ArticleHuman molecular genetics2021
Nanopore direct RNA sequencing detects DUX4-activated repeats and isoforms in human muscle cells.
Article in Human molecular genetics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed, 22 citations in OpenAlex.
- Nanopore Ultra-Long Sequencing for FSHD: From Molecular Diagnosis to Preimplantation Genetic Testing.Genes · 2026Review
- Nanopore direct RNA sequencing and the epitranscriptome: Advances in mapping native RNA landscapes.iMeta · 2026Review
- Identification of cell-type-specific, transcriptionally active transposable elements using long-read RNA-sequencing data-based comprehensive annotation.Genomics & informatics · 2025Article
- DUX4 activates common and context-specific intergenic transcripts and isoforms.Science advances · 2025Article
- Transposon expression and repression in skeletal muscle.Mobile DNA · 2025Review
- Long-read sequencing for diagnosis of genetic myopathies.BMJ neurology open · 2025Review
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- Review
- Genome and RNA sequencing boost neuromuscular diagnoses to 62% from 34% with exome sequencing alone.Annals of clinical and translational neurology · 2024Article
- Species-Specific Transcription Factors Associated with Long Terminal Repeat Promoters of Endogenous Retroviruses: A Comprehensive Review.Biomolecules · 2024Review
- Rapid human genomic DNA cloning into mouse artificial chromosome via direct chromosome transfer from human iPSC and CRISPR/Cas9-mediated translocation.Nucleic acids research · 2024Article
- DUX4-r exerts a neomorphic activity that depends on GTF2I in acute lymphoblastic leukemia.Science advances · 2023Article
- Transcriptome and Genome Analysis Uncovers aNeurology. Genetics · 2023Article
- Effects of Maternal High-Fructose Diet on Long Non-Coding RNAs and Anxiety-like Behaviors in Offspring.International journal of molecular sciences · 2023Article
- Recent advances in cancer fusion transcript detection.Briefings in bioinformatics · 2023Review
- PBSIM3: a simulator for all types of PacBio and ONT long reads.NAR genomics and bioinformatics · 2022Article
- Diagnostic capabilities of nanopore long-read sequencing in muscular dystrophy.Annals of clinical and translational neurology · 2022Article
- Human Endogenous Retroviruses as Gene Expression Regulators: Insights from Animal Models into Human Diseases.Molecules and cells · 2021Review
- Embryonic LTR retrotransposons supply promoter modules to somatic tissues.Genome research · 2021Article
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Authors and funding
6 authors at 4 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Facioscapulohumeral muscular dystrophy (FSHD) is an inherited muscle disease caused by misexpression of the DUX4 gene in skeletal muscle. DUX4 is a transcription factor, which is normally expressed in the cleavage-stage embryo and regulates gene expression involved in early embryonic development. Recent studies revealed that DUX4 also activates the transcription of repetitive elements such as endogenous retroviruses (ERVs), mammalian apparent long terminal repeat (LTR)-retrotransposons and pericentromeric satellite repeats (Human Satellite II). DUX4-bound ERV sequences also create alternative promoters for genes or long non-coding RNAs, producing fusion transcripts. To further understand transcriptional regulation by DUX4, we performed nanopore long-read direct RNA sequencing (dRNA-seq) of human muscle cells induced by DUX4, because long reads show whole isoforms with greater confidence. We successfully detected differential expression of known DUX4-induced genes and discovered 61 differentially expressed repeat loci, which are near DUX4-ChIP peaks. We also identified 247 gene-ERV fusion transcripts, of which 216 were not reported previously. In addition, long-read dRNA-seq clearly shows that RNA splicing is a common event in DUX4-activated ERV transcripts. Long-read analysis showed non-LTR transposons including Alu elements are also transcribed from LTRs. Our findings revealed further complexity of DUX4-induced ERV transcripts. This catalogue of DUX4-activated repetitive elements may provide useful information to elucidate the pathology of FSHD. Also, our results indicate that nanopore dRNA-seq has complementary strengths to conventional short-read complementary DNA sequencing.
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