ArticleBMC genomics2017
Conserved expression of transposon-derived non-coding transcripts in primate stem cells.
Article in BMC genomics, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
20 citing papers in PubMed, 58 citations in OpenAlex.
- Generation and transcriptome profiling of bonobo induced pluripotent stem cells using stealth RNA vectors: a tripartite comparative study with humans and chimpanzees.BMC genomics · 2025Article
- Article
- HERV activation segregates ME/CFS from fibromyalgia while defining a novel nosologic entity.eLife · 2025Article
- Article
- Expression of Transposable Elements throughout theNon-coding RNA · 2024Article
- ARID1A loss derepresses a group of human endogenous retrovirus-H loci to modulate BRD4-dependent transcription.Nature communications · 2022Article
- LINE1 are spliced in non-canonical transcript variants to regulate T cell quiescence and exhaustion.Nature genetics · 2022Article
- HERVH-derived lncRNAs negatively regulate chromatin targeting and remodeling mediated by CHD7.Life science alliance · 2022Article
- Transcriptional dynamics of transposable elements when converting fibroblast cells of Macaca mulatta to neuroepithelial stem cells.BMC genomics · 2021Article
- Transposable element-derived sequences in vertebrate development.Mobile DNA · 2021Review
- Nanopore RNA Sequencing Revealed Long Non-Coding and LTR Retrotransposon-Related RNAs Expressed at Early Stages of Triticale SEED Development.Plants (Basel, Switzerland) · 2020Article
- Transposable elements have contributed human regulatory regions that are activated upon bacterial infection.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2020Article
- Reverse engineering human brain evolution using organoid models.Brain research · 2020Review
- A primate-specific retroviral enhancer wires the XACT lncRNA into the core pluripotency network in humans.Nature communications · 2019Article
- Computational Methods for Mapping, Assembly and Quantification for Coding and Non-coding Transcripts.Computational and structural biotechnology journal · 2019Review
- High-resolution comparative analysis of great ape genomes.Science (New York, N.Y.) · 2018Article
- Article
- LINE-1 retrotransposons in healthy and diseased human brain.Developmental neurobiology · 2018Review
- Silencing of transposable elements may not be a major driver of regulatory evolution in primate iPSCs.eLife · 2018Article
- AFLP-AFLP in silico-NGS approach reveals polymorphisms in repetitive elements in the malignant genome.PloS one · 2018Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors at 3 institutions in 2 countries.
Funding
Abstract
backgroundA significant portion of expressed non-coding RNAs in human cells is derived from transposable elements (TEs). Moreover, it has been shown that various long non-coding RNAs (lncRNAs), which come from the human endogenous retrovirus subfamily H (HERVH), are not only expressed but required for pluripotency in human embryonic stem cells (hESCs).
resultsTo identify additional TE-derived functional non-coding transcripts, we generated RNA-seq data from induced pluripotent stem cells (iPSCs) of four primate species (human, chimpanzee, gorilla, and rhesus) and searched for transcripts whose expression was conserved. We observed that about 30% of TE instances expressed in human iPSCs had orthologous TE instances that were also expressed in chimpanzee and gorilla. Notably, our analysis revealed a number of repeat families with highly conserved expression profiles including HERVH but also MER53, which is known to be the source of a placental-specific family of microRNAs (miRNAs). We also identified a number of repeat families from all classes of TEs, including MLT1-type and Tigger families, that contributed a significant amount of sequence to primate lncRNAs whose expression was conserved.
conclusionsTogether, these results describe TE families and TE-derived lncRNAs whose conserved expression patterns can be used to identify what are likely functional TE-derived non-coding transcripts in primate iPSCs.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.