ArticleGenome biology2021
Systematic functional interrogation of human pseudogenes using CRISPRi.
Article in Genome biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed, 32 citations in OpenAlex.
- A microprotein atlas of the human frontal cortex in Alzheimer's disease.Nature aging · 2026Article
- RNA isoform diversity, splicing variants and switching in single cells of the Alzheimer's disease brain.Communications biology · 2026Article
- From Genomic Fossils to Functional Elements: The Evolving Story of Pseudogenes.Advanced genetics (Hoboken, N.J.) · 2025Review
- MGAT4EP promotes tumor progression and serves as a prognostic marker for breast cancer.Cancer biology & therapy · 2025Article
- Evolutionary analyses of the animal glycosyltransferase family 54 reveals two β1,4-N-acetylglucosaminyltransferase families.iScience · 2025Article
- RNA isoform diversity, splicing variants, and switching in single cells of the Alzheimer's disease brain.Research square · 2025Article
- CRISPR screening approaches in breast cancer research.Cancer metastasis reviews · 2025Review
- Training, Validating, and Testing Machine Learning Prediction Models for Endometrial Cancer Recurrence.JCO precision oncology · 2025Article
- The MHC (Major Histocmpatibility Complex) Exceptional Molecules of Birds and Their Relationship to Diseases.International journal of molecular sciences · 2025Review
- Coding, or non-coding, that is the question.Cell research · 2024Review
- Loss to gain: pseudogenes in microorganisms, focusing on eubacteria, and their biological significance.Applied microbiology and biotechnology · 2024Review
- CRISPR-Cas9-based functional interrogation of unconventional translatome reveals human cancer dependency on cryptic non-canonical open reading frames.Nature structural & molecular biology · 2023Article
- The status of the human gene catalogue.Nature · 2023Review
- Genome annotation: From human genetics to biodiversity genomics.Cell genomics · 2023Review
- Multiomics analyses revealScience advances · 2023Article
- Non-Coding RNAs in Human Health and Diseases.Genes · 2023Article
- Article
- The status of the human gene catalogue.ArXiv · 2023Article
- Different MAPT haplotypes influence expression of total MAPT in postmortem brain tissue.Acta neuropathologica communications · 2023Article
- CRISPR/Cas9 screen uncovers functional translation of cryptic lncRNA-encoded open reading frames in human cancer.The Journal of clinical investigation · 2023Article
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Authors and funding
14 authors at 3 institutions in 3 countries.
Funding
Abstract
backgroundThe human genome encodes over 14,000 pseudogenes that are evolutionary relics of protein-coding genes and commonly considered as nonfunctional. Emerging evidence suggests that some pseudogenes may exert important functions. However, to what extent human pseudogenes are functionally relevant remains unclear. There has been no large-scale characterization of pseudogene function because of technical challenges, including high sequence similarity between pseudogene and parent genes, and poor annotation of transcription start sites.
resultsTo overcome these technical obstacles, we develop an integrated computational pipeline to design the first genome-wide library of CRISPR interference (CRISPRi) single-guide RNAs (sgRNAs) that target human pseudogene promoter-proximal regions. We perform the first pseudogene-focused CRISPRi screen in luminal A breast cancer cells and reveal approximately 70 pseudogenes that affect breast cancer cell fitness. Among the top hits, we identify a cancer-testis unitary pseudogene, MGAT4EP, that is predominantly localized in the nucleus and interacts with FOXA1, a key regulator in luminal A breast cancer. By enhancing the promoter binding of FOXA1, MGAT4EP upregulates the expression of oncogenic transcription factor FOXM1. Integrative analyses of multi-omic data from the Cancer Genome Atlas (TCGA) reveal many unitary pseudogenes whose expressions are significantly dysregulated and/or associated with overall/relapse-free survival of patients in diverse cancer types.
conclusionsOur study represents the first large-scale study characterizing pseudogene function. Our findings suggest the importance of nuclear function of unitary pseudogenes and underscore their underappreciated roles in human diseases. The functional genomic resources developed here will greatly facilitate the study of human pseudogene function.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.