ArticleNucleic acids research2015
Identification of RNA polymerase III-transcribed Alu loci by computational screening of RNA-Seq data.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 49 papers.
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Who cites it
49 citing papers in PubMed, 76 citations in OpenAlex.
- Massively parallel assessment of gene regulatory activity at human cortical-structure-associated variants.Nature neuroscience · 2026Article
- Alu Overexpression Leads to an Increased Double-Stranded RNA Signature in Dermatomyositis.Arthritis & rheumatology (Hoboken, N.J.) · 2026Article
- Long-read RNA sequencing of transposable elements from single cells using CELLO-seq.Nature protocols · 2025Review
- Identification of novel RNA polymerase III promoters in bovine leukemia virus miRNA cluster by cross-taxa analysis of small non-coding RNAs.BMC genomics · 2025Article
- An RNA polymerase III tissue and tumor atlas uncovers context-specific activities linked to 3D epigenome regulatory mechanisms.bioRxiv : the preprint server for biology · 2025Article
- Alu RNA pseudoknot alterations influence SRP9/SRP14 association.RNA (New York, N.Y.) · 2025Article
- Massively parallel jumping assay decodes Alu retrotransposition activity.Nature communications · 2025Article
- Triplexes Color the Chromaverse by Modulating Nucleosome Phasing and Anchoring Chromatin Condensates.International journal of molecular sciences · 2025Review
- lncRNA BC200 is processed into a stable Alu monomer.RNA (New York, N.Y.) · 2024Article
- Adenovirus small E1A directs activation of Alu transcription at YAP/TEAD- and AP-1-bound enhancers through interactions with the EP400 chromatin remodeler.Nucleic acids research · 2024Article
- Inverted Alu repeats: friends or foes in the human transcriptome.Experimental & molecular medicine · 2024Review
- The ancient Z-DNA and Z-RNA specific Zα fold has evolved modern roles in immunity and transcription through the natural selection of flipons.Royal Society open science · 2024Article
- The role of SRP9/SRP14 in regulating Alu RNA.RNA biology · 2024Review
- Article
- Pan-cancer analysis reveals multifaceted roles of retrotransposon-fusion RNAs.bioRxiv : the preprint server for biology · 2023Article
- RNA transcription and degradation of Alu retrotransposons depends on sequence features and evolutionary history.G3 (Bethesda, Md.) · 2022Article
- Global chromosome rearrangement induced by CRISPR-Cas9 reshapes the genome and transcriptome of human cells.Nucleic acids research · 2022Article
- DNA damage contributes to neurotoxic inflammation in Aicardi-Goutières syndrome astrocytes.The Journal of experimental medicine · 2022Article
- An RNA Polymerase III General Transcription Factor Engages in Cell Type-Specific Chromatin Looping.International journal of molecular sciences · 2022Article
- The nuclear and cytoplasmic activities of RNA polymerase III, and an evolving transcriptome for surveillance.Nucleic acids research · 2021Article
Corrections and comments
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Authors and funding
6 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Of the ∼ 1.3 million Alu elements in the human genome, only a tiny number are estimated to be active in transcription by RNA polymerase (Pol) III. Tracing the individual loci from which Alu transcripts originate is complicated by their highly repetitive nature. By exploiting RNA-Seq data sets and unique Alu DNA sequences, we devised a bioinformatic pipeline allowing us to identify Pol III-dependent transcripts of individual Alu elements. When applied to ENCODE transcriptomes of seven human cell lines, this search strategy identified ∼ 1300 Alu loci corresponding to detectable transcripts, with ∼ 120 of them expressed in at least three cell lines. In vitro transcription of selected Alus did not reflect their in vivo expression properties, and required the native 5'-flanking region in addition to internal promoter. We also identified a cluster of expressed AluYa5-derived transcription units, juxtaposed to snaR genes on chromosome 19, formed by a promoter-containing left monomer fused to an Alu-unrelated downstream moiety. Autonomous Pol III transcription was also revealed for Alus nested within Pol II-transcribed genes. The ability to investigate Alu transcriptomes at single-locus resolution will facilitate both the identification of novel biologically relevant Alu RNAs and the assessment of Alu expression alteration under pathological conditions.
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