ArticleDNA research : an international journal for rapid publication of reports on genes and genomes2017
Whole-genome expression analysis of mammalian-wide interspersed repeat elements in human cell lines.
Article in DNA research : an international journal for rapid publication of reports on genes and genomes, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed, 23 citations in OpenAlex.
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- Rewiring of SINE-MIR enhancer topology and Esrrb modulation in expanded and naive pluripotency.Genome biology · 2025Article
- Single chromatin fiber profiling and nucleosome position mapping in the human brain.Cell reports methods · 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
- AML with complex karyotype: extreme genomic complexity revealed by combined long-read sequencing and Hi-C technology.Blood advances · 2023Article
- Alternative splicing and genetic variation of mhc-e: implications for rhesus cytomegalovirus-based vaccines.Communications biology · 2022Article
- Quantitative assessment reveals the dominance of duplicated sequences in germline-derived extrachromosomal circular DNA.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Retrotransposons as Drivers of Mammalian Brain Evolution.Life (Basel, Switzerland) · 2021Review
- Article
- Identification of SNPs Associated with Somatic Cell Score in Candidate Genes in Italian Holstein Friesian Bulls.Animals : an open access journal from MDPI · 2021Article
- Mobile genomics: tools and techniques for tackling transposons.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2020Review
- Cooperative evolution of two different TEs results in lineage-specific novel transcripts in the BLOC1S2 gene.BMC evolutionary biology · 2019Article
- MIR sequences recruit zinc finger protein ZNF768 to expressed genes.Nucleic acids research · 2019Article
- Identification of RNA Polymerase III-Transcribed SINEs at Single-Locus Resolution from RNA Sequencing Data.Non-coding RNA · 2017Review
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
With more than 500,000 copies, mammalian-wide interspersed repeats (MIRs), a sub-group of SINEs, represent ∼2.5% of the human genome and one of the most numerous family of potential targets for the RNA polymerase (Pol) III transcription machinery. Since MIR elements ceased to amplify ∼130 myr ago, previous studies primarily focused on their genomic impact, while the issue of their expression has not been extensively addressed. We applied a dedicated bioinformatic pipeline to ENCODE RNA-Seq datasets of seven human cell lines and, for the first time, we were able to define the Pol III-driven MIR transcriptome at single-locus resolution. While the majority of Pol III-transcribed MIR elements are cell-specific, we discovered a small set of ubiquitously transcribed MIRs mapping within Pol II-transcribed genes in antisense orientation that could influence the expression of the overlapping gene. We also identified novel Pol III-transcribed ncRNAs, deriving from transcription of annotated MIR fragments flanked by unique MIR-unrelated sequences, and confirmed the role of Pol III-specific internal promoter elements in MIR transcription. Besides demonstrating widespread transcription at these retrotranspositionally inactive elements in human cells, the ability to profile MIR expression at single-locus resolution will facilitate their study in different cell types and states including pathological alterations.
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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.