of functional genes, pseudogenes are "genomic fossils" valuable for exploring the dynamics and evolution of genes and genomes. Pseudogene identification is an important problem in computational genomics, and is also critical for obtaining an accurate picture of a genome's structure and function. However, no consensus computational scheme for defining and detecting pseudogenes has been developed thus far. As part of the ENCyclopedia Of DNA Elements (ENCODE) project, we have compared several distinct pseudogene annotation strategies and found that different approaches and parameters often resulted in rather distinct sets of pseudogenes. We subsequently developed a consensus approach for annotating pseudogenes (derived from protein coding genes) in the ENCODE regions, resulting in 201 pseudogenes, two-thirds of which originated from retrotransposition. A survey of orthologs for these pseudogenes in 28 vertebrate genomes showed that a significant fraction ( approximately 80%) of the processed pseudogenes are primate-specific sequences, highlighting the increasing retrotransposition activity in primates. Analysis of sequence conservation and variation also demonstrated that most pseudogenes evolve neutrally, and processed pseudogenes appear to have lost their coding potential immediately or soon after their emergence. In order to explore the functional implication of pseudogene prevalence, we have extensively examined the transcriptional activity of the ENCODE pseudogenes. We performed systematic series of pseudogene-specific RACE analyses. These, together with complementary evidence derived from tiling microarrays and high throughput sequencing, demonstrated that at least a fifth of the 201 pseudogenes are transcribed in one or more cell lines or tissues.
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Registered trials
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